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Li Y, Fu Y, Li Y, Zhang R, Yang J, Ma H, Min L, Zhang X. Reversing anther thermotolerance by manipulating the cis-elements in the promoter of a high-temperature upregulated gene Casein Kinase I in upland cotton. SCIENCE CHINA. LIFE SCIENCES 2025; 68:1558-1569. [PMID: 39821833 DOI: 10.1007/s11427-024-2755-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 10/15/2024] [Indexed: 01/19/2025]
Abstract
High temperature (HT) stress causes male sterility, leading to reduced upland cotton yield. Previously, we identified a key gene, Casein Kinase I (GhCKI), that negatively regulates male fertility in upland cotton under HT. However, conventional genetic manipulations of GhCKI would result in male sterility, hindering its utilization in breeding programs. Here, we engineered quantitative variation for anther thermotolerance-related traits in upland cotton by creating weak promoter alleles of GhCKI genes, using CRISPR/Cas9 and CRISPR/Cpf1 genome editing. Then, we screened and identified two new upland cotton plant lines exhibiting a HT-tolerant phenotype with edited GhCKI promoters, and characterized their corresponding heat-tolerant allelic genotypes. Further research revealed that the primary reason for the HT tolerance of the GhCKI promoter editing mutants is that the trans-acting factors GhMYB73 and GhMYB4, which positively regulate GhCKI expression under HT, failed to bind and activate the expression of GhCKI. Overall, our study not only provides a rapid strategy to generate new beneficial alleles but also offers novel germplasm resources and molecular insights for crop HT tolerance breeding.
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Affiliation(s)
- Yanlong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yinuo Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yaoyao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huanhuan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Qiao L, Tan H, Sun M, Zhang X, Xiao S, Ye Z, Chen Z, Zhang X, Tu L. Bifunctional transcription factor GhMYB4 orchestrates transition from elongation to secondary cell wall synthesis trade-off in cotton fiber. Dev Cell 2025:S1534-5807(25)00294-1. [PMID: 40449490 DOI: 10.1016/j.devcel.2025.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 11/03/2024] [Accepted: 05/07/2025] [Indexed: 06/03/2025]
Abstract
The integration of cell wall expansion and reinforcement is vital for plant cell wall development. Cotton fiber is characterized by the synchronized development of fiber growth and cell wall formation, providing an excellent system for investigating plant cell walls. Here, we found that the often-overlooked transition stage coordinates fiber elongation and secondary cell wall (SCW) synthesis through antagonistic effects of the transcription factor GhMYB4. Knockout of GhMYB4 produced longer and finer fibers, contrasting with overexpression of GhMYB4. We show that GhMYB4 represses fiber elongation through fatty acid and brassinosteroid pathways involving a negative feedback loop with GhRAP2 and GhTCP15, while activating SCW synthesis by inducing cellulose biosynthesis in succession with the GhMYB52-GhFSN1-GhILR3 module. We identify that the bifunctionality of GhMYB4 depends on its interaction with different cis-elements and is executed through distinct transcriptional regulation motifs. Our findings propose a strategy to improve fiber quality by orchestrating wall expansion and stiffness.
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Affiliation(s)
- Lu Qiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Haozhe Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Mengling Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xiao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Shenghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zhengxiu Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zhiwei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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3
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Meng Q, Xie P, Xu Z, Tang J, Hui L, Gu J, Gu X, Jiang S, Rong Y, Zhang J, Udall JA, Grover CE, Zheng K, Chen Q, Kong J, Wang M, Nie X, Lin Z, Jin S, Wendel JF, Zhang X, Yuan D. Pangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L. Nat Commun 2025; 16:4995. [PMID: 40442108 PMCID: PMC12122945 DOI: 10.1038/s41467-025-60254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/19/2025] [Indexed: 06/02/2025] Open
Abstract
Gossypium barbadense is renowned for its superior fiber quality, particularly its extra-long fibers, although its fiber yield is lower compared to G. hirsutum. Here, to further reveal fiber-related genomic variants of G. barbadense, we de novo assemble 12 genomes of G. barbadense that span the wild-to-domesticated continuum, and construct a graph-based pangenome by integrating these assemblies and 17 publicly available tetraploid cotton genome assemblies. We uncover the divergent evolutionary trajectories and subsequent exchanges between G. barbadense and G. hirsutum through investigation of structural variants (SVs). We perform the SV-based GWAS analysis in G. barbadense and identify four, three, and seven candidate SVs for fiber length, fiber strength, and lint percentage, respectively. Furthermore, we detect the underlying candidate genes and uncover the origin and distribution of favorable alleles, and reveal the tradeoff between lint percentage and fiber quality. These pangenome and trait-associated SVs provide insights into and resources for improving cotton fiber.
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Affiliation(s)
- Qingying Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Peihao Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhongping Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiwei Tang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Liuyang Hui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiaqi Gu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xinxin Gu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shihe Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuxuan Rong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jie Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Joshua A Udall
- USDA/Agricultural Research Service, Crop Germplasm Research Unit, College Station, TX, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey Hall, Iowa State University, Ames, IA, USA
| | - Kai Zheng
- Engineering Research Centre of Cotton of Ministry of Education, College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton of Ministry of Education, College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xinhui Nie
- Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey Hall, Iowa State University, Ames, IA, USA
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.
- Engineering Research Centre of Cotton of Ministry of Education, College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
- Agricultural College, Shihezi University, Shihezi, Xinjiang, China.
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Pei Y, Liu Y, Peng J, Pei Y, Zhang T, Miao P, Liu Y, Liu Y, Liu J, Yang Z, Li F, Wang Z. The DNA N6-adenine methylation target gene GhMAF1 promotes fiber initiation at the base of Gossypium ovules. THE NEW PHYTOLOGIST 2025; 246:1015-1031. [PMID: 40065494 DOI: 10.1111/nph.70047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2024] [Accepted: 02/14/2025] [Indexed: 04/11/2025]
Abstract
DNA methylation consists of 5-methylcytosine and N6-methyl deoxyadenosine (6mA) and is crucial in plant development. However, its specific role and potential mechanism to initiate cotton fibers remain unclear. This study employed Oxford Nanopore Technologies (ONT) sequencing to analyze DNA methylation alterations in ZM24 and ZM24 fuzzless-lintless (ZM24fl) during fiber initiation. Our results indicated that DNA 6mA methylation exhibited the most remarkable difference among ovule samples at -2, 0, and 5 d post anthesis of ZM24 and ZM24fl. Subsequently, genes with significant changes in DNA 6mA methylation and transcription during fiber initiation were screened. We found that GhMAF1 displayed significant transcriptional upregulation and 6mA enrichment in its promoter, which could serve as a potential target for DNA 6mA in fiber initiation. Further, we knocked out GhMAF1 using CRISPR-Cas technology and demonstrated that GhMAF1 specifically promotes the initiation of fiber cells at the base of the ovule by mediating the downstream JAZ2/CPC-MML3/MML4 pathway. These findings unveil a novel spatial module of fiber cell initiation on the ovule surface that involves GhMAF1. Ultimately, this work provides significant knowledge for the regulatory network of DNA 6mA modification in fiber initiation to improve fiber yield and quality.
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Affiliation(s)
- Yanfei Pei
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Xinjiang Key Laboratory of Crop Gene Editing and Germplasm Innovation, Institute of Western Agricultural of CAAS, Changji, 831100, Xinjiang, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Yongming Liu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Jun Peng
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Yayue Pei
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Tianen Zhang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Pengfei Miao
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Yuanyuan Liu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Yang Liu
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Ji Liu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Xinjiang Key Laboratory of Crop Gene Editing and Germplasm Innovation, Institute of Western Agricultural of CAAS, Changji, 831100, Xinjiang, China
| | - Fuguang Li
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhi Wang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Xinjiang Key Laboratory of Crop Gene Editing and Germplasm Innovation, Institute of Western Agricultural of CAAS, Changji, 831100, Xinjiang, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
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Guo K, Yang X, Bu T, Lin J, Luo S, Tian H, Xia J, Song W, Li Y, Yu Y, Liu X, Wang W, Teng Z, Liu D, Liu D, Zhang Z. GhIAA14-GhARF7 module coordinates auxin-mediated cellulose biosynthesis during secondary cell wall thickening in cotton fibers. Int J Biol Macromol 2025; 311:143662. [PMID: 40311980 DOI: 10.1016/j.ijbiomac.2025.143662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2025] [Revised: 04/24/2025] [Accepted: 04/28/2025] [Indexed: 05/03/2025]
Abstract
The phytohormone auxin is critical for cotton fiber development, yet its regulatory mechanisms during secondary cell wall (SCW) thickening remain poorly understood. Our investigation revealed that the dynamic patterns of auxin accumulation exhibit stage correlations with fiber development, with lower levels during rapid elongation (5-10 days post-anthesis [DPA]) and significantly higher level during SCW thickening (15-25 DPA). Meanwhile, the auxin content in superior-fiber cotton Gossypium barbadense is higher than in G. hirsutum at SCW thickening stage. Genome-wide characterization identified GhIAA14, a key AUX/IAA transcriptional repressor predominantly expressed during the elongation-SCW transition stage. CRISPR-Cas9-mediated knockout of GhIAA14 resulted in shortened fibers, elevated micronaire values and cell wall thickness of fiber cells. Yeast two-hybrid (Y2H) screening coupled with bimolecular fluorescence complementation (BiFC) revealed physical interaction between GhIAA14 and transcriptional activator GhARF7. Transcriptional upregulation of downstream targets GhMYBL1 and cellulose synthase genes (GhCES4/7/8) in ghiaa14 mutants suggests a regulatory mechanism where GhIAA14 normally represses ARF-mediated SCW thickening under physiological auxin signaling. These findings delineate the mechanism of fiber SCW thickening mediated by an auxin signaling module GhIAA14-GhARF7, providing potential target genes for fiber quality improvement.
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Affiliation(s)
- Kai Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
| | - Xuyuan Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Tonghang Bu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jin Lin
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Siyan Luo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Hongyu Tian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jichun Xia
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Wenhui Song
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Yibing Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Yi Yu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Xueying Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Wenwen Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Zhonghua Teng
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Dajun Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Dexin Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
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Cheng H, Liu S, Zhang Y, Zuo D, Wang Q, Lv L, Yang Y, Hao L, Zhang X, Zhang S, Song G. Comparative single-cell transcriptomic map reveals divergence in leaves between two cotton species at cell type resolution. J Adv Res 2025:S2090-1232(25)00256-5. [PMID: 40228790 DOI: 10.1016/j.jare.2025.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 01/22/2025] [Accepted: 04/10/2025] [Indexed: 04/16/2025] Open
Abstract
INTRODUCTION Leaves are important functional organs in plants that determine yield and quality of crops. Upland cotton and sea-island cotton contribute more than 90% of the cotton fiber production annually. Deciphering and utilizing the diversity of leaf cells and functional genes underlying their divergences will be highly meaningful for cotton breeding. OBJECTIVES To investigate the conserved and divergent cell types of leaves between upland cotton and sea-island cotton, identify functional genes, and explore functional cell types in response to biotic and abiotic stresses in both species. METHODS Nuclei were isolated from leaves of upland cotton CRI12 and sea-island cotton XH21, respectively, and single-nucleus RNA-seq (snRNA-seq) was performed. Based on the orthologous genes, comparative single-cell transcriptomic map (CSCTM) of two cotton species was constructed to investigate conservation and divergence of cell types, and funtional genes were validated by virus induced gene silencing. Combining CSCTM, comparative genomic and transcriptomic analysis, functional cell types were identified in response to biotic and abiotic stresses. RESULTS A total of 22 and 20 distinct clusters were identified representing 6 main cell types in CRI12 and XH21, respectively. CSCTM analysis revealed a sea-island cotton-specific cell cluster, in which specifically expressed GbNF-YA7's role in pathogen resistance was validated. Meanwhile, the divergence of pigment gland development was revealed among cotton species and WRKY15 was identified to influence gossypol content without affecting pigment gland number. Moreover, integrated CSCTM and comparative genomic and transcriptomic analysis revealed genome variations could influence the gene expression in an elaborate cell type-specifc manner, highlighted the function of cotton leaf vascular tissue cells in Verticillium wilt resistance and putative functional differentiation of conserved abiotic stresses response genes. Additionally, different cell types might assume distinct roles in dealing with various stresses, forming a complex stress response system. CONCLUSIONS This study uncovered the conservation and divergence in cell types of leaves of upland cotton and sea-island cotton, which will provide a better understanding of phenotypic variation of the two species.
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Affiliation(s)
- Hailiang Cheng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Shang Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Youping Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Dongyun Zuo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Qiaolian Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Limin Lv
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yi Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Lingyu Hao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Xue Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shuo Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Guoli Song
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China.
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7
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Hu G, Wang Z, Tian Z, Wang K, Ji G, Wang X, Zhang X, Yang Z, Liu X, Niu R, Zhu D, Zhang Y, Duan L, Ma X, Xiong X, Kong J, Zhao X, Zhang Y, Zhao J, He S, Grover CE, Su J, Feng K, Yu G, Han J, Zang X, Wu Z, Pan W, Wendel JF, Ma X. A telomere-to-telomere genome assembly of cotton provides insights into centromere evolution and short-season adaptation. Nat Genet 2025; 57:1031-1043. [PMID: 40097785 DOI: 10.1038/s41588-025-02130-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/14/2025] [Indexed: 03/19/2025]
Abstract
Cotton (Gossypium hirsutum L.) is a key allopolyploid crop with global economic importance. Here we present a telomere-to-telomere assembly of the elite variety Zhongmian 113. Leveraging technologies including PacBio HiFi, Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C, our assembly surpasses previous genomes in contiguity and completeness, resolving 26 centromeric and 52 telomeric regions, 5S rDNA clusters and nucleolar organizer regions. A phylogenetically recent centromere repositioning on chromosome D08 was discovered specific to G. hirsutum, involving deactivation of an ancestral centromere and the formation of a unique, satellite repeat-based centromere. Genomic analyses evaluated favorable allele aggregation for key agronomic traits and uncovered an early-maturing haplotype derived from an 11 Mb pericentric inversion that evolved early during G. hirsutum domestication. Our study sheds light on the genomic origins of short-season adaptation, potentially involving introgression of an inversion from primitively domesticated forms, followed by subsequent haplotype differentiation in modern breeding programs.
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Affiliation(s)
- Guanjing Hu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenyu Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Zunzhe Tian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Gaoxiang Ji
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xingxing Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xianliang Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Zhaoen Yang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xuan Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Ruoyu Niu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - De Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuzhi Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lian Duan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xueyuan Ma
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xianpeng Xiong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jiali Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xianjia Zhao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ya Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junjie Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Shoupu He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA
| | - Junji Su
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Keyun Feng
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Guangrun Yu
- School of Life Sciences, Nantong University, Nantong, China
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, China
| | - Xinshan Zang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Weihua Pan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA
| | - Xiongfeng Ma
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.
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8
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Wu A, Shen T, Lu J, Fu X, Yang M, Sun M, Ma L, Lian B, Wu H, Li Y, Yu S, Wei H, Wang H. GhMYB102 affects cotton fibre elongation and secondary wall thickening by regulating GhIRX10 in cotton. PLANT BIOTECHNOLOGY JOURNAL 2025; 23:1329-1344. [PMID: 39966942 PMCID: PMC11933854 DOI: 10.1111/pbi.14588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Revised: 11/29/2024] [Accepted: 01/02/2025] [Indexed: 02/20/2025]
Abstract
Upland cotton (Gossypium hirsutum) is a principal economic crop and a fundamental raw material for the textile industry. The quality of cotton fibres is significantly influenced by the synthesis of cell wall polysaccharides. This study focuses on GhIRX10, a beta-1,4-xylosyltransferase crucial for xylan backbone synthesis. Overexpression of GhIRX10 enhances xylan synthesis, which impacts fibre elongation and secondary cell wall thickening. GhMYB102, identified as a direct regulator of GhIRX10 expression, was confirmed through comprehensive validation. Overexpression of GhMYB102 resulted in a similar phenotype as OE-GhIRX10: increased cell wall thickness and reduced fibre length. Overexpression of GhMYB102 upregulated the expression of key cell wall synthesis-related genes, including GhCESA4/7/8, GhIRXs, GhCESAs, GhGUXs, GhTBLs, GhXTHs, and GhXXTs. Consequently, the cellulose and hemicellulose contents in OE-GhMYB102 lines were significantly increased. GhMYB102 was also validated as a target gene regulated by GhFSN1 and GhMYB7, with the ability to reciprocally regulate GhFSN1 expression. In summary, we propose a regulatory model where GhMYB102 promotes the expression of GhIRX10 and other cell wall-related genes, thereby affecting fibre quality. This study elucidates the regulatory network of secondary cell wall synthesis in cotton and provides potential targets for improving fibre quality through molecular breeding.
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Affiliation(s)
- Aimin Wu
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
| | - Tong Shen
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
| | - Jianhua Lu
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
| | - Xiaokang Fu
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
| | - Miaoqian Yang
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
| | - Mengxi Sun
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
| | - Liang Ma
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
| | - Boying Lian
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
| | - Hongmei Wu
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
| | - Yiran Li
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
| | - Shuxun Yu
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
| | - Hengling Wei
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‐breeding and Integrated UtilizationZhengzhou UniversityZhengzhouHenanChina
| | - Hantao Wang
- State Key Laboratory of Cotton Bio‐Breeding and Integrated UtilizationInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyangHenanChina
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‐breeding and Integrated UtilizationZhengzhou UniversityZhengzhouHenanChina
- Western Agricultural Research CenterChinese Academy of Agricultural SciencesChangjiXinjiangChina
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9
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Gao S, Liu S, Feng G, Gao J, Wang N, Ai N, Zhou B. Evaluation of resistance to Verticillium wilt in Gossypium hirsutum-Gossypium arboreum introgression lines and identification of putative resistance genes using RNA-seq. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 352:112353. [PMID: 39643248 DOI: 10.1016/j.plantsci.2024.112353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 12/01/2024] [Accepted: 12/04/2024] [Indexed: 12/09/2024]
Abstract
Verticillium wilt (VW), a fungal disease caused by Verticillium dahliae (Vd), is one of the most destructive threats to cotton production. Moreover, widely cultivated upland cotton (Gossypium hirsutum, 2n = 4x = AADD = 52) often demonstrates low resistance to Vd. In contrast, G. arboreum (2n = 2x = AA = 26) shows high resistant to VW, making it a valuable source for breeding, despite the challenges posed by hybridization incompatibility between the two species. Here, a population of introgression lines derived from G. hirsutum and G. arboreum was evaluated for resistance to VW through both glasshouse and field tests. Among these lines, DM11039 demonstrated high resistance to VW. Both DM11039 and the recipient TM-1 underwent transcriptome sequencing during Vd infection at 0, 4, 12, 24, 48, and 96 h post inoculation. The analysis identified differentially expressed genes (DEGs), which were predominantly associated with resistance mechanisms. Based on the results from transcriptome sequencing and weighted correlation network analysis, three DEGs from each parent-G. arboreum and G. hirsutum- in DM11039 were subjected to virus-induced gene silencing in cotton seedlings. The findings revealed that silencing of GaPP2A1, GaPDH-E1, or GaLRK10L-1.2, which are located within the introgression segments from G. arboreum, significantly impaired disease resistance in cotton. This suggests that these genes are potentially linked to the disease phenotype. In contrast, silencing of GHA13G1263, GhZIP1 or GHA10G2498 from G. hirsutum did not result in any changes in disease resistance in DM11039. The results indicate G. arboreum harbors resistance genes to VW. Furthermore, the introgression population presents a valuable resource for future cotton breeding.
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Affiliation(s)
- Shuang Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Susu Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Guoli Feng
- Shihezi Agricultural Science Research Institute, Shihezi, Xinjiang 832000, PR China
| | - Jianbo Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Ningshan Wang
- Shihezi Agricultural Science Research Institute, Shihezi, Xinjiang 832000, PR China
| | - Nijiang Ai
- Shihezi Agricultural Science Research Institute, Shihezi, Xinjiang 832000, PR China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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10
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Zhang X, Li Y, Ge Y, Mao Y, Hu G, Ma Q, Chen E. SEEDSTICK Affects Seed Development by Mediating Cytokinin Levels in Cotton. PHYSIOLOGIA PLANTARUM 2025; 177:e70161. [PMID: 40113449 DOI: 10.1111/ppl.70161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 02/18/2025] [Accepted: 02/24/2025] [Indexed: 03/22/2025]
Abstract
The SEEDSTICK transcription factor is important for flower and seed development, but the underlying molecular mechanisms remain unclear in cotton. In this study, we identified and cloned two STK homolog genes in upland cotton, an economically valuable cultivated crop. Phylogenetic and sequence analyses showed that the C-terminus of both GhSTKs had a conserved -DJJILHLG amino acid sequence and that GhSTK1 and GhSTK2 were very similar to GaAGL11 and GrAGL11, respectively. Quantitative real-time PCR analysis revealed that both GhSTKs were highly expressed in the ovules, and GUS activity was detected in the style and stigma. Subcellular localization experiments showed that GhSTK1 and GhSTK2 were localized to the nucleus. In Arabidopsis, the overexpression of GhSTK1 or GhSTK2 affected floral organ development and seed formation by increasing the transcript levels of the CKX genes and other genes related to floral development. Silencing both GhSTK1 and GhSTK2 increased the expression of GhFT and GhSHP and led to the earlier appearance of cotton buds. Yeast two-hybrid and bimolecular fluorescence complementation assays indicated that the two GhSTK proteins could interact with the GhSEP3 and GhSEP4 proteins. The present results suggest that GhSTK1 and GhSTK2, which have different sequences and expression patterns, might be functionally redundant and influence the regulation of cotton bud and seed development.
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Affiliation(s)
- Xiaohong Zhang
- Collaborative Innovation Center of Modern Biological Breeding, College of Agronomy, Henan Institute of Science and Technology, Xinxiang, Henan, P.R, China
| | - Yifan Li
- Collaborative Innovation Center of Modern Biological Breeding, College of Agronomy, Henan Institute of Science and Technology, Xinxiang, Henan, P.R, China
| | - Yunjie Ge
- Collaborative Innovation Center of Modern Biological Breeding, College of Agronomy, Henan Institute of Science and Technology, Xinxiang, Henan, P.R, China
| | - Yuhao Mao
- Collaborative Innovation Center of Modern Biological Breeding, College of Agronomy, Henan Institute of Science and Technology, Xinxiang, Henan, P.R, China
| | - Genhai Hu
- Collaborative Innovation Center of Modern Biological Breeding, College of Agronomy, Henan Institute of Science and Technology, Xinxiang, Henan, P.R, China
| | - Qifeng Ma
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R, China
| | - Eryong Chen
- Collaborative Innovation Center of Modern Biological Breeding, College of Agronomy, Henan Institute of Science and Technology, Xinxiang, Henan, P.R, China
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11
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Kun W, Shoupu H, Yuxian Z. Cotton2035: From genomics research to optimized breeding. MOLECULAR PLANT 2025; 18:298-312. [PMID: 39844464 DOI: 10.1016/j.molp.2025.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2024] [Revised: 01/08/2025] [Accepted: 01/12/2025] [Indexed: 01/24/2025]
Abstract
Cotton is the world's most important natural fiber crop and serves as an ideal model for studying plant genome evolution, cell differentiation, elongation, and cell wall biosynthesis. The first draft genome assembly for Gossypium raimondii, completed in 2012, marked the beginning of global efforts in studying cotton genomics. Over the past decade, the cotton research community has continued to assemble and refine the genomes for both wild and cultivated Gossypium species. With the accumulation of de novo genome assemblies and resequencing data across virous cotton populations, significant progress has been made in uncovering the genetic basis of key agronomic traits. Achieving the goal of cotton genomics-to-breeding (G2B) will require a deeper understanding of the spatiotemporal regulatory mechanisms involved in genome information storage and expression. We advocate for a cotton ENCODE project to systematically decode the functional elements and regulatory networks within the cotton genome. Technological advances, particularly on single-cell sequencing and high-resolution spatiotemporal omics, will be essential for elucidating these regulatory mechanisms. By integrating multi-omics data, genome editing tools, and artificial intelligence, these efforts will empower the genomics-driven strategies needed for future cotton G2B breeding.
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Affiliation(s)
- Wang Kun
- College of Life Sciences, Wuhan University, Wuhan 430072, China; Institute for Advanced Studies, Wuhan University, Wuhan 430072, China; Hubei Hongshan Laboratory, Wuhan 430072, China.
| | - He Shoupu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572000, China.
| | - Zhu Yuxian
- College of Life Sciences, Wuhan University, Wuhan 430072, China; Institute for Advanced Studies, Wuhan University, Wuhan 430072, China; Hubei Hongshan Laboratory, Wuhan 430072, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China.
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12
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Wang W, Liu D, Zhang T, Guo K, Liu X, Liu D, Chen L, Yang J, Teng Z, Zou Y, Ma J, Wang Y, Yang X, Guo X, Sun X, Zhang J, Xiao Y, Paterson AH, Zhang Z. Natural variation in GhROPGEF5 contributes to longer and stronger cotton fibers. THE NEW PHYTOLOGIST 2025; 245:1090-1105. [PMID: 39575696 DOI: 10.1111/nph.20286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 11/03/2024] [Indexed: 01/11/2025]
Abstract
Length and strength are key parameters impacting the quality of textiles that can be produced from cotton fibers, and therefore are important considerations in cotton breeding. Through map-based cloning and function analysis, we demonstrated that GhROPGEF5, encoding a ROP guanine nucleotide exchange factor, was the gene controlling fiber length and strength at qFSA10.1. Evolutionary analysis revealed that a base deletion in the third exon of GhROPGEF5 resulting in superior fiber length and strength was a rare mutation occurring in a tiny percentage of Upland cottons, with reduced fiber yield hindering its spread. GhROPGEF5 interacted with and activated GhROP10. Knockout or mutation of GhROPGEF5 resulted a loss of the ability to activate GhROP10. Knockout of GhROPGEF5 or GhROP10 affected the expression of many downstream genes associated with fiber elongation and secondary wall deposition, prolonged fiber elongation and delayed secondary wall deposition, producing denser fiber helices and increasing fiber length and strength. These results revealed new molecular aspects of fiber development and revealed a rare favorable allele for improving fiber quality in cotton breeding.
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Affiliation(s)
- Wenwen Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Dexin Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Tingfu Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Kai Guo
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Xueying Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Dajun Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Lei Chen
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Jinming Yang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Zhonghua Teng
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Ying Zou
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Junrui Ma
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Yi Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Xinrui Yang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Xin Guo
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Xiaoting Sun
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Jian Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Yuehua Xiao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
| | - Andrew H Paterson
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Zhengsheng Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
- Chongqing Key Laboratory of Crop Molecular Improvement, Southwest University, Chongqing, 400716, China
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13
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Zhang Y, Zhang H, Zhang Y, Wang D, Meng X, Chen J. Utilizing physiologies, transcriptomics, and metabolomics to unravel key genes and metabolites of Salvia miltiorrhiza Bge. seedlings in response to drought stress. FRONTIERS IN PLANT SCIENCE 2025; 15:1484688. [PMID: 39877738 PMCID: PMC11772496 DOI: 10.3389/fpls.2024.1484688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 12/16/2024] [Indexed: 01/31/2025]
Abstract
Drought stress inhibits Salvia miltiorrhiza Bunge (S. miltiorrhiza) seedling growth and yield. Here, we studied the effects of drought stress on the different parts of S. miltiorrhiza seedlings through physiological, transcriptomic, and metabolomics analyses, and identified key genes and metabolites related to drought tolerance. Physiological analysis showed that drought stress increased the accumulation of hydrogen peroxide (H2O2), enhanced the activity of peroxidase (POD), decreased the activity of catalase (CAT) and the contents of chlorophyll b and total chlorophyll, reduced the degree of photosynthesis, enhanced oxidative damage in S. miltiorrhiza seedlings, and inhibited the growth of S. miltiorrhiza plants. Transcriptome analyses revealed 383 genes encoding transcription factors and 80 genes encoding plant hormones as hypothetical regulators of drought resistance in S. miltiorrhiza plants. Moreover, differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) are involved in a variety of biological processes, such as proline and glycine betaine metabolism, and biosynthesis of tanshinones and phenolic acids. Additionally, it has barely been reported that the AHL gene family may be involved in regulating the neocryptotanshinone biosynthesis. In conclusion, our results suggest that drought stress inhibits S. miltiorrhiza seedling growth by enhancing membrane lipid peroxidation, attenuating the antioxidant system, photosynthesis, and regulating proline and glycine betaine metabolism, transcription factors and plant hormones, and tanshinones and phenolic acid metabolism pathways. This study provides new insights into the complex mechanisms by which S. miltiorrhiza responds to drought stress.
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Affiliation(s)
| | | | | | | | | | - Juan Chen
- Institute of Chinese Materia Medica, Shaanxi Provincial Academy of Traditional Chinese
Medicine, Xi’an, Shaanxi, China
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14
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Wang K, Ren K, Luo Y, Zheng P, Mao X, Yan H, Wang Q, He J. Improved quality of cottonseed meal: effect of cottonseed protein isolate on growth performance, nutrient digestibility, and intestinal health in growing pigs. J Anim Sci 2025; 103:skaf057. [PMID: 40036897 PMCID: PMC12019961 DOI: 10.1093/jas/skaf057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Accepted: 02/27/2025] [Indexed: 03/06/2025] Open
Abstract
Cottonseed meal (CSM) is abundant in proteins that have the potential to substitute for conventionally utilized protein supplements for animals. However, the presence of anti-nutritional factors in CSM, particularly free gossypol, has limited its application. This study evaluated the nutritional value of a cottonseed protein isolate (CPI) derived from CSM using an alkaline extraction and acid precipitation process and explored its effect on intestinal health in growing pigs. 32 Duroc-Landrace-Yorkshire castrated male pigs (initial body weight 19 ± 2 kg) were divided into 4 treatment groups: nitrogen-free diet, corn-soybean meal diet (CSD), cottonseed meal diet (CSMD, where CSM replaced 35% of the nitrogen in CSD), CPI diet (CPID, where CPI replaced 35% of the nitrogen in CSD). Our study revealed that, as compared to the CSM, the CPI exhibited significantly higher crude protein content and lower levels of crude fiber, neutral detergent fiber, acid detergent fiber, and free gossypol (P < 0.01). Interestingly, CPI feeding significantly decreased the ratio of gain to feed (G:F) in growing pigs (P = 0.012). Moreover, CPI also showed an improved apparent and true digestibility of protein, as well as enhanced nitrogen utilization in growing pigs (P < 0.05). The metabolizable energy of CPI was significantly higher than that of CSM (P < 0.01). Additionally, CPI showed higher apparent ileal digestibility and standardized ileal digestibility for amino acids such as arginine, aspartic acid, glutamic acid, and serine (P < 0.05). Importantly, CPI feeding improved the intestinal health in pigs as indicated by increases in villus height and digestive enzyme activities (P < 0.05), as well as increases in the production of short-chain fatty acid and beneficial microbiota (0.05 ≤ P < 0.10). The results not only showed an improved quality of CPI as compared to the CSM but also indicated a beneficial effect of CPI on growth performance and intestinal health in growing pigs. These attributes should make it an attractive candidate to substitute for conventionally utilized protein supplements like soybean meal.
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Affiliation(s)
- Kang Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
- Key Laboratory of Animal Disease-resistant Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
| | - Kaizheng Ren
- Institute of Animal Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
- Key Laboratory of Animal Disease-resistant Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
| | - Yuheng Luo
- Institute of Animal Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
- Key Laboratory of Animal Disease-resistant Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
| | - Ping Zheng
- Institute of Animal Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
- Key Laboratory of Animal Disease-resistant Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
| | - Xiangbing Mao
- Institute of Animal Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
- Key Laboratory of Animal Disease-resistant Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
| | - Hui Yan
- Institute of Animal Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
- Key Laboratory of Animal Disease-resistant Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
| | - Quyuan Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
- Key Laboratory of Animal Disease-resistant Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
| | - Jun He
- Institute of Animal Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
- Key Laboratory of Animal Disease-resistant Nutrition, Sichuan Agricultural University, Sichuan Province, 611130, People’s Republic of China
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15
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Li H, Liu L, Kong X, Wang X, Si A, Zhao F, Huang Q, Yu Y, Chen Z. Time-Course Transcriptomics Analysis Reveals Molecular Mechanisms of Salt-Tolerant and Salt-Sensitive Cotton Cultivars in Response to Salt Stress. Int J Mol Sci 2025; 26:329. [PMID: 39796184 PMCID: PMC11719879 DOI: 10.3390/ijms26010329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 12/29/2024] [Accepted: 12/30/2024] [Indexed: 01/13/2025] Open
Abstract
Salt stress is an environmental factor that limits plant seed germination, growth, and survival. We performed a comparative RNA sequencing transcriptome analysis during germination of the seeds from two cultivars with contrasting salt tolerance responses. A transcriptomic comparison between salt-tolerant cotton cv Jin-mian 25 and salt-sensitive cotton cv Su-mian 3 revealed both similar and differential expression patterns between the two genotypes during salt stress. The expression of genes related to aquaporins, kinases, reactive oxygen species (ROS) scavenging, trehalose biosynthesis, and phytohormone biosynthesis and signaling that include ethylene (ET), gibberellin (GA), abscisic acid (ABA), jasmonic acid (JA), and brassinosteroid (BR) were systematically investigated between the cultivars. Despite the involvement of these genes in cotton's response to salt stress in positive or negative ways, their expression levels were mostly similar in both genotypes. Interestingly, a PXC2 gene (Ghir_D08G025150) was identified, which encodes a leucine-rich repeat receptor-like protein kinase (LRR-RLK). This gene showed an induced expression pattern after salt stress treatment in salt-tolerant cv Jin-mian 25 but not salt-sensitive cv Su-mian 3. Our multifaceted transcriptome approach illustrated a differential response to salt stress between salt-tolerant and salt-sensitive cotton.
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Affiliation(s)
- Hang Li
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (H.L.); (L.L.); (X.K.); (X.W.); (A.S.); (F.Z.); (Q.H.)
| | - Li Liu
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (H.L.); (L.L.); (X.K.); (X.W.); (A.S.); (F.Z.); (Q.H.)
| | - Xianhui Kong
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (H.L.); (L.L.); (X.K.); (X.W.); (A.S.); (F.Z.); (Q.H.)
| | - Xuwen Wang
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (H.L.); (L.L.); (X.K.); (X.W.); (A.S.); (F.Z.); (Q.H.)
| | - Aijun Si
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (H.L.); (L.L.); (X.K.); (X.W.); (A.S.); (F.Z.); (Q.H.)
| | - Fuxiang Zhao
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (H.L.); (L.L.); (X.K.); (X.W.); (A.S.); (F.Z.); (Q.H.)
| | - Qian Huang
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (H.L.); (L.L.); (X.K.); (X.W.); (A.S.); (F.Z.); (Q.H.)
| | - Yu Yu
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (H.L.); (L.L.); (X.K.); (X.W.); (A.S.); (F.Z.); (Q.H.)
| | - Zhiwen Chen
- Engineering Research Center of Coal-Based Ecological Carbon Sequestration Technology of the Ministry of Education, Key Laboratory of Graphene Forestry Application of National Forest and Grass Administration, Shanxi Datong University, Datong 037009, China
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16
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Dong Z, Jin S, Fan R, Sun P, Shao L, Zhao T, Jiang H, Zhang Z, Shang H, Guan X, Hu Y, Zhang T, Zhu F, Fang L. High-quality genome of Firmiana hainanensis provides insights into the evolution of Malvaceae subfamilies and the mechanism of their wood density formation. J Genet Genomics 2024:S1673-8527(24)00362-X. [PMID: 39709049 DOI: 10.1016/j.jgg.2024.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Revised: 12/10/2024] [Accepted: 12/10/2024] [Indexed: 12/23/2024]
Abstract
The Malvaceae family, the most diverse family in the order Malvales, consists of nine subfamilies. Within the Firmiana genus of the Sterculioideae subfamily, most species are considered globally vulnerable, yet their genomes remain unexplored. Here, we present a chromosome-level genome assembly for a representative Firmiana species, F. hainanensis, 2n = 40, totaling 1536 Mb. Phylogenomic analysis shows that F. hainanensis and Durio zibethinus have the closest evolutionary relationship, with an estimated divergence time of approximately 21 MYA and distinct polyploidization events in their histories. Evolutionary trajectory analyses indicate that fissions and fusions may play a crucial role in chromosome number variation (2n = 14 to 2n = 96). Analysis of repetitive elements among Malvaceae reveals that the Tekay subfamily (belonging to the Gypsy group) contributes to variation in genome size (ranging from 324 Mb to 1620 Mb). Additionally, genes associated with P450, peroxidase, and microtubules, and thereby related to cell wall biosynthesis, are significantly contracted in F. hainanensis, potentially leading to its lower wood density relative to Hopea hainanensis. Overall, our study provides insights into the evolution of chromosome number, genome size, and the genetic basis of cell wall biosynthesis in Malvaceae species.
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Affiliation(s)
- Zeyu Dong
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Key Lab of Plant Factory for Plant Factory Generation-Adding Breeding of Ministry of Agriculture and Rural Affairs, The Advanced Seed Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Institute of Zhejiang University, Sanya, Hainan 572025, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Shangkun Jin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Key Lab of Plant Factory for Plant Factory Generation-Adding Breeding of Ministry of Agriculture and Rural Affairs, The Advanced Seed Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Rui Fan
- Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan 571533, China
| | - Pengcheng Sun
- College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Lei Shao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Key Lab of Plant Factory for Plant Factory Generation-Adding Breeding of Ministry of Agriculture and Rural Affairs, The Advanced Seed Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Institute of Zhejiang University, Sanya, Hainan 572025, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Key Lab of Plant Factory for Plant Factory Generation-Adding Breeding of Ministry of Agriculture and Rural Affairs, The Advanced Seed Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Institute of Zhejiang University, Sanya, Hainan 572025, China
| | - Haojie Jiang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Key Lab of Plant Factory for Plant Factory Generation-Adding Breeding of Ministry of Agriculture and Rural Affairs, The Advanced Seed Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhiyuan Zhang
- Hainan Institute of Zhejiang University, Sanya, Hainan 572025, China
| | - Haihong Shang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Key Lab of Plant Factory for Plant Factory Generation-Adding Breeding of Ministry of Agriculture and Rural Affairs, The Advanced Seed Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Institute of Zhejiang University, Sanya, Hainan 572025, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Key Lab of Plant Factory for Plant Factory Generation-Adding Breeding of Ministry of Agriculture and Rural Affairs, The Advanced Seed Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Institute of Zhejiang University, Sanya, Hainan 572025, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Key Lab of Plant Factory for Plant Factory Generation-Adding Breeding of Ministry of Agriculture and Rural Affairs, The Advanced Seed Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Institute of Zhejiang University, Sanya, Hainan 572025, China
| | - Fuyuan Zhu
- College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Key Lab of Plant Factory for Plant Factory Generation-Adding Breeding of Ministry of Agriculture and Rural Affairs, The Advanced Seed Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Institute of Zhejiang University, Sanya, Hainan 572025, China.
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17
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Cheng C, Zhang F, Li L, Ni Z. Identification and Analysis of the Plasma Membrane H +-ATPase Gene Family in Cotton and Its Roles in Response to Salt Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:3510. [PMID: 39771208 PMCID: PMC11728463 DOI: 10.3390/plants13243510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 12/09/2024] [Accepted: 12/11/2024] [Indexed: 01/16/2025]
Abstract
Plant plasma membrane (PM) H+-ATPase functions as a proton-motive force by exporting cellular protons to establish a transmembrane chemical gradient of H+ ions and an accompanying electrical gradient. These gradients are crucial for plant growth and development and for plant responses to abiotic and biotic stresses. In this study, a comprehensive identification of the PM H+-ATPase gene family was conducted across four cotton species. Specifically, 14 genes were identified in the diploid species Gossypium arboreum and Gossypium raimondii, whereas 39 and 43 genes were identified in the tetraploid species Gossypium hirsutum and Gossypium barbadense, respectively. The characteristics of this gene family were subsequently compared and analyzed using bioinformatics. Chromosomal localization and collinearity analyses elucidated the distribution characteristics of this gene family within the cotton genomes. Gene structure and phylogenetic analyses demonstrated the conservation of this family across cotton species, whereas the examination of cis-acting elements in gene promoters highlighted their involvement in environmental stress and hormone response categories. An expression profile analysis revealed eight genes whose expression was upregulated under salt stress conditions, and quantitative real-time PCR results suggested that the cotton PM H+-ATPase genes may play crucial roles in conferring resistance to salt stress. These findings establish a robust foundation for subsequent investigations into the functions of cotton PM H+-ATPase genes and may offer valuable insights for selecting genes for resistance breeding programs.
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Affiliation(s)
- Cong Cheng
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (C.C.); (L.L.)
- College of Life Science, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Fengyuan Zhang
- College of Life Science, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Li Li
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (C.C.); (L.L.)
- College of Life Science, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Zhiyong Ni
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (C.C.); (L.L.)
- College of Life Science, Xinjiang Agricultural University, Urumqi 830052, China;
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18
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Li T, Jia W, Li L, Xu S, Xu R. GhCNGC31 is critical for conferring resistance to Verticillium wilt in cotton. PLANT MOLECULAR BIOLOGY 2024; 115:2. [PMID: 39666136 DOI: 10.1007/s11103-024-01533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 11/11/2024] [Indexed: 12/13/2024]
Abstract
In the past decades, cyclic nucleotide-gated ion channels (CNGCs) have been extensively studied in diploid species Arabidopsis thaliana. However, the functional diversification of CNGCs in crop plants, mostly polyploid, remains poorly understood. In allotetraploid Upland cotton (Gossypium hirsutum), GhCNGC31 is one of the multiple orthologs of AtCNGC2, being present in the plasma membrane, capable of interacting with itself and binding to calmodulins and cyclic nucleotides. GhCNGC31 knockdown plants exhibited slight growth inhibition, and became more susceptible to Verticillium dahliae infection, which was associated with the reduced lignin and flavonoid accumulation, impaired ROS (reactive oxygen species) burst, and down-regulation of defense-related genes PR1, JAZ2, LOX2, and RBOH10. RNA-Seq analysis identified 1817 differentially expressed genes from GhCNGC31 knockdown, of which 1184 (65%) were responsive to V. dahliae infection and accounted for 57% among a total of 2065 V. dahliae-responsive genes identified in this study. These GhCNGC31-regulated genes mainly function with cell wall organization and biogenesis, cellular carbohydrate metabolic or biosynthetic process, cellular component macromolecule biosynthetic process, and rhythmic process. They are significantly enriched in the pathways of plant MAPK signaling, plant-pathogen interaction, phenylpropanoid biosynthesis, and plant hormone signal transduction. A set of transcription factors (TFs) and resistance (R) genes are among the GhCNGC31-regulated genes, which are significantly over-represented with the TCP and WRKY TFs families, as well as with the R genes of T (TIR) and TNL (TIR-NB-LRR) classes. Together, our results unraveled a critical role of GhCNGC31 for conferring resistance to Verticillium wilt in cotton.
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Affiliation(s)
- Tianming Li
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Wenjing Jia
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Lin Li
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Shi Xu
- Henan Seed Industry Development Center, Zhengzhou, 450000, China
| | - Ruqiang Xu
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, 450001, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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19
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Zhang L, Wen X, Chen X, Zhou Y, Wang K, Zhu Y. GhCASPL1 regulates secondary cell wall thickening in cotton fibers by stabilizing the cellulose synthase complex on the plasma membrane. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:2632-2647. [PMID: 39315818 PMCID: PMC11622535 DOI: 10.1111/jipb.13777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 08/26/2024] [Accepted: 08/30/2024] [Indexed: 09/25/2024]
Abstract
Cotton (Gossypium hirsutum) fibers are elongated single cells that rapidly accumulate cellulose during secondary cell wall (SCW) thickening, which requires cellulose synthase complex (CSC) activity. Here, we describe the CSC-interacting factor CASPARIAN STRIP MEMBRANE DOMAIN-LIKE1 (GhCASPL1), which contributes to SCW thickening by influencing CSC stability on the plasma membrane. GhCASPL1 is preferentially expressed in fiber cells during SCW biosynthesis and encodes a MARVEL domain protein. The ghcaspl1 ghcaspl2 mutant exhibited reduced plant height and produced mature fibers with fewer natural twists, lower tensile strength, and a thinner SCW compared to the wild type. Similarly, the Arabidopsis (Arabidopsis thaliana) caspl1 caspl2 double mutant showed a lower cellulose content and thinner cell walls in the stem vasculature than the wild type but normal plant morphology. Introducing the cotton gene GhCASPL1 successfully restored the reduced cellulose content of the Arabidopsis caspl1 caspl2 mutant. Detergent treatments, ultracentrifugation assays, and enzymatic assays showed that the CSC in the ghcaspl1 ghcaspl2 double mutant showed reduced membrane binding and decreased enzyme activity compared to the wild type. GhCASPL1 binds strongly to phosphatidic acid (PA), which is present in much higher amounts in thickening fiber cells compared to ovules and leaves. Mutating the PA-binding site in GhCASPL1 resulted in the loss of its colocalization with GhCesA8, and it failed to localize to the plasma membrane. PA may alter membrane structure to facilitate protein-protein interactions, suggesting that GhCASPL1 and PA collaboratively stabilize the CSC. Our findings shed light on CASPL functions and the molecular machinery behind SCW biosynthesis in cotton fibers.
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Affiliation(s)
- Li Zhang
- Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Xingpeng Wen
- Institute for Advanced StudiesWuhan UniversityWuhan430072China
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life SciencesWuhan UniversityWuhan430072China
- TaiKang Center for Life and Medical SciencesWuhan UniversityWuhan430072China
| | - Xin Chen
- State Key Laboratory of Protein and Plant Gene Research, College of Life SciencesPeking UniversityBeijing100871China
| | - Yifan Zhou
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life SciencesWuhan UniversityWuhan430072China
| | - Kun Wang
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life SciencesWuhan UniversityWuhan430072China
| | - Yuxian Zhu
- Institute for Advanced StudiesWuhan UniversityWuhan430072China
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life SciencesWuhan UniversityWuhan430072China
- TaiKang Center for Life and Medical SciencesWuhan UniversityWuhan430072China
- State Key Laboratory of Protein and Plant Gene Research, College of Life SciencesPeking UniversityBeijing100871China
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20
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Yang Z, Li G, Zhang Y, Li F, Zhou T, Ye J, Wang X, Zhang X, Sun Z, Tao X, Wu M, Wu J, Li Y. Crop antiviral defense: Past and future perspective. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2617-2634. [PMID: 39190125 DOI: 10.1007/s11427-024-2680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/09/2024] [Indexed: 08/28/2024]
Abstract
Viral pathogens not only threaten the health and life of humans and animals but also cause enormous crop yield losses and contribute to global food insecurity. To defend against viral pathogens, plants have evolved an intricate immune system to perceive and cope with such attacks. Although most of the fundamental studies were carried out in model plants, more recent research in crops has provided new insights into the antiviral strategies employed by crop plants. We summarize recent advances in understanding the biological roles of cellular receptors, RNA silencing, RNA decay, hormone signaling, autophagy, and ubiquitination in manipulating crop host-mediated antiviral responses. The potential functions of circular RNAs, the rhizosphere microbiome, and the foliar microbiome of crops in plant-virus interactions will be fascinating research directions in the future. These findings will be beneficial for the development of modern crop improvement strategies.
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Affiliation(s)
- Zhirui Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Guangyao Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Jian Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianbing Wang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100049, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Xiaorong Tao
- Department of Plant Pathology, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ming Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianguo Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yi Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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21
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Chen Y, Yang R, Wang H, Xiao X, Xing B, Li Y, Liu Q, Lu Q, Peng R, Chen G, Wang Y, Li P. Genome-Wide Identification of the Oxidative Stress 3 ( OXS3) Gene Family and Analysis of Its Expression Pattern During Ovule Development and Under Abiotic Stress in Cotton. BIOLOGY 2024; 13:903. [PMID: 39596858 PMCID: PMC11591572 DOI: 10.3390/biology13110903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Revised: 10/19/2024] [Accepted: 10/22/2024] [Indexed: 11/29/2024]
Abstract
Oxidative Stress 3 (OXS3) encodes a plant-specific protein that makes great contributions to a plant's stress tolerance. However, reports on genome-wide identification and expression pattern analyses of OXS3 were only found for Arabidopsis, wheat, and rice. The genus Gossypium (cotton) serves as an ideal model for studying allopolyploidy. Therefore, two diploid species (G. raimondii and G. arboreum) and two tetraploid species (G. hirsutum and G. barbadense) were chosen in this study for a bioinformatics analysis, resulting in 12, 12, 22, and 23 OXS3 members, respectively. A phylogenetic tree was constructed using 69 cotton OXS3 genes alongside 8 Arabidopsis, 10 rice, and 9 wheat genes, which were classified into three groups (Group 1-3). A consistent evolutionary relationship with the phylogenetic tree was observed in our structural analysis of the cotton OXS3 genes and the clustering of six conserved motifs. Gene duplication analysis across the four representative Gossypium species suggested that whole-genome duplication, segmental duplication, and tandem duplication might play significant roles in the expansion of the OXS3 gene family. Some existing elements responsive to salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) were identified by cis-regulatory element analysis in the promoter regions, which could influence the expression levels of cotton OXS3 genes. Furthermore, the expression patterns of the GhOXS3 gene were examined in different tissues or organs, as well as in developing ovules and fibers, with the highest expression observed in ovules. GhOXS3 genes exhibited a more pronounced regulatory response to abiotic stresses, of which ten GhOXS3 genes showed similar expression patterns under cold, heat, salt, and drought treatments. These observations were verified by quantitative real-time PCR experiments. These findings enhance our understanding of the evolutionary relationships and expression patterns of the OXS3 gene family and provide valuable insights for the identification of vital candidate genes for trait improvement in cotton breeding.
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Affiliation(s)
- Yu Chen
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (Y.C.); (R.Y.); (H.W.); (X.X.); (B.X.); (Y.L.); (Q.L.); (Q.L.); (R.P.)
| | - Rui Yang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (Y.C.); (R.Y.); (H.W.); (X.X.); (B.X.); (Y.L.); (Q.L.); (Q.L.); (R.P.)
- Xinjiang Production and Construction Corps Seventh Division Agricultural Research Institute, Kuitun 833200, China
| | - Haojie Wang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (Y.C.); (R.Y.); (H.W.); (X.X.); (B.X.); (Y.L.); (Q.L.); (Q.L.); (R.P.)
| | - Xianghui Xiao
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (Y.C.); (R.Y.); (H.W.); (X.X.); (B.X.); (Y.L.); (Q.L.); (Q.L.); (R.P.)
| | - Baoguang Xing
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (Y.C.); (R.Y.); (H.W.); (X.X.); (B.X.); (Y.L.); (Q.L.); (Q.L.); (R.P.)
| | - Yanfang Li
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (Y.C.); (R.Y.); (H.W.); (X.X.); (B.X.); (Y.L.); (Q.L.); (Q.L.); (R.P.)
| | - Qiankun Liu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (Y.C.); (R.Y.); (H.W.); (X.X.); (B.X.); (Y.L.); (Q.L.); (Q.L.); (R.P.)
| | - Quanwei Lu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (Y.C.); (R.Y.); (H.W.); (X.X.); (B.X.); (Y.L.); (Q.L.); (Q.L.); (R.P.)
| | - Renhai Peng
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (Y.C.); (R.Y.); (H.W.); (X.X.); (B.X.); (Y.L.); (Q.L.); (Q.L.); (R.P.)
| | - Guodong Chen
- College of Agriculture, Tarim University, Alar 843300, China
| | - Yongbo Wang
- Cotton Sciences Research Institute of Hunan, Changde 415101, China
| | - Pengtao Li
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (Y.C.); (R.Y.); (H.W.); (X.X.); (B.X.); (Y.L.); (Q.L.); (Q.L.); (R.P.)
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22
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Liu Y, Wei Z, Pei Y, Yang L, Zou X, Pei Y, Zhang T, Miao P, Gan L, Liu J, Yang Z, Peng J, Li F, Wang Z. Membrane Interactions of GET1 and GET2 Facilitate Fiber Cell Initiation through the Guided Entry of the TA Protein Pathway in Cotton. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:24283-24299. [PMID: 39467771 DOI: 10.1021/acs.jafc.4c06208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/30/2024]
Abstract
The guided entry of TA proteins (GET) pathway, which is responsible for the post-translational targeting and insertion of the tail-anchored (TA) protein into the endoplasmic reticulum (ER), plays an important role in physiological processes such as protein sorting, vesicle trafficking, cell apoptosis, and enzymatic reactions in which the GET1/2 complex is indispensable. However, a comprehensive study of the GET1 and GET2 genes and the GET pathway in cotton has not yet been carried out. Here, 12 GET1 and 21 GET2 genes were identified in nine representative plant species, and the phylogenetic relationships, gene structures, protein motifs, cis-regulatory elements (CREs), and temporal and spatial expression profiles were analyzed thoroughly. Our study indicated that GhGET1s and GhGET2s might be localized on ER membranes. According to expression profiling and CREs analysis, GhGET2-A02 was identified as a promising candidate for fiber cell development, interacting with two GhGET1s in the membrane, with a binding bias toward GhGET1-A06. Silencing of GhGET1-A06 or GhGET2-A02 reduced fiber initiation and elongation. In summary, our research provides important evidence for understanding the gene families and functions of GET1 and GET2 in cotton and provides clues for molecular breeding of high-quality cotton fiber varieties.
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Affiliation(s)
- Yang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
- Hainan Seed Industry Laboratory, Sanya 572000, China
| | - Zhenzhen Wei
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Yanfei Pei
- Hainan Seed Industry Laboratory, Sanya 572000, China
| | - Lu Yang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
| | - Xianyan Zou
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Yayue Pei
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Tianen Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
| | - Pengfei Miao
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
| | - Lei Gan
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Ji Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Jun Peng
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
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23
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Wang B, Wang Z, Tang Y, Zhong N, Wu J. Cotton BOP1 mediates SUMOylation of GhBES1 to regulate fibre development and plant architecture. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:3054-3067. [PMID: 39003587 PMCID: PMC11500983 DOI: 10.1111/pbi.14428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 06/05/2024] [Accepted: 06/27/2024] [Indexed: 07/15/2024]
Abstract
The Arabidopsis BLADE-ON-PETIOLE (BOP) genes are primarily known for their roles in regulating leaf and floral patterning. However, the broader functions of BOPs in regulating plant traits remain largely unexplored. In this study, we investigated the role of the Gossypium hirsutum BOP1 gene in the regulation of fibre length and plant height through the brassinosteroid (BR) signalling pathway. Transgenic cotton plants overexpressing GhBOP1 display shorter fibre lengths and reduced plant height compared to the wild type. Conversely, GhBOP1 knockdown led to increased plant height and longer fibre, indicating a connection with phenotypes influenced by the BR pathway. Our genetic evidence supports the notion that GhBOP1 regulates fibre length and plant height in a GhBES1-dependent manner, with GhBES1 being a major transcription factor in the BR signalling pathway. Yeast two-hybrid, luciferase complementation assay and pull-down assay results demonstrated a direct interaction between GhBOP1 and GhSUMO1, potentially forming protein complexes with GhBES1. In vitro and in vivo SUMOylation analyses revealed that GhBOP1 functions in an E3 ligase-like manner to mediate GhBES1 SUMOylation and subsequent degradation. Therefore, our study not only uncovers a novel mechanism of GhBES1 SUMOylation but also provides significant insights into how GhBOP1 regulates fibre length and plant height by controlling GhBES1 accumulation.
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Affiliation(s)
- Bingting Wang
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Zhian Wang
- Institute of Cotton Research, Shanxi Agricultural UniversityYunchengChina
| | - Ye Tang
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Naiqin Zhong
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Jiahe Wu
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
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24
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Cheng S, Zhu QH, Sun J. Special Issue: Cotton Molecular Genomics and Genetics 2.0. Int J Mol Sci 2024; 25:11255. [PMID: 39457039 PMCID: PMC11508491 DOI: 10.3390/ijms252011255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 10/17/2024] [Indexed: 10/28/2024] Open
Abstract
Cotton is a multiuse economic crop cultivated worldwide [...].
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Affiliation(s)
- Shuaishuai Cheng
- Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832000, China;
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Jie Sun
- Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832000, China;
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25
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Saleem MS, Khan SH, Ahmad A, Rana IA, Naveed ZA, Khan AI. The 4Fs of cotton: genome editing of cotton for fiber, food, feed, and fuel to achieve zero hunger. Front Genome Ed 2024; 6:1401088. [PMID: 39328243 PMCID: PMC11424549 DOI: 10.3389/fgeed.2024.1401088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 08/27/2024] [Indexed: 09/28/2024] Open
Abstract
Cotton is globally known for its high-priority cellulose-rich natural fiber. In addition to providing fiber for the textile industry, it is an important source material for edible oil, livestock feed, and fuel products. Global warming and the growing population are the major challenges to the world's agriculture and the potential risks to food security. In this context, improving output traits in cotton is necessary to achieve sustainable cotton production. During the last few years, high throughput omics techniques have aided in identifying crucial genes associated with traits of cotton fiber, seed, and plant architecture which could be targeted with more precision and efficiency through the CIRPSR/Cas-mediated genome editing technique. The various CRISPR/Cas systems such as CRISPR/Cas9, CRISPR/nCas9, and CRISPR/Cas12a have been employed to edit cotton genes associated with a wide range of traits including fiber length, flowering, leaf colour, rooting, seed oil, plant architecture, gossypol content, somatic embryogenesis, and biotic and abiotic stresses tolerance, highlighting its effectiveness in editing the cotton genome. Thus, CRISPR/Cas-mediated genome editing has emerged as a technique of choice to tailor crop phenotypes for better yield potential and environmental resilience. The review covers a comprehensive analysis of cotton phenotypic traits and their improvement with the help of the latest genome editing tools to improve fiber, food, feed, and fuel-associated genes of cotton to ensure food security.
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Affiliation(s)
- Muhammad Sulyman Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Aftab Ahmad
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Iqrar Ahmad Rana
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Zunaira Afzal Naveed
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Azeem Iqbal Khan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
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26
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Suo Q, Fang N, Zeng J, Yan F, Zhu X, Wang Y, Yu W, Chen J, Liang A, Li Y, Kong J, Xiao Y. R2R3 MYB Transcription Factor GhMYB201 Promotes Cotton Fiber Elongation via Cell Wall Loosening and Very-Long-Chain Fatty Acid Synthesis. Int J Mol Sci 2024; 25:9559. [PMID: 39273506 PMCID: PMC11395274 DOI: 10.3390/ijms25179559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 08/30/2024] [Accepted: 08/31/2024] [Indexed: 09/15/2024] Open
Abstract
Cotton fiber is the leading natural textile material, and fiber elongation plays an essential role in the formation of cotton yield and quality. Although a number of components in the molecular network controlling cotton fiber elongation have been reported, a lot of players still need to be functionally dissected to understand the regulatory mechanism of fiber elongation comprehensively. In the present study, an R2R3-MYB transcription factor gene, GhMYB201, was characterized and functionally verified via CRISPR/Cas9-mediated gene editing. GhMYB201 was homologous to Arabidopsis AtMYB60, and both coding genes (GhMYB201At and GhMYB201Dt) were preferentially expressed in elongating cotton fibers. Knocking-out of GhMYB201 significantly reduced the rate and duration of fiber elongation, resulting in shorter and coarser mature fibers. It was found that GhMYB201 could bind and activate the transcription of cell wall loosening genes (GhRDLs) and also β-ketoacyl-CoA synthase genes (GhKCSs) to enhance very-long-chain fatty acid (VLCFA) levels in elongating fibers. Taken together, our data demonstrated that the transcription factor GhMYB201s plays an essential role in promoting fiber elongation via activating genes related to cell wall loosening and VLCFA biosynthesis.
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Affiliation(s)
- Qingwei Suo
- Chongqing Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Nianjuan Fang
- Chongqing Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jianyan Zeng
- Chongqing Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Fulin Yan
- Chongqing Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Xi Zhu
- Chongqing Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yi Wang
- Chongqing Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Wanting Yu
- Chongqing Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Junmin Chen
- Chongqing Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Aimin Liang
- Chongqing Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yaohua Li
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Yuehua Xiao
- Chongqing Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
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27
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Huang G, Bao Z, Feng L, Zhai J, Wendel JF, Cao X, Zhu Y. A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development. Nat Genet 2024; 56:1953-1963. [PMID: 39147922 DOI: 10.1038/s41588-024-01877-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 07/18/2024] [Indexed: 08/17/2024]
Abstract
Assembly of complete genomes can reveal functional genetic elements missing from draft sequences. Here we present the near-complete telomere-to-telomere and contiguous genome of the cotton species Gossypium raimondii. Our assembly identified gaps and misoriented or misassembled regions in previous assemblies and produced 13 centromeres, with 25 chromosomal ends having telomeres. In contrast to satellite-rich Arabidopsis and rice centromeres, cotton centromeres lack phased CENH3 nucleosome positioning patterns and probably evolved by invasion from long terminal repeat retrotransposons. In-depth expression profiling of transposable elements revealed a previously unannotated DNA transposon (MuTC01) that interacts with miR2947 to produce trans-acting small interfering RNAs (siRNAs), one of which targets the newly evolved LEC2 (LEC2b) to produce phased siRNAs. Systematic genome editing experiments revealed that this tripartite module, miR2947-MuTC01-LEC2b, controls the morphogenesis of complex folded embryos characteristic of Gossypium and its close relatives in the cotton tribe. Our study reveals a trans-acting siRNA-based tripartite regulatory pathway for embryo development in higher plants.
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Affiliation(s)
- Gai Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Institute for Advanced Studies, Wuhan University, Wuhan, China.
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Zhigui Bao
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Li Feng
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuxian Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Institute for Advanced Studies, Wuhan University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
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28
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Xu F, Li G, He S, Zeng Z, Wang Q, Zhang H, Yan X, Hu Y, Tian H, Luo M. Sphingolipid inhibitor response gene GhMYB86 controls fiber elongation by regulating microtubule arrangement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1898-1914. [PMID: 38995105 DOI: 10.1111/jipb.13740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024]
Abstract
Although the cell membrane and cytoskeleton play essential roles in cellular morphogenesis, the interaction between the membrane and cytoskeleton is poorly understood. Cotton fibers are extremely elongated single cells, which makes them an ideal model for studying cell development. Here, we used the sphingolipid biosynthesis inhibitor, fumonisin B1 (FB1), and found that it effectively suppressed the myeloblastosis (MYB) transcription factor GhMYB86, thereby negatively affecting fiber elongation. A direct target of GhMYB86 is GhTUB7, which encodes the tubulin protein, the major component of the microtubule cytoskeleton. Interestingly, both the overexpression of GhMYB86 and GhTUB7 caused an ectopic microtubule arrangement at the fiber tips, and then leading to shortened fibers. Moreover, we found that GhMBE2 interacted with GhMYB86 and that FB1 and reactive oxygen species induced its transport into the nucleus, thereby enhancing the promotion of GhTUB7 by GhMYB86. Overall, we established a GhMBE2-GhMYB86-GhTUB7 regulation module for fiber elongation and revealed that membrane sphingolipids affect fiber elongation by altering microtubule arrangement.
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Affiliation(s)
- Fan Xu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Guiming Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Shengyang He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Dianjiang No.1 Middle School of Chongqing, Chongqing, 408300, China
| | - Zhifeng Zeng
- Yushan No.1 Senior High School, Shangrao, 334700, China
| | - Qiaoling Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Hongju Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Xingying Yan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Yulin Hu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Huidan Tian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Ming Luo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400715, China
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29
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Zhong A, Zou X, Wei Z, Gan L, Peng J, Li Y, Wang Z, Liu Y. Cotton Pectate Lyase GhPEL48_Dt Promotes Fiber Initiation Mediated by Histone Acetylation. PLANTS (BASEL, SWITZERLAND) 2024; 13:2356. [PMID: 39273840 PMCID: PMC11397362 DOI: 10.3390/plants13172356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/18/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024]
Abstract
GhPEL48_Dt, a Pectate lyase (PEL, EC4.2.2.2), is a crucial enzyme involved in cell-wall modification and pectin degradation. Studies have shown that the GhPEL48_Dt also plays a significant role in cotton-fiber development; however, the specific function and regulatory mechanism of GhPEL48_Dt in cotton-fiber development are still not fully understood. Here, we found that the histone deacetylase inhibitor-Trichostatin A significantly reduces the transcript levels of GhPEL48_Dt and its enzyme activity. Further, silencing of GhPEL48_Dt significantly inhibits the initiation and elongation of cotton fibers by promoting pectin degradation, and the heterologous expression of GhPEL48_Dt promotes the development of trichomes and root hairs in Arabidopsis, which suggests that GhPEL48_Dt plays a positive and conserved role in single cell i.e., fiber, root hair, and leaf trichome development. Collectively, this paper provides a comprehensive analysis of the fundamental characteristics and functions of GhPEL48_Dt in fiber development, including the regulatory role of histone acetylation on GhPEL48_Dt, which contributes to the understanding of pectin degradation pathways and establishes a theoretical foundation for elucidating its regulatory mechanism.
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Affiliation(s)
- Anlin Zhong
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Xianyan Zou
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Zhenzhen Wei
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Lei Gan
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Jun Peng
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Yonghui Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Yuanyuan Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
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30
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Li P, Chen Y, Yang R, Sun Z, Ge Q, Xiao X, Yang S, Li Y, Liu Q, Zhang A, Xing B, Wu B, Du X, Liu X, Tang B, Gong J, Lu Q, Shi Y, Yuan Y, Peng R, Shang H. Co-Expression Network Analysis and Introgressive Gene Identification for Fiber Length and Strength Reveal Transcriptional Differences in 15 Cotton Chromosome Substitution Segment Lines and Their Upland and Sea Island Parents. PLANTS (BASEL, SWITZERLAND) 2024; 13:2308. [PMID: 39204744 PMCID: PMC11359254 DOI: 10.3390/plants13162308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/04/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Fiber length (FL) and strength (FS) are the core indicators for evaluating cotton fiber quality. The corresponding stages of fiber elongation and secondary wall thickening are of great significance in determining FL and FS formation, respectively. QTL mapping and high-throughput sequencing technology have been applied to dissect the molecular mechanism of fiber development. In this study, 15 cotton chromosome segment substitution lines (CSSLs) with significant differences in FL and FS, together with their recurrent parental Gossypium hirsutum line CCRI45 and donor parent G. barbadense line Hai1, were chosen to conduct RNA-seq on developing fiber samples at 10 days post anthesis (DPA) and 20 DPA. Differentially expressed genes (DEGs) were obtained via pairwise comparisons among all 24 samples (each one with three biological repeats). A total of 969 DEGs related to FL-high, 1285 DEGs to FS-high, and 997 DEGs to FQ-high were identified. The functional enrichment analyses of them indicated that the GO terms of cell wall structure and ROS, carbohydrate, and phenylpropanoid metabolism were significantly enriched, while the GO terms of glucose and polysaccharide biosynthesis, and brassinosteroid and glycosylphosphatidylinositol metabolism could make great contributions to FL and FS formation, respectively. Weighted gene co-expressed network analyses (WGCNA) were separately conducted for analyzing FL and FS traits, and their corresponding hub DEGs were screened in significantly correlated expression modules, such as EXPA8, XTH, and HMA in the fiber elongation and WRKY, TDT, and RAC-like 2 during secondary wall thickening. An integrated analysis of these hub DEGs with previous QTL identification results successfully identified a total of 33 candidate introgressive DEGs with non-synonymous mutations between the Gh and Gb species. A common DEG encoding receptor-like protein kinase 1 was reported to likely participate in fiber secondary cell thickening regulation by brassionsteroid signaling. Such valuable information was conducive to enlightening the developing mechanism of cotton fiber and also provided an abundant gene pool for further molecular breeding.
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Affiliation(s)
- Pengtao Li
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
| | - Yu Chen
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (R.Y.); (Z.S.); (Q.G.)
| | - Rui Yang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (R.Y.); (Z.S.); (Q.G.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- Xinjiang Production and Construction Corps Seventh Division Agricultural Research Institute, Kuitun 833200, China
| | - Zhihao Sun
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (R.Y.); (Z.S.); (Q.G.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Qun Ge
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (R.Y.); (Z.S.); (Q.G.)
| | - Xianghui Xiao
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
| | - Shuhan Yang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
| | - Yanfang Li
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
| | - Qiankun Liu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (R.Y.); (Z.S.); (Q.G.)
| | - Aiming Zhang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
| | - Baoguang Xing
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
| | - Bei Wu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
| | - Xue Du
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
| | - Xiaoyan Liu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
| | - Baomeng Tang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (R.Y.); (Z.S.); (Q.G.)
| | - Juwu Gong
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (R.Y.); (Z.S.); (Q.G.)
| | - Quanwei Lu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (R.Y.); (Z.S.); (Q.G.)
| | - Yuzhen Shi
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (R.Y.); (Z.S.); (Q.G.)
| | - Youlu Yuan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (R.Y.); (Z.S.); (Q.G.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- Agricultural Technology Popularization Center of Kashgar, Kashgar 844000, China
| | - Renhai Peng
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China; (P.L.); (Y.C.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Haihong Shang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
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Ma J, Yang L, Dang Y, Shahzad K, Song J, Jia B, Wang L, Feng J, Wang N, Pei W, Wu M, Zhang X, Zhang J, Wu J, Yu J. Deciphering the dynamic expression network of fiber elongation and the functional role of the GhTUB5 gene for fiber length in cotton based on an introgression population of upland cotton. J Adv Res 2024:S2090-1232(24)00324-2. [PMID: 39106927 DOI: 10.1016/j.jare.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/02/2024] [Accepted: 08/02/2024] [Indexed: 08/09/2024] Open
Abstract
INTRODUCTION Interspecific introgression between Gossypium hirsutum and G. barbadense allows breeding cotton with outstanding fiber length (FL). However, the dynamic gene regulatory network of FL-related genes has not been characterized, and the functional mechanism through which the hub gene GhTUB5 mediates fiber elongation has yet to be determined. METHODS Coexpression analyses of 277 developing fiber transcriptomes integrated with QTL mapping using 250 introgression lines of different FL phenotypes were conducted to identify genes related to fiber elongation. The function of GhTUB5 was determined by ectopic expression of two TUB5 alleles in Arabidopsis and knockout of GhTUB5 in upland cotton. Yeast two-hybrid, split-luciferase and pull-down assays were conducted to screen for interacting proteins, and upstream genes were identified by yeast one-hybrid, dual-LUC and electrophoretic mobility shift assays. RESULTS The 32,612, 30,837 and 30,277 genes expressed at 5, 10 and 15 days postanthesis (dpa) were grouped into 19 distinct coexpression modules, and 988 genes in the MEblack module were enriched in the cell wall process and exhibited significant associations with FL. A total of 20 FL-QTLs were identified, each explaining 3.34-16.04 % of the phenotypic variance in the FL. Furthermore, several FL-QTLs contained 15 genes that were differentially expressed in the MEblack module including the tubulin beta gene (TUB5). Compared with the wild type, the overexpression of GhTUB5 and GbTUB5 in Arabidopsis suppressed root cell length but promoted cellulose synthesis. Knockout of GhTUB5 resulted in longer fiber lines. Protein-based experiments revealed that GhTUB5 interacts with GhZFP6. Additionally, GhTUB5 was directly activated by GhHD-ZIP7, a homeobox-leucine zipper transcription factor, and its paralogous gene was previously reported to mediate fiber elongation. CONCLUSION This study opens a new avenue to dissect functional mechanism of cotton fiber elongation. Our findings provide some molecular details on how GhTUB5 mediates the FL phenotype in cotton.
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Affiliation(s)
- Jianjiang Ma
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Liupeng Yang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuanyue Dang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Kashif Shahzad
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jikun Song
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bing Jia
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Juanjuan Feng
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Nuohan Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Man Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, USA.
| | - Jianyong Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
| | - Jiwen Yu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China; Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China.
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Zhao N, Guo A, Wang W, Li B, Wang M, Zhou Z, Jiang K, Aierxi A, Wang B, Adjibolosoo D, Xia Z, Li H, Cui Y, Kong J, Hua J. GbPP2C80 Interacts with GbWAKL14 to Negatively Co-Regulate Resistance to Fusarium and Verticillium wilt via MPK3 and ROS Signaling in Sea Island Cotton. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309785. [PMID: 38889299 PMCID: PMC11321686 DOI: 10.1002/advs.202309785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/21/2024] [Indexed: 06/20/2024]
Abstract
Fusarium wilt (FW) is widespread in global cotton production, but the mechanism underlying FW resistance in superior-fiber-quality Sea Island cotton is unclear. This study reveals that FW resistance has been the target of genetic improvement of Sea Island cotton in China since the 2010s. The key nonsynonymous single nucleotide polymorphism (SNP, T/C) of gene Gbar_D03G001670 encoding protein phosphatase 2C 80 (PP2C80) results in an amino acid shift (L/S), which is significantly associated with FW resistance of Sea Island cotton. Silencing GbPP2C80 increases FW resistance in Sea Island cotton, whereas overexpressing GbPP2C80 reduces FW resistance in Arabidopsis. GbPP2C80 and GbWAKL14 exist synergistically in Sea Island cotton accessions with haplotype forms "susceptible-susceptible" (TA) and "resistant-resistant" (CC), and interact with each other. CRISPR/Cas9-mediated knockout of GbWAKL14 enhances FW and Verticillium wilt (VW) resistance in upland cotton and overexpression of GbWAKL14 and GbPP2C80 weakens FW and VW resistance in Arabidopsis. GbPP2C80 and GbWAKL14 respond to FW and VW by modulating reactive oxygen species (ROS) content via affecting MPK3 expression. In summary, two tandem genes on chromosome D03, GbPP2C80, and GbWAKL14, functions as cooperative negative regulators in cotton wilt disease defense, providing novel genetic resources and molecular markers for the development of resistant cotton cultivars.
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Affiliation(s)
- Nan Zhao
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100193China
| | - Anhui Guo
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100193China
| | - Weiran Wang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesUrumqiXinjiang830091China
| | - Bin Li
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100193China
| | - Meng Wang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesUrumqiXinjiang830091China
| | - Zixin Zhou
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesUrumqiXinjiang830091China
| | - Kaiyun Jiang
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100193China
| | - Alifu Aierxi
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesUrumqiXinjiang830091China
| | - Baoliang Wang
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100193China
| | - Daniel Adjibolosoo
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100193China
| | - Zhanghao Xia
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100193China
| | - Huijing Li
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100193China
| | - Yanan Cui
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100193China
| | - Jie Kong
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesUrumqiXinjiang830091China
| | - Jinping Hua
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100193China
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Sun Y, Han Y, Liu B, Jiang M, Sheng K, Li H, Yang P, Zhu QH, Sun J, Chen J, Zhu S, Zhao T. GoPGS regulates cotton pigment gland size and contributes to biotic stress tolerance through jasmonic acid pathways. THE NEW PHYTOLOGIST 2024; 243:839-845. [PMID: 38845449 DOI: 10.1111/nph.19884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/19/2024] [Indexed: 07/05/2024]
Affiliation(s)
- Yue Sun
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yifei Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Bin Liu
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100094, China
| | - Meng Jiang
- Institute of Hainan, Zhejiang University, Hangzhou, 310058, China
| | - Kuang Sheng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Huazu Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ping Yang
- Agricultural Experiment Station, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, 2601, ACT, Australia
| | - Jie Sun
- Agricultural College, Shihezi University, Shihezi, 832003, China
| | - Jinhong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Institute of Hainan, Zhejiang University, Hangzhou, 310058, China
| | - Shuijin Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Institute of Hainan, Zhejiang University, Hangzhou, 310058, China
| | - Tianlun Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Institute of Hainan, Zhejiang University, Hangzhou, 310058, China
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Li Y, Shen W, Zhang X, Cui Y, Zhao Y, Guo Y, Li X, Wang S, Song G, Wang P, Ma J, Lin J. Single-cell characterization of major components of plant cell walls in situ by Raman spectroscopy. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1772-1774. [PMID: 38644446 DOI: 10.1007/s11427-024-2542-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 04/23/2024]
Affiliation(s)
- Yujian Li
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Weiwei Shen
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xi Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yaning Cui
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yuanyuan Zhao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yayu Guo
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaojuan Li
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuizhong Wang
- Beijing Key Laboratory of Lignocellulosic Chemistry, Engineering Research Center of Forestry Biomass Materials and Energy, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Guoyong Song
- Beijing Key Laboratory of Lignocellulosic Chemistry, Engineering Research Center of Forestry Biomass Materials and Energy, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Pu Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Jianfeng Ma
- Key lab of Bamboo and Rattan Science & Technology, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Jinxing Lin
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China.
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Zhang S, Cai X, Wei J, Wang H, Liu C, Li X, Tang L, Zhou X, Zhang J. GhWRKY40 Interacts with an Asparaginase GhAP D6 Involved in Fiber Development in Upland Cotton ( Gossypium hirsutum L.). Genes (Basel) 2024; 15:979. [PMID: 39202340 PMCID: PMC11353873 DOI: 10.3390/genes15080979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/15/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Fiber quality improvement is a primary goal in cotton breeding. Identification of fiber quality-related genes and understanding the underlying molecular mechanisms are essential prerequisites. Previously, studies determined that silencing the gene GhWRKY40 resulted in longer cotton fibers; however, both the underlying mechanisms and whether this transcription factor is additionally involved in the regulation of cotton fiber strength/fineness are unknown. In the current study, we verified that GhWRKY40 influences the fiber strength, fiber fineness, and fiber surface structure by using virus-induced gene silencing (VIGS). Potential proteins that may interact with the nucleus-localized GhWRKY40 were screened in a yeast two-hybrid (Y2H) nuclear-system cDNA library constructed from fibers at 0, 10, and 25 days post-anthesis (DPA) in two near-isogenic lines differing in fiber length and strength. An aspartyl protease/asparaginase-related protein, GhAPD6, was identified and confirmed by Y2H and split-luciferase complementation assays. The expression of GhAPD6 was approximately 30-fold higher in the GhWRKY40-VIGS lines at 10 DPA and aspartyl protease activity was significantly upregulated in the GhWRKY40-VIGS lines at 10-20 DPA. This study suggested that GhWRKY40 may interact with GhAPD6 to regulate fiber development in cotton. The results provide a theoretical reference for the selection and breeding of high-quality cotton fibers assisted by molecular technology.
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Affiliation(s)
- Sujun Zhang
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China; (S.Z.); (X.C.); (H.W.); (C.L.); (X.L.); (L.T.); (X.Z.)
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang 050051, China
| | - Xiao Cai
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China; (S.Z.); (X.C.); (H.W.); (C.L.); (X.L.); (L.T.); (X.Z.)
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang 050051, China
| | - Jingyan Wei
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Haitao Wang
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China; (S.Z.); (X.C.); (H.W.); (C.L.); (X.L.); (L.T.); (X.Z.)
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang 050051, China
| | - Cunjing Liu
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China; (S.Z.); (X.C.); (H.W.); (C.L.); (X.L.); (L.T.); (X.Z.)
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang 050051, China
| | - Xinghe Li
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China; (S.Z.); (X.C.); (H.W.); (C.L.); (X.L.); (L.T.); (X.Z.)
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang 050051, China
| | - Liyuan Tang
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China; (S.Z.); (X.C.); (H.W.); (C.L.); (X.L.); (L.T.); (X.Z.)
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang 050051, China
| | - Xiaodong Zhou
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China; (S.Z.); (X.C.); (H.W.); (C.L.); (X.L.); (L.T.); (X.Z.)
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang 050051, China
| | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China; (S.Z.); (X.C.); (H.W.); (C.L.); (X.L.); (L.T.); (X.Z.)
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang 050051, China
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Liu L, Grover CE, Kong X, Jareczek J, Wang X, Si A, Wang J, Yu Y, Chen Z. Expression profile analysis of cotton fiber secondary cell wall thickening stage. PeerJ 2024; 12:e17682. [PMID: 38993976 PMCID: PMC11238726 DOI: 10.7717/peerj.17682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/13/2024] [Indexed: 07/13/2024] Open
Abstract
To determine the genes associated with the fiber strength trait in cotton, three different cotton cultivars were selected: Sea Island cotton (Xinhai 32, with hyper-long fibers labeled as HL), and upland cotton (17-24, with long fibers labeled as L, and 62-33, with short fibers labeled as S). These cultivars were chosen to assess fiber samples with varying qualities. RNA-seq technology was used to analyze the expression profiles of cotton fibers at the secondary cell wall (SCW) thickening stage (20, 25, and 30 days post-anthesis (DPA)). The results showed that a large number of differentially expressed genes (DEGs) were obtained from the three assessed cotton cultivars at different stages of SCW development. For instance, at 20 DPA, Sea Island cotton (HL) had 6,215 and 5,364 DEGs compared to upland cotton 17-24 (L) and 62-33 (S), respectively. Meanwhile, there were 1,236 DEGs between two upland cotton cultivars, 17-24 (L) and 62-33 (S). Gene Ontology (GO) term enrichment identified 42 functions, including 20 biological processes, 11 cellular components, and 11 molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified several pathways involved in SCW synthesis and thickening, such as glycolysis/gluconeogenesis, galactose metabolism, propanoate metabolism, biosynthesis of unsaturated fatty acids pathway, valine, leucine and isoleucine degradation, fatty acid elongation pathways, and plant hormone signal transduction. Through the identification of shared DEGs, 46 DEGs were found to exhibit considerable expressional differences at different fiber stages from the three cotton cultivars. These shared DEGs have functions including REDOX enzymes, binding proteins, hydrolases (such as GDSL thioesterase), transferases, metalloproteins (cytochromatin-like genes), kinases, carbohydrates, and transcription factors (MYB and WRKY). Therefore, RT-qPCR was performed to verify the expression levels of nine of the 46 identified DEGs, an approach which demonstrated the reliability of RNA-seq data. Our results provided valuable molecular resources for clarifying the cell biology of SCW biosynthesis during fiber development in cotton.
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Affiliation(s)
- Li Liu
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Xianhui Kong
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China
| | - Josef Jareczek
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Xuwen Wang
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China
| | - Aijun Si
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China
| | - Juan Wang
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China
| | - Yu Yu
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China
| | - Zhiwen Chen
- Engineering Research Center of Coal-based Ecological Carbon Sequestration Technology of the Ministry of Education, Key Laboratory of Graphene Forestry Application of National Forest and Grass Administration, Shanxi Datong University, Datong, China
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37
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Guang H, Xiaoyang G, Zhian W, Ye W, Peng W, Linfang S, Bingting W, Anhong Z, Fuguang L, Jiahe W. The cotton MYB33 gene is a hub gene regulating the trade-off between plant growth and defense in Verticillium dahliae infection. J Adv Res 2024; 61:1-17. [PMID: 37648022 PMCID: PMC11258673 DOI: 10.1016/j.jare.2023.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/16/2023] [Accepted: 08/26/2023] [Indexed: 09/01/2023] Open
Abstract
INTRODUCTION Sessile plants engage in trade-offs between growth and defense capacity in response to fluctuating environmental cues. MYB is an important transcription factor that plays many important roles in controlling plant growth and defense. However, the mechanism behind how it keeps a balance between these two physiological processes is still largely unknown. OBJECTIVES Our work focuses on the dissection of the molecular mechanism by which GhMYB33 regulates plant growth and defense. METHODS The CRISPR/Cas9 technique was used to generate mutants for deciphering GhMYB33 functions. Yeast two-hybrid, luciferase complementary imaging, and co-immunoprecipitation assays were used to prove that proteins interact with each other. We used the electrophoretic mobility shift assay, yeast one-hybrid, and luciferase activity assays to analyze GhMYB33 acting as a promoter. A β-glucuronidase fusion reporter and 5' RNA ligase mediated amplification of cDNA ends analysis showed that ghr-miR319c directedly cleaved the GhMYB33 mRNA. RESULTS Overexpressing miR319c-resistant GhMYB33 (rGhMYB33) promoted plant growth, accompanied by a significant decline in resistance against Verticillium dahliae. Conversely, its knockout mutant, ghmyb33, demonstrated growth restriction and concomitant augmentation of V. dahliae resistance. GhMYB33 was found to couple with the DELLA protein GhGAI1 and bind to the specific cis-elements of GhSPL9 and GhDFR1 promoters, thereby modulating internode elongation and plant resistance in V. dahliae infection. The ghr-miR319c was discovered to target and suppress GhMYB33 expression. The overexpression of ghr-miR319c led to enhanced plant resistance and a simultaneous reduction in plant height. CONCLUSION Our findings demonstrate that GhMYB33 encodes a hub protein and controls the expression of GhSPL9 and GhDFR1, implicating a pivotal role for the miR319c-MYB33 module to regulate the trade-offs between plant growth and defense.
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Affiliation(s)
- Hu Guang
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ge Xiaoyang
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wang Zhian
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng 044000, China
| | - Wang Ye
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wang Peng
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shi Linfang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wang Bingting
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhang Anhong
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng 044000, China
| | - Li Fuguang
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Wu Jiahe
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Yi C, Liu Q, Huang Y, Liu C, Guo X, Fan C, Zhang K, Liu Y, Han F. Non-B-form DNA is associated with centromere stability in newly-formed polyploid wheat. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1479-1488. [PMID: 38639838 DOI: 10.1007/s11427-023-2513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/18/2023] [Indexed: 04/20/2024]
Abstract
Non-B-form DNA differs from the classic B-DNA double helix structure and plays a crucial regulatory role in replication and transcription. However, the role of non-B-form DNA in centromeres, especially in polyploid wheat, remains elusive. Here, we systematically analyzed seven non-B-form DNA motif profiles (A-phased DNA repeat, direct repeat, G-quadruplex, inverted repeat, mirror repeat, short tandem repeat, and Z-DNA) in hexaploid wheat. We found that three of these non-B-form DNA motifs were enriched at centromeric regions, especially at the CENH3-binding sites, suggesting that non-B-form DNA may create a favorable loading environment for the CENH3 nucleosome. To investigate the dynamics of centromeric non-B form DNA during the alloploidization process, we analyzed DNA secondary structure using CENH3 ChIP-seq data from newly formed allotetraploid wheat and its two diploid ancestors. We found that newly formed allotetraploid wheat formed more non-B-form DNA in centromeric regions compared with their parents, suggesting that non-B-form DNA is related to the localization of the centromeric regions in newly formed wheat. Furthermore, non-B-form DNA enriched in the centromeric regions was found to preferentially form on young LTR retrotransposons, explaining CENH3's tendency to bind to younger LTR. Collectively, our study describes the landscape of non-B-form DNA in the wheat genome, and sheds light on its potential role in the evolution of polyploid centromeres.
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Affiliation(s)
- Congyang Yi
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhong Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chang Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianrui Guo
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaolan Fan
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kaibiao Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fangpu Han
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Sun R, Wu Y, Zhang X, Lv M, Yu D, Sun Y. Chromosome-level genome assembly and annotation of a potential model organism Gossypium arboreum ZB-1. Sci Data 2024; 11:620. [PMID: 38866802 PMCID: PMC11169495 DOI: 10.1038/s41597-024-03481-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Recent advancements in plant regeneration and synthetic polyploid creation have been documented in Gossypium arboreum ZB-1. These developments make ZB-1 a potential model within the Gossypium genus for investigating gene function and polyploidy. This work generated the sequence and annotation of the ZB-1 genome. The contig-level genome was constructed using the PacBio high-fidelity reads, encompassing 81 contigs with an N50 length of 112.12 Mb. The Hi-C data assisted the construction of the chromosome-level genome, which consists of 13 pseudo-chromosomes and 39 un-anchored contigs, with a total length of about 1.67 Gb. Repetitive sequences accounted for about 69.7% of the genome in length. Based on ab initio and evidence-based prediction, we have identified 48,021 protein-coding genes in the ZB-1 genome. Comparative genomics analysis revealed conserved gene content and arrangement between ZB-1 and G. arboreum SXY1. The single nucleotide polymorphism occurrence rate between ZB-1 and SXY1 was about 0.54 per 1,000 nucleotides. This study enriched the genomic resources for further exploration into cotton regeneration and polyploidy mechanisms.
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Affiliation(s)
- Rongnan Sun
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Yuqing Wu
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Xinyu Zhang
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Minghua Lv
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Dongliang Yu
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China.
| | - Yuqiang Sun
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China.
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Hui F, Tang X, Li B, Alariqi M, Xu Z, Meng Q, Hu Y, Wang G, Zhang Y, Zhang X, Jin S. Robust CRISPR/Mb2Cas12a genome editing tools in cotton plants. IMETA 2024; 3:e209. [PMID: 38898989 PMCID: PMC11183160 DOI: 10.1002/imt2.209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
The efficiency and accuracy of the CRISPR/Mb2Cas12a system were demonstrated in cotton, achieving an efficiency of over 90% at target sites. Notably, Mb2Cas12a exhibited significant tolerance under different temperatures ranging from 22°C to 32°C. Additionally, the Mb2Cas12a system revealed effective editing at more relaxed VTTV PAM sites in the cotton genome, which expanded the genome editing range by approximately 2.6-fold than the wide-type LbCas12a. Finally, a multiplex genome editing system was also developed based on Mb2Cas12a, enabling simultaneous editing of eight target sites using a single crRNA cassette.
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Affiliation(s)
- Fengjiao Hui
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xu Tang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life SciencesSouthwest UniversityChongqingChina
| | - Bo Li
- Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural SciencesXinjiang Key Laboratory of Crop BiotechnologyUrumqiChina
| | - Muna Alariqi
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhongping Xu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Qingying Meng
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yongxue Hu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Guanying Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yong Zhang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life SciencesSouthwest UniversityChongqingChina
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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Li W, Chen X, Yu J, Zhu Y. Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution, lignin biosynthesis regulation, and stress tolerance. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1266-1279. [PMID: 38763999 DOI: 10.1007/s11427-024-2580-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/26/2024] [Indexed: 05/21/2024]
Abstract
Durian (Durio zibethinus) is a tropical fruit that has a unique flavor and aroma. It occupies a significant phylogenetic position within the Malvaceae family. Extant core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling, resulting in an abundant genomic diversity. However, the ancestral karyotypes of the Malvaceae family, as well as the evolution trajectory leading to the 28 chromosomes in durian, remain poorly understood. Here, we report the high-quality assembly of the durian genome with comprehensive comparative genomic analyses. By analyzing the collinear blocks between cacao and durian, we inferred 11 Malvaceae ancestral karyotypes. These blocks were present in a single-copy form in cacao and mainly in triplicates in durian, possibly resulting from a recent whole genome triplication (WGT) event that led to hexaploidization of the durian genome around 20 (17-24) million years ago. A large proportion of the duplicated genes in durian, such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis, are derived directly from whole genome duplication, which makes it an important force in reshaping its genomic architecture. Transcriptome studies have revealed that genes involved in feruloyl-CoA formations were highly preferentially expressed in fruit peels, indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl lignins. Among all the analyzed transcription factors (TFs), members of the heat shock factor family (HSF) were the most significantly upregulated under heat stress. All subfamilies of genes encoding heat shock proteins (HSPs) in the durian genome appear to have undergone expansion. The potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally verified. Our study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian genome. We also provide insights into the mechanism underlying lignin biosynthesis and heat stress tolerance.
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Affiliation(s)
- Wanwan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Xin Chen
- The State Key Laboratory of Protein and Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jianing Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
| | - Yuxian Zhu
- The Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
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Chen Y, Xiao X, Yang R, Sun Z, Yang S, Zhang H, Xing B, Li Y, Liu Q, Lu Q, Shi Y, Yuan Y, Miao C, Li P. Genome-wide identification and expression-pattern analysis of sulfate transporter (SULTR) gene family in cotton under multiple abiotic stresses and fiber development. Funct Integr Genomics 2024; 24:108. [PMID: 38773054 DOI: 10.1007/s10142-024-01387-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
Sulfate transporter (SULTR) proteins are in charge of the transport and absorption on sulfate substances, and have been reported to play vital roles in the biological processes of plant growth and stress response. However, there were few reports of genome-wide identification and expression-pattern analysis of SULTRs in Hibiscus mutabilis. Gossypium genus is a ideal model for studying the allopolyploidy, therefore two diploid species (G. raimondii and G. arboreum) and two tetraploid species (G. hirsutum and G. barbadense) were chosen in this study to perform bioinformatic analyses, identifying 18, 18, 35, and 35 SULTR members, respectively. All the 106 cotton SULTR genes were utilized to construct the phylogenetic tree together with 11 Arabidopsis thaliana, 13 Oryza sativa, and 8 Zea mays ones, which was divided into Group1-Group4. The clustering analyses of gene structures and 10 conserved motifs among the cotton SULTR genes showed the consistent evolutionary relationship with the phylogenetic tree, and the results of gene-duplication identification among the four representative Gossypium species indicated that genome-wide or segment duplication might make main contributions to the expansion of SULTR gene family in cotton. Having conducted the cis-regulatory element analysis in promoter region, we noticed that the existing salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) elements could have influences with expression levels of cotton SULTR genes. The expression patterns of GhSULTR genes were also investigated on the 7 different tissues or organs and the developing ovules and fibers, most of which were highly expressed in root, stem, sepal, receptacel, ovule at 10 DPA, and fiber at 20 and 25 DPA. In addition, more active regulatory were observed in GhSULTR genes responding to multiple abiotic stresses, and 12 highly expressed genes showed the similar expression patterns in the quantitative Real-time PCR experiments under cold, heat, salt, and drought treatments. These findings broaden our insight into the evolutionary relationships and expression patterns of the SULTR gene family in cotton, and provide the valuable information for further screening the vital candidate genes on trait improvement.
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Affiliation(s)
- Yu Chen
- Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, 455000, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xianghui Xiao
- Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, 455000, China
| | - Rui Yang
- Xinjiang Production and Construction Corps Seventh Division Agricultural Research Institute, Kuitun, 833200, China
| | - Zhihao Sun
- Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, 455000, China
| | - Shuhan Yang
- Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, 455000, China
| | - Haibo Zhang
- Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, 455000, China
| | - Baoguang Xing
- Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, 455000, China
| | - Yanfang Li
- Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, 455000, China
| | - Qiankun Liu
- Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, 455000, China
| | - Quanwei Lu
- Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China
| | - Yuzhen Shi
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, 455000, China
| | - Youlu Yuan
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, 455000, China.
| | - Chen Miao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Pengtao Li
- Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China.
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, 455000, China.
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Shao L, Jin S, Chen J, Yang G, Fan R, Zhang Z, Deng Q, Han J, Ma X, Dong Z, Lu H, Hu W, Wang K, Hu L, Shen Z, Huang S, Zhao T, Guan X, Hu Y, Zhang T, Fang L. High-quality genomes of Bombax ceiba and Ceiba pentandra provide insights into the evolution of Malvaceae species and differences in their natural fiber development. PLANT COMMUNICATIONS 2024; 5:100832. [PMID: 38321741 PMCID: PMC11121743 DOI: 10.1016/j.xplc.2024.100832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/15/2023] [Accepted: 02/01/2024] [Indexed: 02/08/2024]
Abstract
Members of the Malvaceae family, including Corchorus spp., Gossypium spp., Bombax spp., and Ceiba spp., are important sources of natural fibers. In the past decade, the genomes of several Malvaceae species have been assembled; however, the evolutionary history of Malvaceae species and the differences in their fiber development remain to be clarified. Here, we report the genome assembly and annotation of two natural fiber plants from the Malvaceae, Bombax ceiba and Ceiba pentandra, whose assembled genome sizes are 783.56 Mb and 1575.47 Mb, respectively. Comparative analysis revealed that whole-genome duplication and Gypsy long terminal repeat retroelements have been the major causes of differences in chromosome number (2n = 14 to 2n = 96) and genome size (234 Mb to 2676 Mb) among Malvaceae species. We also used comparative genomic analyses to reconstruct the ancestral Malvaceae karyotype with 11 proto-chromosomes, providing new insights into the evolutionary trajectories of Malvaceae species. MYB-MIXTA-like 3 is relatively conserved among the Malvaceae and functions in fiber cell-fate determination in the epidermis. It appears to perform this function in any tissue where it is expressed, i.e. in fibers on the endocarp of B. ceiba and in ovule fibers of cotton. We identified a structural variation in a cellulose synthase gene and a higher copy number of cellulose synthase-like genes as possible causes of the finer, less spinnable, weaker fibers of B. ceiba. Our study provides two high-quality genomes of natural fiber plants and offers insights into the evolution of Malvaceae species and differences in their natural fiber formation and development through multi-omics analysis.
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Affiliation(s)
- Lei Shao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Shangkun Jin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guangsui Yang
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Rui Fan
- Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Zhiyuan Zhang
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Qian Deng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jin Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaowei Ma
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zeyu Dong
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hejun Lu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wanying Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Lisong Hu
- Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Zhen Shen
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Surong Huang
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
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Huang J, Ma S, Zhou M, Liu Z, Liang Q. Cytochemical localization and synthesis mechanism of the glucomannan in pseudobulbs of Bletilla striata Reichb. f. HORTICULTURE RESEARCH 2024; 11:uhae092. [PMID: 38799126 PMCID: PMC11116825 DOI: 10.1093/hr/uhae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/25/2024] [Indexed: 05/29/2024]
Abstract
The dried pseudobulbs of Bletilla striata, an important traditional Chinese medicine named BaiJi, have an extraordinary polysaccharide content and excellent prospects for medicinal effects. However, the distribution and molecular mechanism underlying biosynthesis are poorly understood. In this study, chemical and immunologic analyses were performed in representative tissues of B. striata, and the results showed that what are conventionally termed Bletilla striata polysaccharides (BSPs) are water-soluble polysaccharides deposited only in pseudobulbs. The structural component of BSPs is glucomannan, with a mannose:glucose mass ratio of ~3:2. BSPs are present in the parenchyma of the pseudobulbs in cells known as glucomannan idioblasts and distributed in the cytoplasm within cellular membranes, but are not contained in the vacuole. Comparative transcriptomics and bioinformatics analyses mapped the pathway from sucrose to BSP and identified BsGPI, BsmanA, and BsCSLAs as the key genes of BSP biosynthesis, suggesting that the functional differentiation of the cellulose synthase-like family A (CSLA) may be critical for the flow of glucomannan to the BSP or cell wall. Subsequently, virus-mediated gene silencing showed that silencing of two CSLAs (Bs03G11846 and Bs03G11849) led to a decrease in BSP content, and yeast two-hybrid and luciferase complementation experiments confirmed that four CSLAs (Bs03G11846, Bs03G11847, Bs03G11848, and Bs03G11849) can form homo- or heterodimers, suggesting that multiple CSLAs may form a large complex that functions in BSP synthesis. Our results provide cytological evidence of BSP and describe the isolation and characterization of candidate genes involved in BSP synthesis, laying a solid foundation for further research on its regulation mechanisms and the genetic engineering breeding of B. striata.
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Affiliation(s)
- Junfeng Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Shuang Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Ming Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhihao Liu
- Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi City 435002, China
| | - Qiong Liang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Zhang J, Meng Q, Wang Q, Zhang H, Tian H, Wang T, Xu F, Yan X, Luo M. Cotton sphingosine kinase GhLCBK1 participates in fiber cell elongation by affecting sphingosine-1-phophate and auxin synthesis. Int J Biol Macromol 2024; 267:131323. [PMID: 38574912 DOI: 10.1016/j.ijbiomac.2024.131323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/30/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024]
Abstract
Sphingolipids serve as essential components of biomembrane and possess significant bioactive properties. Sphingosine-1-phophate (S1P) plays a key role in plant resistance to stress, but its specific impact on plant growth and development remains to be fully elucidated. Cotton fiber cells are an ideal material for investigating the growth and maturation of plant cells. In this study, we examined the content and composition of sphingosine (Sph) and S1P throughout the progression of fiber cell development. The content of S1P elevated gradually during fiber elongation but declined during the transition stage. Exogenous application of S1P promoted fiber elongation while using of FTY720 (an antagonist of S1P), and DMS (an inhibitor of LCBK) hindered fiber elongation. Cotton Long Chain Base Kinase 1 (GhLCBK1) was notably expressed during the fiber elongation stage, containing all conserved domains of LCBK protein and localized in the endoplasmic reticulum. Overexpression GhLCBK1 increased the S1P content and promoted fiber elongation while retarded secondary cell wall (SCW) deposition. Conversely, downregulation of GhLCBK1 reduced the S1P levels, and suppressed fiber elongation, and accelerated SCW deposition. Transcriptome analysis revealed that upregulating GhLCBK1 or applying S1P induced the expression of GhEXPANSIN and auxin related genes. Furthermore, the levels of IAA were elevated and reduced in the fibers when up-regulating or down-regulating GhLCBK1, respectively. Our investigation demonstrated that GhLCBK1 and its product S1P facilitated the elongation of fiber cells by affecting auxin biosynthesis. This study contributes novel insights into the intricate regulatory pathways involved in fiber cell elongation, identifying GhLCBK1 as a potential target gene and laying the groundwork for enhancing fiber quality via genetic manipulation.
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Affiliation(s)
- Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Qian Meng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Qiaoling Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Hongju Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Huidan Tian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Tiantian Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Fan Xu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xingying Yan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Ming Luo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China.
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Tang L, Liu C, Li X, Wang H, Zhang S, Cai X, Zhang J. An aldehyde dehydrogenase gene, GhALDH7B4_A06, positively regulates fiber strength in upland cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1377682. [PMID: 38736450 PMCID: PMC11082362 DOI: 10.3389/fpls.2024.1377682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/09/2024] [Indexed: 05/14/2024]
Abstract
High fiber strength (FS) premium cotton has significant market demand. Consequently, enhancing FS is a major objective in breeding quality cotton. However, there is a notable lack of known functionally applicable genes that can be targeted for breeding. To address this issue, our study used specific length-amplified fragment sequencing combined with bulk segregant analysis to study FS trait in an F2 population. Subsequently, we integrated these results with previous quantitative trait locus mapping results regarding fiber quality, which used simple sequence repeat markers in F2, F2:3, and recombinant inbred line populations. We identified a stable quantitative trait locus qFSA06 associated with FS located on chromosome A06 (90.74-90.83 Mb). Within this interval, we cloned a gene, GhALDH7B4_A06, which harbored a critical mutation site in coding sequences that is distinct in the two parents of the tested cotton line. In the paternal parent Ji228, the gene is normal and referred to as GhALDH7B4_A06O; however, there is a nonsense mutation in the maternal parent Ji567 that results in premature termination of protein translation, and this gene is designated as truncated GhALDH7B4_A06S. Validation using recombinant inbred lines and gene expression analysis revealed that this mutation site is correlated with cotton FS. Virus-induced gene silencing of GhALDH7B4 in cotton caused significant decreases in FS and fiber micronaire. Conversely, GhALDH7B4_A06O overexpression in Arabidopsis boosted cell wall component contents in the stem. The findings of our study provide a candidate gene for improving cotton fiber quality through molecular breeding.
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Affiliation(s)
| | | | | | | | | | | | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, Hebei, China
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Li C, Zhao J, Liu Z, Yang Y, Lai C, Ma J, Aierxi A. Comparative Transcriptomic Analysis of Gossypium hirsutum Fiber Development in Mutant Materials ( xin w 139) Provides New Insights into Cotton Fiber Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:1127. [PMID: 38674536 PMCID: PMC11054599 DOI: 10.3390/plants13081127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/02/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024]
Abstract
Cotton is the most widely planted fiber crop in the world, and improving cotton fiber quality has long been a research hotspot. The development of cotton fibers is a complex process that includes four consecutive and overlapping stages, and although many studies on cotton fiber development have been reported, most of the studies have been based on cultivars that are promoted in production or based on lines that are used in breeding. Here, we report a phenotypic evaluation of Gossypium hirsutum based on immature fiber mutant (xin w 139) and wild-type (Xin W 139) lines and a comparative transcriptomic study at seven time points during fiber development. The results of the two-year study showed that the fiber length, fiber strength, single-boll weight and lint percentage of xin w 139 were significantly lower than those of Xin W 139, and there were no significant differences in the other traits. Principal component analysis (PCA) and cluster analysis of the RNA-sequencing (RNA-seq) data revealed that these seven time points could be clearly divided into three different groups corresponding to the initiation, elongation and secondary cell wall (SCW) synthesis stages of fiber development, and the differences in fiber development between the two lines were mainly due to developmental differences after twenty days post anthesis (DPA). Differential expression analysis revealed a total of 5131 unique differentially expressed genes (DEGs), including 290 transcription factors (TFs), between the 2 lines. These DEGs were divided into five clusters. Each cluster functional category was annotated based on the KEGG database, and different clusters could describe different stages of fiber development. In addition, we constructed a gene regulatory network by weighted correlation network analysis (WGCNA) and identified 15 key genes that determined the differences in fiber development between the 2 lines. We also screened seven candidate genes related to cotton fiber development through comparative sequence analysis and qRT-PCR; these genes included three TFs (GH_A08G1821 (bHLH), GH_D05G3074 (Dof), and GH_D13G0161 (C3H)). These results provide a theoretical basis for obtaining an in-depth understanding of the molecular mechanism of cotton fiber development and provide new genetic resources for cotton fiber research.
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Affiliation(s)
- Chunping Li
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.L.); (Z.L.); (Y.Y.); (C.L.)
| | - Jieyin Zhao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China;
| | - Zhongshan Liu
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.L.); (Z.L.); (Y.Y.); (C.L.)
| | - Yanlong Yang
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.L.); (Z.L.); (Y.Y.); (C.L.)
| | - Chengxia Lai
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.L.); (Z.L.); (Y.Y.); (C.L.)
| | - Jun Ma
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.L.); (Z.L.); (Y.Y.); (C.L.)
| | - Alifu Aierxi
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.L.); (Z.L.); (Y.Y.); (C.L.)
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48
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Li J, Zhao Y, Wu Z, Wang X. Editorial: Crop improvement by omics and bioinformatics. FRONTIERS IN PLANT SCIENCE 2024; 15:1391334. [PMID: 38633453 PMCID: PMC11022161 DOI: 10.3389/fpls.2024.1391334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024]
Affiliation(s)
- Jun Li
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Zhichao Wu
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Xueqiang Wang
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Yazhouwan National Laboratory, Sanya, Hainan, China
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49
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Liu S, Cheng H, Zhang Y, He M, Zuo D, Wang Q, Lv L, Lin Z, Song G. Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement. Genes (Basel) 2024; 15:378. [PMID: 38540437 PMCID: PMC10970022 DOI: 10.3390/genes15030378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 06/14/2024] Open
Abstract
Genomic data in Gossypium provide numerous data resources for the cotton genomics community. However, to fill the gap between genomic analysis and breeding field work, detecting the featured genomic items of a subset cohort is essential for geneticists. We developed FPFinder v1.0 software to identify a subset of the cohort's fingerprint genomic sites. The FPFinder was developed based on the term frequency-inverse document frequency algorithm. With the short-read sequencing of an elite cotton pedigree, we identified 453 pedigree fingerprint genomic sites and found that these pedigree-featured sites had a role in cotton development. In addition, we applied FPFinder to evaluate the geographical bias of fiber-length-related genomic sites from a modern cotton cohort consisting of 410 accessions. Enriching elite sites in cultivars from the Yangtze River region resulted in the longer fiber length of Yangze River-sourced accessions. Apart from characterizing functional sites, we also identified 12,536 region-specific genomic sites. Combining the transcriptome data of multiple tissues and samples under various abiotic stresses, we found that several region-specific sites contributed to environmental adaptation. In this research, FPFinder revealed the role of the cotton pedigree fingerprint and region-specific sites in cotton development and environmental adaptation, respectively. The FPFinder can be applied broadly in other crops and contribute to genetic breeding in the future.
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Affiliation(s)
- Shang Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Hailiang Cheng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
- Zhengzhou Research Base, Zhengzhou University, Zhengzhou 450001, China
| | - Youping Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Man He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Dongyun Zuo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Qiaolian Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Limin Lv
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Zhongxv Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Guoli Song
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
- Zhengzhou Research Base, Zhengzhou University, Zhengzhou 450001, China
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50
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Yang Y, Li X, Li C, Zhang H, Tuerxun Z, Hui F, Li J, Liu Z, Chen G, Cai D, Chen X, Li B. Isolation and Functional Characterization of a Constitutive Promoter in Upland Cotton ( Gossypium hirsutum L.). Int J Mol Sci 2024; 25:1917. [PMID: 38339199 PMCID: PMC10855717 DOI: 10.3390/ijms25031917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Multiple cis-acting elements are present in promoter sequences that play critical regulatory roles in gene transcription and expression. In this study, we isolated the cotton FDH (Fiddlehead) gene promoter (pGhFDH) using a real-time reverse transcription-PCR (qRT-PCR) expression analysis and performed a cis-acting elements prediction analysis. The plant expression vector pGhFDH::GUS was constructed using the Gateway approach and was used for the genetic transformation of Arabidopsis and upland cotton plants to obtain transgenic lines. Histochemical staining and a β-glucuronidase (GUS) activity assay showed that the GUS protein was detected in the roots, stems, leaves, inflorescences, and pods of transgenic Arabidopsis thaliana lines. Notably, high GUS activity was observed in different tissues. In the transgenic lines, high GUS activity was detected in different tissues such as leaves, stalks, buds, petals, androecium, endosperm, and fibers, where the pGhFDH-driven GUS expression levels were 3-10-fold higher compared to those under the CaMV 35S promoter at 10-30 days post-anthesis (DPA) during fiber development. The results indicate that pGhFDH can be used as an endogenous constitutive promoter to drive the expression of target genes in various cotton tissues to facilitate functional genomic studies and accelerate cotton molecular breeding.
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Affiliation(s)
- Yang Yang
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Xiaorong Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Chenyu Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China
| | - Hui Zhang
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Zumuremu Tuerxun
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Fengjiao Hui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
| | - Juan Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Zhigang Liu
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Guo Chen
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Darun Cai
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Xunji Chen
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Bo Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
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