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Danso B, Ackah M, Jin X, Ayittey DM, Amoako FK, Zhao W. Genome-Wide Analysis of the Xyloglucan Endotransglucosylase/Hydrolase ( XTH) Gene Family: Expression Pattern during Magnesium Stress Treatment in the Mulberry Plant ( Morus alba L.) Leaves. PLANTS (BASEL, SWITZERLAND) 2024; 13:902. [PMID: 38592929 PMCID: PMC10975095 DOI: 10.3390/plants13060902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 03/01/2024] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
Abstract
Mulberry (Morus alba L.), a significant fruit tree crop, requires magnesium (Mg) for its optimal growth and productivity. Nonetheless, our understanding of the molecular basis underlying magnesium stress tolerance in mulberry plants remains unexplored. In our previous study, we identified several differential candidate genes associated with Mg homeostasis via transcriptome analysis, including the xyloglucan endotransglucosylase/hydrolase (XTH) gene family. The XTH gene family is crucial for plant cell wall reconstruction and stress responses. These genes have been identified and thoroughly investigated in various plant species. However, there is no research pertaining to XTH genes within the M. alba plant. This research systematically examined the M. alba XTH (MaXTH) gene family at the genomic level using a bioinformatic approach. In total, 22 MaXTH genes were discovered and contained the Glyco_hydro_16 and XET_C conserved domains. The MaXTHs were categorized into five distinct groups by their phylogenetic relationships. The gene structure possesses four exons and three introns. Furthermore, the MaXTH gene promoter analysis reveals a plethora of cis-regulatory elements, mainly stress responsiveness, phytohormone responsiveness, and growth and development. GO analysis indicated that MaXTHs encode proteins that exhibit xyloglucan xyloglucosyl transferase and hydrolase activities in addition to cell wall biogenesis as well as xyloglucan and carbohydrate metabolic processes. Moreover, a synteny analysis unveiled an evolutionary relationship between the XTH genes in M. alba and those in three other species: A. thaliana, P. trichocarpa, and Zea mays. Expression profiles from RNA-Seq data displayed distinct expression patterns of XTH genes in M. alba leaf tissue during Mg treatments. Real-time quantitative PCR analysis confirmed the expression of the MaXTH genes in Mg stress response. Overall, this research enhances our understanding of the characteristics of MaXTH gene family members and lays the foundation for future functional genomic study in M. alba.
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Affiliation(s)
- Blessing Danso
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (B.D.)
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Michael Ackah
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (B.D.)
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Xin Jin
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (B.D.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Derek M. Ayittey
- School of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201308, China
| | - Frank Kwarteng Amoako
- Institute of Plant Nutrition and Soil Science, Kiel University, Hermann-Rodewald-Straße 2, 24118 Kiel, Germany;
| | - Weiguo Zhao
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (B.D.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
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Wu A, Lian B, Hao P, Fu X, Zhang M, Lu J, Ma L, Yu S, Wei H, Wang H. GhMYB30-GhMUR3 affects fiber elongation and secondary wall thickening in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:694-712. [PMID: 37988560 DOI: 10.1111/tpj.16523] [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: 05/20/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Xyloglucan, an important hemicellulose, plays a crucial role in maintaining cell wall structure and cell elongation. However, the effects of xyloglucan on cotton fiber development are not well understood. GhMUR3 encodes a xyloglucan galactosyltransferase that is essential for xyloglucan synthesis and is highly expressed during fiber elongation. In this study, we report that GhMUR3 participates in cotton fiber development under the regulation of GhMYB30. Overexpression GhMUR3 affects the fiber elongation and cell wall thickening. Transcriptome showed that the expression of genes involved in secondary cell wall synthesis was prematurely activated in OE-MUR3 lines. In addition, GhMYB30 was identified as a key regulator of GhMUR3 by Y1H, Dual-Luc, and electrophoretic mobility shift assay (EMSA) assays. GhMYB30 directly bound the GhMUR3 promoter and activated GhMUR3 expression. Furthermore, DAP-seq of GhMYB30 was performed to identify its target genes in the whole genome. The results showed that many target genes were associated with fiber development, including cell wall synthesis-related genes, BR-related genes, reactive oxygen species pathway genes, and VLCFA synthesis genes. It was demonstrated that GhMYB30 may regulate fiber development through multiple pathways. Additionally, GhMYB46 was confirmed to be a target gene of GhMYB30 by EMSA, and GhMYB46 was significantly increased in GhMYB30-silenced lines, indicating that GhMYB30 inhibited GhMYB46 expression. Overall, these results revealed that GhMUR3 under the regulation of GhMYB30 and plays an essential role in cotton fiber elongation and secondary wall thickening. Additionally, GhMYB30 plays an important role in the regulation of fiber development and regulates fiber secondary wall synthesis by inhibiting the expression of GhMYB46.
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Affiliation(s)
- Aimin Wu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430000, Hubei, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Boying Lian
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Pengbo Hao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaokang Fu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meng Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jianhua Lu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Liang Ma
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Shuxun Yu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430000, Hubei, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hengling Wei
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hantao Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
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Gao Y, Wang L, Li D, Qi D, Fang F, Luo Y, Zhang H, Zhang S. Genome-wide characterization of the xyloglucan endotransglucosylase/hydrolase family genes and their response to plant hormone in sugar beet. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108239. [PMID: 38113720 DOI: 10.1016/j.plaphy.2023.108239] [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: 07/06/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
Xyloglucan endotransglucosylase/hydrolases (XTHs) play a crucial role in plant growth and development. However, their functional response to phytohormone in sugar beet still remains obscure. In this study, we identified 30 putative BvXTH genes in the sugar beet genome. Phylogenetic and evolutionary relationship analysis revealed that they were clustered into three groups and have gone through eight tandem duplication events under purifying selection. Gene structure and motif composition analysis demonstrated that they were highly conserved and all contained one conserved glycoside hydrolase family 16 domain (Glyco_hydro_16) and one xyloglucan endotransglycosylase C-terminus (XET_C) domain. Transcriptional expression analysis exhibited that all BvXTHs were ubiquitously expressed in leaves, root hairs and tuberous roots, and most of them were up-regulated by brassinolide (BR), jasmonic acid (JA), abscisic acid (ABA) and gibberellic acid (GA3). Further mutant complementary experiment demonstrated that expression of BvXTH17 rescued the retarded growth phenotype of xth22, an Arabidopsis knock out mutant of AtXTH22. The findings in our work provide fundamental information on the structure and evolutionary relationship of the XTH family genes in sugar beet, and reveal the potential function of BvXTH17 in plant growth and hormone response.
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Affiliation(s)
- Yachao Gao
- Sugar Beet Physiological Research Institute, Inner Mongolia Agricultural University, Hohhot, China.
| | - Limin Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China.
| | - Dong Li
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China
| | - Dazhuang Qi
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China.
| | - Fengyan Fang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China.
| | - Yuankai Luo
- Sugar Beet Physiological Research Institute, Inner Mongolia Agricultural University, Hohhot, China.
| | - Hongxia Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China.
| | - Shaoying Zhang
- Sugar Beet Physiological Research Institute, Inner Mongolia Agricultural University, Hohhot, China.
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Wen X, Chen Z, Yang Z, Wang M, Jin S, Wang G, Zhang L, Wang L, Li J, Saeed S, He S, Wang Z, Wang K, Kong Z, Li F, Zhang X, Chen X, Zhu Y. A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2214-2256. [PMID: 36899210 DOI: 10.1007/s11427-022-2278-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 03/12/2023]
Abstract
Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.
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Affiliation(s)
- Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Maojun Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianying Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sumbul Saeed
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Li H, Tao H, Xiao Y, Qin L, Lan C, Cheng B, Roberts JA, Zhang X, Lu X. ZmXYL modulates auxin-induced maize growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1699-1715. [PMID: 37300848 DOI: 10.1111/tpj.16348] [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: 07/27/2022] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
Plant architecture, lodging resistance, and yield are closely associated with height. In this paper, we report the identification and characterization of two allelic EMS-induced mutants of Zea mays, xyl-1, and xyl-2 that display dwarf phenotypes. The mutated gene, ZmXYL, encodes an α-xylosidase which functions in releasing xylosyl residue from a β-1,4-linked glucan chain. Total α-xylosidase activity in the two alleles is significantly decreased compared to wild-type plants. Loss-of-function mutants of ZmXYL resulted in a decreased xylose content, an increased XXXG content in xyloglucan (XyG), and a reduced auxin content. We show that auxin has an antagonistic effect with XXXG in promoting cell divisions within mesocotyl tissue. xyl-1 and xyl-2 were less sensitive to IAA compared to B73. Based on our study, a model is proposed that places XXXG, an oligosaccharide derived from XyG and the substrate of ZmXYL, as having a negative impact on auxin homeostasis resulting in the dwarf phenotypes of the xyl mutants. Our results provide a insight into the roles of oligosaccharides released from plant cell walls as signals in mediating plant growth and development.
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Affiliation(s)
- Haiyan Li
- National Engineering Laboratory of Crop Stress Resistance, School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Huifang Tao
- National Engineering Laboratory of Crop Stress Resistance, School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Yao Xiao
- National Engineering Laboratory of Crop Stress Resistance, School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Li Qin
- Institute of Advanced Agricultural Technology, Qilu Normal University, Jinan, 250200, China
| | - Chen Lan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, China
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance, School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Jeremy A Roberts
- Faculty of Science and Engineering, School of Biological & Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, China
| | - Xiaoduo Lu
- National Engineering Laboratory of Crop Stress Resistance, School of Life Science, Anhui Agricultural University, Hefei, 230036, China
- Institute of Advanced Agricultural Technology, Qilu Normal University, Jinan, 250200, China
- Lab of Molecular Breeding by Design in Maize Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572000, China
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Jareczek JJ, Grover CE, Hu G, Xiong X, Arick Ii MA, Peterson DG, Wendel JF. Domestication over Speciation in Allopolyploid Cotton Species: A Stronger Transcriptomic Pull. Genes (Basel) 2023; 14:1301. [PMID: 37372480 DOI: 10.3390/genes14061301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Cotton has been domesticated independently four times for its fiber, but the genomic targets of selection during each domestication event are mostly unknown. Comparative analysis of the transcriptome during cotton fiber development in wild and cultivated materials holds promise for revealing how independent domestications led to the superficially similar modern cotton fiber phenotype in upland (G. hirsutum) and Pima (G. barbadense) cotton cultivars. Here we examined the fiber transcriptomes of both wild and domesticated G. hirsutum and G. barbadense to compare the effects of speciation versus domestication, performing differential gene expression analysis and coexpression network analysis at four developmental timepoints (5, 10, 15, or 20 days after flowering) spanning primary and secondary wall synthesis. These analyses revealed extensive differential expression between species, timepoints, domestication states, and particularly the intersection of domestication and species. Differential expression was higher when comparing domesticated accessions of the two species than between the wild, indicating that domestication had a greater impact on the transcriptome than speciation. Network analysis showed significant interspecific differences in coexpression network topology, module membership, and connectivity. Despite these differences, some modules or module functions were subject to parallel domestication in both species. Taken together, these results indicate that independent domestication led G. hirsutum and G. barbadense down unique pathways but that it also leveraged similar modules of coexpression to arrive at similar domesticated phenotypes.
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Affiliation(s)
- Josef J Jareczek
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
- Biology Department, Bellarmine University, Louisville, KY 40205, USA
| | - Corrinne E Grover
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
| | - Guanjing Hu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, 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 518120, 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 518120, China
| | - Mark A Arick Ii
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jonathan F Wendel
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
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Han J, Liu Y, Shen Y, Li W. A Surprising Diversity of Xyloglucan Endotransglucosylase/Hydrolase in Wheat: New in Sight to the Roles in Drought Tolerance. Int J Mol Sci 2023; 24:9886. [PMID: 37373033 DOI: 10.3390/ijms24129886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Drought has become a major limiting factor for wheat productivity, and its negative impact on crop growth is anticipated to increase with climate deterioration in arid areas. Xyloglucan endoglycosylases/hydrolases (XTHs) are involved in constructing and remodeling cell wall structures and play an essential role in regulating cell wall extensibility and stress responses. However, there are no systematic studies on the wheat XTH gene family. In this study, 71 wheat XTH genes (TaXTHs) were characterized and classified into three subgroups through phylogenetic analysis. Genomic replication promoted the expansion of TaXTHs. We found a catalytically active motif and a potential N-linked glycosylation domain in all TaXTHs. Further expression analysis revealed that many TaXTHs in the roots and shoots were significantly associated with drought stress. The wheat TaXTH12.5a gene was transferred into Arabidopsis to verify a possible role of TaXTHs in stress response. The transgenic plants possessed higher seed germination rates and longer roots and exhibited improved tolerance to drought. In conclusion, bioinformatics and gene expression pattern analysis indicated that the TaXTH genes played a role in regulating drought response in wheat. The expression of TaXTH12.5a enhanced drought tolerance in Arabidopsis and supported the XTH genes' role in regulating drought stress response in plants.
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Affiliation(s)
- Junjie Han
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832003, China
| | - Yichen Liu
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832003, China
| | - Yiting Shen
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832003, China
| | - Weihua Li
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832003, China
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8
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Yang Z, Liu Z, Ge X, Lu L, Qin W, Qanmber G, Liu L, Wang Z, Li F. Brassinosteroids regulate cotton fiber elongation by modulating very-long-chain fatty acid biosynthesis. THE PLANT CELL 2023; 35:2114-2131. [PMID: 36861340 DOI: 10.1093/plcell/koad060] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/02/2023] [Accepted: 02/27/2023] [Indexed: 05/30/2023]
Abstract
Brassinosteroid (BR), a growth-promoting phytohormone, regulates many plant growth processes including cell development. However, the mechanism by which BR regulates fiber growth is poorly understood. Cotton (Gossypium hirsutum) fibers are an ideal single-cell model in which to study cell elongation due to their length. Here we report that BR controls cotton fiber elongation by modulating very-long-chain fatty acid (VLCFA) biosynthesis. BR deficiency reduces the expression of 3-ketoacyl-CoA synthases (GhKCSs), the rate-limiting enzymes involved in VLCFA biosynthesis, leading to lower saturated VLCFA contents in pagoda1 (pag1) mutant fibers. In vitro ovule culture experiments show that BR acts upstream of VLCFAs. Silencing of BRI1-EMS-SUPPRESOR 1.4 (GhBES1.4), encoding a master transcription factor of the BR signaling pathway, significantly reduces fiber length, whereas GhBES1.4 overexpression produces longer fibers. GhBES1.4 regulates endogenous VLCFA contents and directly binds to BR RESPONSE ELEMENTS (BRREs) in the GhKCS10_At promoter region, which in turn regulates GhKCS10_At expression to increase endogenous VLCFA contents. GhKCS10_At overexpression promotes cotton fiber elongation, whereas GhKCS10_At silencing inhibits cotton fiber growth, supporting a positive regulatory role for GhKCS10_At in fiber elongation. Overall, these results uncover a mechanism of fiber elongation through crosstalk between BR and VLCFAs at the single-cell level.
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Affiliation(s)
- Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China
| | - Zhao Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan, China
| | - Xiaoyang Ge
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan, China
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan, China
| | - Wenqiang Qin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan, China
| | - Ghulam Qanmber
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan, China
| | - Le Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China
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9
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Li Y, Si Z, Wang G, Shi Z, Chen J, Qi G, Jin S, Han Z, Gao W, Tian Y, Mao Y, Fang L, Hu Y, Chen H, Zhu X, Zhang T. Genomic insights into the genetic basis of cotton breeding in China. MOLECULAR PLANT 2023; 16:662-677. [PMID: 36738104 DOI: 10.1016/j.molp.2023.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/08/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
The excellent Upland cotton (Gossypium hirsutum) cultivars developed since 1949 have made a huge contribution to cotton production in China, the world's largest producer and consumer of cotton. However, the genetic and genomic basis for the improvements of these cotton cultivars remains largely unclear. In this study, we selected 16 Upland cotton cultivars with important historical status in Chinese cotton breeding and constructed a multiparent, advanced generation, intercross (MAGIC) population comprising 920 recombinant inbred lines. A genome-wide association study using the MAGIC population identified 54 genomic loci associated with lint yield and fiber quality. Of them, 25 (46.30%) pleiotropic genomic loci cause simultaneous changes of lint yield and/or fiber quality traits, revealing complex trade-offs and linkage drags in Upland cotton agronomic traits. Deep sequencing data of 11 introduced ancestor cultivars and publicly available resequencing datasets of 839 cultivars developed in China during the past 70 years were integrated to explore the historical distribution and origin of the elite or selected alleles. Interestingly, 85% of these elite alleles were selected and fixed from different American ancestors, consistent with cotton breeding practices in China. However, seven elite alleles of native origin that are responsible for Fusarium wilt resistance, early maturing, good-quality fiber, and other characteristics were not found in American ancestors but have greatly contributed to Chinese cotton breeding and wide cultivation. Taken together, these results provide a genetic basis for further improving cotton cultivars and reveal that the genetic composition of Chinese cotton cultivars is narrow and mainly derived from early introduced American varieties.
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Affiliation(s)
- Yiqian Li
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guoping Wang
- Xinjiang Production and Construction Corps Seventh Division Agricultural Research Institute, Kuintun, China
| | - Zhuolin Shi
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guoan Qi
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shangkun Jin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zegang Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wenhao Gao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yue Tian
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China; College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yun Mao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hong Chen
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture, Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xiefei Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
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10
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Liu L, Chen G, Li S, Gu Y, Lu L, Qanmber G, Mendu V, Liu Z, Li F, Yang Z. A brassinosteroid transcriptional regulatory network participates in regulating fiber elongation in cotton. PLANT PHYSIOLOGY 2023; 191:1985-2000. [PMID: 36542688 PMCID: PMC10022633 DOI: 10.1093/plphys/kiac590] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/02/2022] [Accepted: 12/02/2022] [Indexed: 05/30/2023]
Abstract
Brassinosteroids (BRs) participate in the regulation of plant growth and development through BRI1-EMS-SUPPRESSOR1 (BES1)/BRASSINAZOLE-RESISTANT1 (BZR1) family transcription factors. Cotton (Gossypium hirsutum) fibers are highly elongated single cells, and BRs play a vital role in the regulation of fiber elongation. However, the mode of action on how BR is involved in the regulation of cotton fiber elongation remains unexplored. Here, we generated GhBES1.4 over expression lines and found that overexpression of GhBES1.4 promoted fiber elongation, whereas silencing of GhBES1.4 reduced fiber length. DNA affinity purification and sequencing (DAP-seq) identified 1,531 target genes of GhBES1.4, and five recognition motifs of GhBES1.4 were identified by enrichment analysis. Combined analysis of DAP-seq and RNA-seq data of GhBES1.4-OE/RNAi provided mechanistic insights into GhBES1.4-mediated regulation of cotton fiber development. Further, with the integrated approach of GWAS, RNA-seq, and DAP-seq, we identified seven genes related to fiber elongation that were directly regulated by GhBES1.4. Of them, we showed Cytochrome P450 84A1 (GhCYP84A1) and 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (GhHMG1) promote cotton fiber elongation. Overall, the present study established the role of GhBES1.4-mediated gene regulation and laid the foundation for further understanding the mechanism of BR participation in regulating fiber development.
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Affiliation(s)
- Le Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Guoquan Chen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Shengdong Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yu Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Ghulam Qanmber
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Venugopal Mendu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Zhao Liu
- Author for correspondence: (Z.Y.), (F.L.), (Z.L.)
| | - Fuguang Li
- Author for correspondence: (Z.Y.), (F.L.), (Z.L.)
| | - Zuoren Yang
- Author for correspondence: (Z.Y.), (F.L.), (Z.L.)
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11
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Li N, Zhang Y, Wang X, Ma H, Sun Y, Li G, Zhang S. Integration of Transcriptomic and Proteomic Profiles Reveals Multiple Levels of Genetic Regulation of Taproot Growth in Sugar Beet ( Beta vulgaris L.). FRONTIERS IN PLANT SCIENCE 2022; 13:882753. [PMID: 35909753 PMCID: PMC9326478 DOI: 10.3389/fpls.2022.882753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Sugar beet taproot growth and development is a complex biological process involving morphogenesis and dry matter accumulation. However, the molecular regulatory mechanisms underlying taproot growth and development remain elusive. We performed a correlation analysis of the proteome and transcriptome in two cultivars (SD13829 and BS02) at the start and the highest points of the taproot growth rate. The corresponding correlation coefficients were 0.6189, 0.7714, 0.6803, and 0.7056 in four comparison groups. A total of 621 genes were regulated at both transcriptional and translational levels, including 190, 71, 140, and 220 in the BS59-VS-BS82, BS59-VS-SD59, BS82-VS-SD82, and SD59-VS-SD82 groups, respectively. Ten, 32, and 68 correlated-DEGs-DEPs (cor-DEGs-DEPs) were significantly enrdiched in the proteome and transcriptome of the BS59-VS-BS82, SD59-VS-SD82, and BS82-VS-SD82 groups, respectively, which included ribonuclease 1-like protein, DEAD-box ATP-dependent RNA helicase, TolB protein, heat shock protein 83, 20 kDa chaperonin, polygalacturonase, endochitinase, brassinolide and gibberellin receptors (BRI1 and GID1), and xyloglucan endotransglucosylase/hydrolase (XTH). In addition, Beta vulgaris XTH could enhance the growth and development of Arabidopsis primary roots by improving cell growth in the root tip elongation zone. These findings suggested that taproot growth and expansion might be regulated at transcriptional and posttranscriptional levels and also may be attributed to cell wall metabolism to improve cell wall loosening and elongation.
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12
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Zhu J, Tang G, Xu P, Li G, Ma C, Li P, Jiang C, Shan L, Wan S. Genome-wide identification of xyloglucan endotransglucosylase/hydrolase gene family members in peanut and their expression profiles during seed germination. PeerJ 2022; 10:e13428. [PMID: 35602895 PMCID: PMC9121870 DOI: 10.7717/peerj.13428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/21/2022] [Indexed: 01/14/2023] Open
Abstract
Seed germination marks the beginning of a new plant life cycle. Improving the germination rate of seeds and the consistency of seedling emergence in the field could improve crop yields. Many genes are involved in the regulation of seed germination. Our previous study found that some peanut XTHs (xyloglucan endotransglucosylases/hydrolases) were expressed at higher levels at the newly germinated stage. However, studies of the XTH gene family in peanut have not been reported. In this study, a total of 58 AhXTH genes were identified in the peanut genome. Phylogenetic analysis showed that these AhXTHs, along with 33 AtXTHs from Arabidopsis and 61 GmXTHs from soybean, were classified into three subgroups: the I/II, IIIA and IIIB subclades. All AhXTH genes were unevenly distributed on the 18 peanut chromosomes, with the exception of chr. 07 and 17, and they had relatively conserved exon-intron patterns, most with three to four introns. Through chromosomal distribution pattern and synteny analysis, it was found that the AhXTH family experienced many replication events, including 42 pairs of segmental duplications and 23 pairs of tandem duplications, during genome evolution. Conserved motif analysis indicated that their encoded proteins contained the conserved ExDxE domain and N-linked glycosylation sites and displayed the conserved secondary structural loops 1-3 in members of the same group. Expression profile analysis of freshly harvested seeds, dried seeds, and newly germinated seeds using transcriptome data revealed that 26 AhXTH genes, which account for 45% of the gene family, had relatively higher expression levels at the seed germination stage, implying the important roles of AhXTHs in regulating seed germination. The results of quantitative real-time PCR also confirmed that some AhXTHs were upregulated during seed germination. The results of GUS histochemical staining showed that AhXTH4 was mainly expressed in germinated seeds and etiolated seedlings and had higher expression levels in elongated hypocotyls. AhXTH4 was also verified to play a crucial role in the cell elongation of hypocotyls during seed germination.
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Affiliation(s)
- Jieqiong Zhu
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Guiying Tang
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Pingli Xu
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Guowei Li
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Changle Ma
- College of Life Science, Shandong Normal University, Jinan, China
| | - Pengxiang Li
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Chunyu Jiang
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Lei Shan
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Shubo Wan
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
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13
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Zhang J, Mei H, Lu H, Chen R, Hu Y, Zhang T. Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development. FRONTIERS IN PLANT SCIENCE 2022; 13:864529. [PMID: 35463423 PMCID: PMC9022538 DOI: 10.3389/fpls.2022.864529] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Gossypium hirsutum and Gossypium barbadense are the widely cultivated tetraploid cottons around the world, which evolved great differences in the fiber yield and quality due to the independent domestication process. To reveal the genetic basis of the difference, we integrated 90 samples from ten time points during the fiber developmental period for investigating the dynamics of gene expression changes associated with fiber in G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 and acc. 3-79. Globally, 44,484 genes expressed in all three cultivars account for 61.14% of the total genes. About 61.39% (N = 3,412) of the cotton transcription factors were involved in fiber development, which consisted of 58 cotton TF families. The differential analysis of intra- and interspecies showed that 3 DPA had more expression changes. To discover the genes with temporally changed expression profiles during the whole fiber development, 1,850 genes predominantly expressed in G. hirsutum and 1,050 in G. barbadense were identified, respectively. Based on the weighted gene co-expression network and time-course analysis, several candidate genes, mainly involved in the secondary cell wall synthesis and phytohormones, were identified in this study, underlying possibly the transcriptional regulation and molecular mechanisms of the fiber quality differences between G. barbadense and G. hirsutum. The quantitative real-time PCR validation of the candidate genes was consistent with the RNA-seq data. Our study provides a strong rationale for the analysis of gene function and breeding of high-quality cotton.
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14
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Pei L, Huang X, Liu Z, Tian X, You J, Li J, Fang DD, Lindsey K, Zhu L, Zhang X, Wang M. Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation. Genome Biol 2022; 23:45. [PMID: 35115029 PMCID: PMC8812185 DOI: 10.1186/s13059-022-02616-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022] Open
Abstract
Background Despite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications in this process. Results To interrogate its significance, we establish the dynamic three-dimensional (3D) genome architecture of the allotetraploid cotton fiber, representing a typical single cell undergoing staged development in plants. We show that the subgenome-relayed switching of the chromatin compartment from active to inactive is coupled with the silencing of developmentally repressed genes, pinpointing subgenome-coordinated contribution to fiber development. We identify 10,571 topologically associating domain-like (TAD-like) structures, of which 25.6% are specifically organized in different stages and 75.23% are subject to partition or fusion between two subgenomes. Notably, dissolution of intricate TAD-like structure cliques showing long-range interactions represents a prominent characteristic at the later developmental stage. Dynamic chromatin loops are found to mediate the rewiring of gene regulatory networks that exhibit a significant difference between the two subgenomes, implicating expression bias of homologous genes. Conclusions This study sheds light on the spatial-temporal asymmetric chromatin structures of two subgenomes in the cotton fiber and offers a new insight into the regulatory orchestration of cell differentiation in plants. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02616-y.
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Affiliation(s)
- Liuling Pei
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianhui Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xuehan Tian
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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15
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Li X, Liu W, Ren Z, Wang X, Liu J, Yang Z, Zhao J, Pei X, Liu Y, He K, Zhang F, Zhang Z, Yang D, Ma X, Li W. Glucose regulates cotton fiber elongation by interacting with brassinosteroid. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:711-726. [PMID: 34636403 DOI: 10.1093/jxb/erab451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/09/2021] [Indexed: 05/18/2023]
Abstract
In plants, glucose (Glc) plays important roles, as a nutrient and signal molecule, in the regulation of growth and development. However, the function of Glc in fiber development of upland cotton (Gossypium hirsutum) is unclear. Here, using gas chromatography-mass spectrometry (GC-MS), we found that the Glc content in fibers was higher than that in ovules during the fiber elongation stage. In vitro ovule culture revealed that lower Glc concentrations promoted cotton fiber elongation, while higher concentrations had inhibitory effects. The hexokinase inhibitor N-acetylglucosamine (NAG) inhibited cotton fiber elongation in the cultured ovules, indicating that Glc-mediated fiber elongation depends on the Glc signal transduced by hexokinase. RNA sequencing (RNA-seq) analysis and hormone content detection showed that 150mM Glc significantly activated brassinosteroid (BR) biosynthesis, and the expression of signaling-related genes was also increased, which promoted fiber elongation. In vitro ovule culture clarified that BR induced cotton fiber elongation in a dose-dependent manner. In hormone recovery experiments, only BR compensated for the inhibitory effects of NAG on fiber elongation in a Glc-containing medium. However, the ovules cultured with the BR biosynthetic inhibitor brassinazole and from the BR-deficient cotton mutant pag1 had greatly reduced fiber elongation at all the Glc concentrations tested. This demonstrates that Glc does not compensate for the inhibition of fiber elongation caused by BR biosynthetic defects, suggesting that the BR signaling pathway works downstream of Glc during cotton fiber elongation. Altogether, our study showed that Glc plays an important role in cotton fibre elongation, and crosstalk occurs between Glc and BR signaling during modulation of fiber elongation.
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Affiliation(s)
- Xinyang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wei Liu
- Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Zhongying Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyu Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yangai Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kunlun He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhiqiang Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Daigang Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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16
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The Xyloglucan Endotransglucosylase/Hydrolase Gene XTH22/TCH4 Regulates Plant Growth by Disrupting the Cell Wall Homeostasis in Arabidopsis under Boron Deficiency. Int J Mol Sci 2022; 23:ijms23031250. [PMID: 35163179 PMCID: PMC8836128 DOI: 10.3390/ijms23031250] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/15/2022] [Accepted: 01/21/2022] [Indexed: 11/17/2022] Open
Abstract
TCH4 is a xyloglucan endotransglucosylase/hydrolase (XTH) family member. Extensive studies have shown that XTHs are very important in cell wall homeostasis for plant growth and development. Boron (B), as an essential micronutrient for plants, plays an essential role in the cross-linking of cell wall pectin. However, the effect of B on cell wall organization is unclear. This study aimed to explore the mechanism of plant adaption to B stress by investigating the role of TCH4 in cell wall homeostasis. We conducted both plate and hydroponic cultures of wild-type Col-0 and overexpression and gene knockout lines of XTH22/TCH4 to analyze the phenotype, components, and characteristics of the cell wall using immunofluorescence, atomic force microscopy (AFM), and transmission electron microscopy (TEM). B deficiency induces the expression of TCH4. The overexpression lines of TCH4 presented more sensitivity to B deficiency than the wild-type Col-0, while the knockout lines of TCH4 were more resistant to low B stress. Up-regulation of TCH4 influenced the ratio of chelator-soluble pectin to alkali-soluble pectin and decreased the degree of methylesterification of pectin under B-deficient conditions. Moreover, we found that B deficiency disturbed the arrangement of cellulose, enlarged the gap between cellulose microfibrils, and decreased the mechanical strength of the cell wall, leading to the formation of a thickened and deformed triangular region of the cell wall. These symptoms were more profound in the TCH4 overexpression lines. Consistently, compared with Col-0, the O2- and MDA contents in the TCH4 overexpression lines increased under B-deficient conditions. This study identified the B-deficiency-induced TCH4 gene, which regulates cell wall homeostasis to influence plant growth under B-deficient conditions.
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17
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Yang Z, Zhang R, Zhou Z. The XTH Gene Family in Schima superba: Genome-Wide Identification, Expression Profiles, and Functional Interaction Network Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:911761. [PMID: 35783982 PMCID: PMC9243642 DOI: 10.3389/fpls.2022.911761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/31/2022] [Indexed: 05/04/2023]
Abstract
Xyloglucan endotransglucosylase/hydrolase (XTH), belonging to glycoside hydrolase family 16, is one of the key enzymes in plant cell wall remodeling. Schima superba is an important timber and fireproof tree species in southern China. However, little is known about XTHs in S. superba. In the present study, a total of 34 SsuXTHs were obtained, which were classified into three subfamilies based on the phylogenetic relationship and unevenly distributed on 18 chromosomes. Furthermore, the intron-exon structure and conserved motif composition of them supported the classification and the members belonging to the same subfamily shared similar gene structures. Segmental and tandem duplication events did not lead to SsuXTH gene family expansion, and strong purifying selection pressures during evolution led to similar structure and function of SsuXTH gene family. The interaction network and cis-acting regulatory elements analysis revealed the SsuXTH expression might be regulated by multiple hormones, abiotic stresses and transcription factors. Finally, expression profiles and GO enrichment analysis showed most of the tandem repeat genes were mainly expressed in the phloem and xylem and they mainly participated in glycoside metabolic processes through the transfer and hydrolysis of xyloglucan in the cell wall and then regulated fiber elongation.
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Affiliation(s)
- Zhongyi Yang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Tree Breeding, Hangzhou, China
| | - Rui Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Tree Breeding, Hangzhou, China
- *Correspondence: Rui Zhang,
| | - Zhichun Zhou
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Tree Breeding, Hangzhou, China
- Zhichun Zhou,
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Yang J, Gao L, Liu X, Zhang X, Wang X, Wang Z. Comparative transcriptome analysis of fiber and nonfiber tissues to identify the genes preferentially expressed in fiber development in Gossypium hirsutum. Sci Rep 2021; 11:22833. [PMID: 34819523 PMCID: PMC8613186 DOI: 10.1038/s41598-021-01829-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 11/02/2021] [Indexed: 02/06/2023] Open
Abstract
Cotton is an important natural fiber crop and economic crop worldwide. The quality of cotton fiber directly determines the quality of cotton textiles. Identifying cotton fiber development-related genes and exploring their biological functions will not only help to better understand the elongation and development mechanisms of cotton fibers but also provide a theoretical basis for the cultivation of new cotton varieties with excellent fiber quality. In this study, RNA sequencing technology was used to construct transcriptome databases for different nonfiber tissues (root, leaf, anther and stigma) and fiber developmental stages (7 days post-anthesis (DPA), 14 DPA, and 26 DPA) of upland cotton Coker 312. The sizes of the seven transcriptome databases constructed ranged from 4.43 to 5.20 Gb, corresponding to approximately twice the genome size of Gossypium hirsutum (2.5 Gb). Among the obtained clean reads, 83.32% to 88.22% could be compared to the upland cotton TM-1 reference genome. By analyzing the differential gene expression profiles of the transcriptome libraries of fiber and nonfiber tissues, we obtained 1205, 1135 and 937 genes with significantly upregulated expression at 7 DPA, 14 DPA and 26 DPA, respectively, and 124, 179 and 213 genes with significantly downregulated expression. Subsequently, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed, which revealed that these genes were mainly involved in catalytic activity, carbohydrate metabolism, the cell membrane and organelles, signal transduction and other functions and metabolic pathways. Through gene annotation analysis, many transcription factors and genes related to fiber development were screened. Thirty-six genes were randomly selected from the significantly upregulated genes in fiber, and expression profile analysis was performed using qRT-PCR. The results were highly consistent with the gene expression profile analyzed by RNA-seq, and all of the genes were specifically or predominantly expressed in fiber. Therefore, our RNA sequencing-based comparative transcriptome analysis will lay a foundation for future research to provide new genetic resources for the genetic engineering of improved cotton fiber quality and for cultivating new transgenic cotton germplasms for fiber quality improvement.
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Affiliation(s)
- Jiangtao Yang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lihua Gao
- School of Life Sciences, Langfang Normal University, Langfang, 065000, China
| | - Xiaojing Liu
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaochun Zhang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xujing Wang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhixing Wang
- Biotechnology Research Institute, MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Wu Z, Cui C, Xing A, Xu X, Sun Y, Tian Z, Li X, Zhu J, Wang G, Wang Y. Identification and response analysis of xyloglucan endotransglycosylase/hydrolases (XTH) family to fluoride and aluminum treatment in Camellia sinensis. BMC Genomics 2021; 22:761. [PMID: 34696727 PMCID: PMC8547062 DOI: 10.1186/s12864-021-08056-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Xyloglucan endotransglycosylase/hydrolases (XTH) can disrupt and reconnect the xyloglucan chains, modify the cellulose-xyloglucan complex structure in the cell wall to reconstruct the cell wall. Previous studies have reported that XTH plays a key role in the aluminum (Al) tolerance of tea plants (Camellia sinensis), which is a typical plant that accumulates Al and fluoride (F), but its role in F resistance has not been reported. RESULTS Here, 14 CsXTH genes were identified from C. sinensis and named as CsXTH1-14. The phylogenetic analysis revealed that CsXTH members were divided into 3 subclasses, and conserved motif analysis showed that all these members included catalytic active region. Furthermore, the expressions of all CsXTH genes showed tissue-specific and were regulated by Al3+ and F- treatments. CsXTH1, CsXTH4, CsXTH6-8 and CsXTH11-14 were up-regulated under Al3+ treatments; CsXTH1-10 and CsXTH12-14 responded to different concentrations of F- treatments. The content of xyloglucan oligosaccharide determined by immunofluorescence labeling increased to the highest level at low concentrations of Al3+ or F- treatments (0.4 mM Al3+ or 8 mg/L F-), accompanying by the activity of XET (Xyloglucan endotransglucosylase) peaked. CONCLUSION In conclusion, CsXTH activities were regulated by Al or F via controlling the expressions of CsXTH genes and the content of xyloglucan oligosaccharide in C. sinensis roots was affected by Al or F, which might finally influence the elongation of roots and the growth of plants.
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Affiliation(s)
- Zichen Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chuanlei Cui
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Anqi Xing
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaohan Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiqiang Tian
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuyan Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiangyuan Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Genmei Wang
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuhua Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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20
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Gao Y, Chen Y, Song Z, Zhang J, Lv W, Zhao H, Huo X, Zheng L, Wang F, Zhang J, Zhang T. Comparative Dynamic Transcriptome Reveals the Delayed Secondary-Cell-Wall Thickening Results in Altered Lint Percentage and Fiber Elongation in a Chromosomal Segment Substitution Line of Cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:756434. [PMID: 34759948 PMCID: PMC8573213 DOI: 10.3389/fpls.2021.756434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Lint percentage (LP) is an important yield component in cotton that is usually affected by initial fiber number and cell wall thickness. To explore how fiber cell wall development affects LP, phenotypic identification and dynamic transcriptome analysis were conducted using a single segment substitution line of chromosome 15 (SL15) that harbors a major quantitative trait locus (QTL) for LP. Compared to its recurrent parent LMY22, SL15 did not differ in initial fiber number, but the fiber cell wall thickness and single-fiber weight decreased significantly, altering LP. The comparative transcriptome profiles revealed that the secondary cell wall (SCW) development phase of SL15 was relatively delayed. Meanwhile, the expression of genes related to cell expansion decreased more slightly in SL15 with fiber development, resulting in relatively higher expression at SL15_25D than at LMY22_25D. SCW development-related genes, such as GhNACs and GhMYBs, in the putative NAC-MYB-CESA network differentially expressed at SL15_25D, along with the lower expression of CESA6, CSLC12, and CSLA2. The substituted chromosomal interval was further investigated, and found 6 of 146 candidate genes were differentially expressed in all four cell development periods including 10, 15, 20 and 25 DPA. Genetic variation and co-expression analysis showed that GH_D01G0052, GH_D01G0099, GH_D01G0100, and GH_D01G0140 may be important candidate genes associated with qLP-C15-1. Our results provide novel insights into cell wall development and its relationship with LP, which is beneficial for lint yield and fiber quality improvement.
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Affiliation(s)
- Yang Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhangqiang Song
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Wanyu Lv
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Han Zhao
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xuehan Huo
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Ling Zheng
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Furong Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Plant Precision Breeding Academy, Zhejiang University, Hangzhou, China
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21
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Huang G, Huang JQ, Chen XY, Zhu YX. Recent Advances and Future Perspectives in Cotton Research. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:437-462. [PMID: 33428477 DOI: 10.1146/annurev-arplant-080720-113241] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cotton is not only the world's most important natural fiber crop, but it is also an ideal system in which to study genome evolution, polyploidization, and cell elongation. With the assembly of five different cotton genomes, a cotton-specific whole-genome duplication with an allopolyploidization process that combined the A- and D-genomes became evident. All existing A-genomes seemed to originate from the A0-genome as a common ancestor, and several transposable element bursts contributed to A-genome size expansion and speciation. The ethylene production pathway is shown to regulate fiber elongation. A tip-biased diffuse growth mode and several regulatory mechanisms, including plant hormones, transcription factors, and epigenetic modifications, are involved in fiber development. Finally, we describe the involvement of the gossypol biosynthetic pathway in the manipulation of herbivorous insects, the role of GoPGF in gland formation, and host-induced gene silencing for pest and disease control. These new genes, modules, and pathways will accelerate the genetic improvement of cotton.
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Affiliation(s)
- Gai Huang
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China;
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jin-Quan Huang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Ya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu-Xian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China;
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22
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Seven M, Derman ÜC, Harvey AJ. Enzymatic characterization of ancestral/group-IV clade xyloglucan endotransglycosylase/hydrolase enzymes reveals broad substrate specificities. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1660-1673. [PMID: 33825243 DOI: 10.1111/tpj.15262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 05/14/2023]
Abstract
Xyloglucan endotransglycosylase/hydrolase (XTH) enzymes play important roles in cell wall remodelling. Although previous studies have shown a pathway of evolution for XTH genes from bacterial licheninases, through plant endoglucanases (EG16), the order of development within the phylogenetic clades of true XTHs is yet to be elucidated. In addition, recent studies have revealed interesting and potentially useful patterns of transglycosylation beyond the standard xyloglucan-xyloglucan donor/acceptor substrate activities. To study evolutionary relationships and to search for enzymes with useful broad substrate specificities, genes from the 'ancestral' XTH clade of two monocots, Brachypodium distachyon and Triticum aestivum, and two eudicots, Arabidopsis thaliana and Populus tremula, were investigated. Specific activities of the heterologously produced enzymes showed remarkably broad substrate specificities. All the enzymes studied had high activity with the cellulose analogue HEC (hydroxyethyl cellulose) as well as with mixed-link β-glucan as donor substrates, when compared with the standard xyloglucan. Even more surprising was the wide range of acceptor substrates that these enzymes were able to catalyse reactions with, opening a broad range of possible roles for these enzymes, both within plants and in industrial, pharmaceutical and medical fields. Genome screening and expression analyses unexpectedly revealed that genes from this clade were found only in angiosperm genomes and were predominantly or solely expressed in reproductive tissues. We therefore posit that this phylogenetic group is significantly different and should be renamed as the group-IV clade.
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Affiliation(s)
- Merve Seven
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, 34755, Turkey
| | - Ü Cem Derman
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, 34755, Turkey
| | - Andrew J Harvey
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, 34755, Turkey
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23
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Weighted Gene Co-Expression Network Analysis Reveals Hub Genes Contributing to Fuzz Development in Gossypium arboreum. Genes (Basel) 2021; 12:genes12050753. [PMID: 34067654 PMCID: PMC8156360 DOI: 10.3390/genes12050753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 12/19/2022] Open
Abstract
Fuzzless mutants are ideal materials to decipher the regulatory network and mechanism underlying fuzz initiation and formation. In this study, we utilized two Gossypium arboreum accessions differing in fuzz characteristics to explore expression pattern differences and discriminate genes involved in fuzz development using RNA sequencing. Gene ontology (GO) analysis was conducted and found that DEGs were mainly enriched in the regulation of transcription, metabolic processes and oxidation–reduction-related processes. Weighted gene co-expression network analysis discerned the MEmagenta module highly associated with a fuzz/fuzzless trait, which included a total of 50 hub genes differentially expressed between two materials. GaFZ, which negatively regulates trichome and fuzz formation, was found involved in MEmagenta cluster1. In addition, twenty-eight hub genes in MEmagenta cluster1 were significantly up-regulated and expressed in fuzzless mutant DPL972. It is noteworthy that Ga04G1219 and Ga04G1240, which, respectively, encode Fasciclin-like arabinogalactan protein 18(FLA18) and transport protein, showed remarkable differences of expression level and implied that they may be involved in protein glycosylation to regulate fuzz formation and development. This module and hub genes identified in this study will provide new insights on fiber and fuzz formation and be useful for the molecular design breeding of cotton genetic improvement.
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24
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Zhu QH, Stiller W, Moncuquet P, Gordon S, Yuan Y, Barnes S, Wilson I. Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant. G3-GENES GENOMES GENETICS 2021; 11:1-14. [PMID: 33704434 PMCID: PMC8022719 DOI: 10.1093/g3journal/jkaa042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022]
Abstract
Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0-6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.
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Affiliation(s)
- Qian-Hao Zhu
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
| | | | - Philippe Moncuquet
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
| | - Stuart Gordon
- CSIRO Agriculture and Food, Waurn Ponds, VIC 3216, Australia
| | - Yuman Yuan
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
| | - Scott Barnes
- CSIRO Manufacturing, Waurn Ponds, VIC 3216, Australia
| | - Iain Wilson
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
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25
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Pei W, Song J, Wang W, Ma J, Jia B, Wu L, Wu M, Chen Q, Qin Q, Zhu H, Hu C, Lei H, Gao X, Hu H, Zhang Y, Zhang J, Yu J, Qu Y. Quantitative Trait Locus Analysis and Identification of Candidate Genes for Micronaire in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense. FRONTIERS IN PLANT SCIENCE 2021; 12:763016. [PMID: 34777444 PMCID: PMC8579039 DOI: 10.3389/fpls.2021.763016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/22/2021] [Indexed: 05/08/2023]
Abstract
Cotton is the most important fiber crop and provides indispensable natural fibers for the textile industry. Micronaire (MIC) is determined by fiber fineness and maturity and is an important component of fiber quality. Gossypium barbadense L. possesses long, strong and fine fibers, while upland cotton (Gossypium hirsutum L.) is high yielding with high MIC and widely cultivated worldwide. To identify quantitative trait loci (QTLs) and candidate genes for MIC in G. barbadense, a population of 250 backcross inbred lines (BILs), developed from an interspecific cross of upland cotton CRI36 × Egyptian cotton (G. barbadense) Hai7124, was evaluated in 9 replicated field tests. Based on a high-density genetic map with 7709 genotyping-by-sequencing (GBS)-based single-nucleotide polymorphism (SNP) markers, 25 MIC QTLs were identified, including 12 previously described QTLs and 13 new QTLs. Importantly, two stable MIC QTLs (qMIC-D03-2 on D03 and qMIC-D08-1 on D08) were identified. Of a total of 338 genes identified within the two QTL regions, eight candidate genes with differential expression between TM-1 and Hai7124 were identified. Our research provides valuable information for improving MIC in cotton breeding.
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Affiliation(s)
- Wenfeng Pei
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Jikun Song
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wenkui Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianjiang Ma
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bing Jia
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Luyao Wu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Qin Qin
- Western Agriculture Research Centre, Chinese Academy of Agricultural Sciences, Changji, China
| | - Haiyong Zhu
- Western Agriculture Research Centre, Chinese Academy of Agricultural Sciences, Changji, China
| | - Chengcheng Hu
- Western Agriculture Research Centre, Chinese Academy of Agricultural Sciences, Changji, China
| | - Hai Lei
- Seed Management Station, Department of Agriculture and Rural Affairs of Xinjiang, Urumqi, China
| | - Xuefei Gao
- Join Hope Seed Co., Ltd., Changji, China
| | - Haijun Hu
- Join Hope Seed Co., Ltd., Changji, China
| | - Yu Zhang
- Join Hope Seed Co., Ltd., Changji, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Jinfa Zhang,
| | - Jiwen Yu
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Jiwen Yu,
| | - Yanying Qu
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- Yanying Qu,
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26
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Sertse D, You FM, Ravichandran S, Soto-Cerda BJ, Duguid S, Cloutier S. Loci harboring genes with important role in drought and related abiotic stress responses in flax revealed by multiple GWAS models. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:191-212. [PMID: 33047220 DOI: 10.1007/s00122-020-03691-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/18/2020] [Indexed: 05/19/2023]
Abstract
QTNs associated with drought tolerance traits and indices were identified in a flax mini-core collection through multiple GWAS models and phenotyping at multiple locations under irrigated and non-irrigated field conditions. Drought is a critical phenomenon challenging today's agricultural sector. Crop varieties adapted to moisture deficit are becoming vital. Flax can be greatly affected by limiting moisture conditions, especially during the early development and reproductive stages. Here, a mini-core collection comprising genotypes from more than 20 major growing countries was evaluated for 11 drought-related traits in irrigated and non-irrigated fields for 3 years. Heritability of the traits ranged from 44.7 to 86%. Six of the 11 traits showed significant phenotypic difference between irrigated and non-irrigated conditions. A genome-wide association study (GWAS) was performed for these six traits and their corresponding stress indices based on 106 genotypes and 12,316 single nucleotide polymorphisms (SNPs) using six multi-locus and one single-locus models. The SNPs were then assigned to 8050 linkage disequilibrium (LD) blocks to which a restricted two-stage multi-locus multi-allele GWAS was applied. A total of 144 quantitative trait nucleotides (QTNs) and 13 LD blocks were associated with at least one trait or stress index. Of these, 16 explained more than 15% of the genetic variance. Most large-effect QTN loci harbored gene(s) previously predicted to play role(s) in the associated traits. Genes mediating responses to abiotic stresses resided at loci associated with stress indices. Flax genes Lus10009480 and Lus10030150 that are predicted to encode WAX INDUCER1 and STRESS-ASSOCIATED PROTEIN (SAP), respectively, are among the important candidates detected. Accessions with multiple favorable alleles outperformed others for grain yield, thousand seed weight and fiber/biomass in non-irrigated conditions, suggesting their potential usefulness in breeding and genomic selection.
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Affiliation(s)
- Demissew Sertse
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Braulio J Soto-Cerda
- Agriaquaculture Nutritional Genomic Centre (CGNA), Las Heras 350, 4781158, Temuco, Chile
| | - Scott Duguid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, Canada
| | - Sylvie Cloutier
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada.
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada.
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Wu D, Liu A, Qu X, Liang J, Song M. Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L. BMC Genomics 2020; 21:782. [PMID: 33176678 PMCID: PMC7656703 DOI: 10.1186/s12864-020-07153-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/14/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out. RESULTS In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor. CONCLUSIONS We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.
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Affiliation(s)
- Di Wu
- Qufu Normal University, College of Life Science, Qufu, 273165, P.R. China
| | - Anqi Liu
- Qufu Normal University, College of Life Science, Qufu, 273165, P.R. China
| | - Xiaoyu Qu
- Qufu Normal University, College of Life Science, Qufu, 273165, P.R. China
| | - Jiayi Liang
- Qufu Normal University, College of Life Science, Qufu, 273165, P.R. China
| | - Min Song
- Qufu Normal University, College of Life Science, Qufu, 273165, P.R. China.
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Shang X, Zhu L, Duan Y, Guo W. A cotton α1,3-/4-fucosyltransferase-encoding gene, FucT4, plays an important role in cell elongation and is significantly associated with fiber quality. Mol Genet Genomics 2020; 295:1141-1153. [PMID: 32462532 DOI: 10.1007/s00438-020-01687-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/11/2020] [Indexed: 11/25/2022]
Abstract
Fucosylation, one of the key posttranslational modifications, plays an important role in plants. It is involved in the development, signal transduction, reproduction, and disease resistance. α1,3-/4-Fucosyltransferase is responsible for transferring L-fucose from GDP-L-fucose to the N-glycan to exert fucosylational functions. However, the roles of the fucosyltransferase gene in cotton remain unknown. This study provided a comprehensive investigation of its possible functions. A genome-wide analysis identified four, four, eight, and eight FucT genes presented in the four sequenced cotton species, diploid Gossypium raimondii, G. arboreum, tetraploid G. hirsutum acc. TM-1, and G. barbadense cv. H7124, respectively. These FucTs were classified into two groups, with FucT4 homologs alone as a group. We isolated FucT4 in TM-1 and H7124, and named it GhFucT4 and GbFucT4, respectively. Quantitative RT-PCR and transcriptome data demonstrated that GhFucT4 had the highest expression levels in fibers among all GhFucT genes. Association studies and QTL co-localization supported the possible involvement of GhFucT4 in cotton fiber development. GhFucT4 and GbFucT4 shared high sequence identities, and FucT4 had higher expression in H7124 fiber tissues compared with TM-1. Furthermore, ectopic expression of FucT4 in transgenic Arabidopsis promoted root cell elongation, upregulated expression of genes related to cell wall loosening, and led to longer primary root. These results collectively indicate that FucT4 plays an important role in promoting cell elongation and modulating fiber development, which could be utilized to improve fiber quality traits in cotton breeding.
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Affiliation(s)
- Xiaoguang Shang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lijie Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yujia Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.
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Zhang H, Tan J, Zhang M, Huang S, Chen X. Comparative Transcriptomic Analysis of Two Bottle Gourd Accessions Differing in Fruit Size. Genes (Basel) 2020; 11:genes11040359. [PMID: 32230807 PMCID: PMC7230174 DOI: 10.3390/genes11040359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
The bottle gourd (Lagenaria siceraria) is an important horticultural and medicinal crop with high nutritional value. This study aimed at examining the molecular regulation of fruit size in bottle gourd. We performed transcriptome sequencing of two bottle gourd cultivars differing in their fruit size. The average fruit length and weight of the cultivar Hang (39.48 cm/624.4 g) were higher than those of the cultivar USA (10.34 cm/152.8 g) at maturity. Transcriptome sequencing and assembly resulted in 89,347 unigenes. A total of 1250 differentially expressed genes (DEG) were found between the two cultivars, including 422 upregulated genes and 828 downregulated genes in Hang as compared to USA. Genes related to cell wall metabolism, phytohormones, cell cycle, and cell division showed significant differential expression between the two cultivars. DEGs encoding transcription factors (TF) from nine TF families were also identified. The ethylene response factor family was the most enriched among these families. Our study provides a basis for further investigations of the molecular regulation of fruit size in bottle gourd.
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Li M, Xie F, He Q, Li J, Liu J, Sun B, Luo Y, Zhang Y, Chen Q, Zhang F, Gong R, Wang Y, Wang X, Tang H. Expression Analysis of XTH in Stem Swelling of Stem Mustard and Selection of Reference Genes. Genes (Basel) 2020; 11:genes11010113. [PMID: 31968559 PMCID: PMC7016721 DOI: 10.3390/genes11010113] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 02/05/2023] Open
Abstract
Accurate analysis of gene expression requires selection of appropriate reference genes. In this study, we report analysis of eight candidate reference genes (ACTIN, UBQ, EF-1α, UBC, IF-4α, TUB, PP2A, and HIS), which were screened from the genome and transcriptome data in Brassica juncea. Four statistical analysis softwares geNorm, NormFinder, BestKeeper, and RefFinder were used to test the reliability and stability of gene expression of the reference genes. To further validate the stability of reference genes, the expression levels of two CYCD3 genes (BjuB045330 and BjuA003219) were studied. In addition, all genes in the xyloglucan endotransglucosylase/hydrolase (XTH) family were identified in B. juncea and their patterns at different periods of stem enlargement were analyzed. Results indicated that UBC and TUB genes showed stable levels of expression and are recommended for future research. In addition, XTH genes were involved in regulation of stem enlargement expression. These results provide new insights for future research aiming at exploring important functional genes, their expression patterns and regulatory mechanisms for mustard development.
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Affiliation(s)
- Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Fangjie Xie
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Qi He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Jie Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Jiali Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Fen Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Ronggao Gong
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: ; Tel.: +86-288-629-1949
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Khan AQ, Li Z, Ahmed MM, Wang P, Zhang X, Tu L. Eriodictyol can modulate cellular auxin gradients to efficiently promote in vitro cotton fibre development. BMC PLANT BIOLOGY 2019; 19:443. [PMID: 31651240 PMCID: PMC6814110 DOI: 10.1186/s12870-019-2054-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/25/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Flavonoids have essential roles in flower pigmentation, fibre development and disease resistance in cotton. Previous studies show that accumulation of naringenin in developing cotton fibres significantly affects fibre growth. This study focused on determining the effects of the flavonoids naringenin, dihydrokaempferol, dihydroquerectin and eriodictyol on fibre development in an in vitro system. RESULTS 20 μM eriodictyol treatment produced a maximum fibre growth, in terms of fibre length and total fibre units. To gain insight into the associated transcriptional regulatory networks, RNA-seq analysis was performed on eriodictyol-treated elongated fibres, and computational analysis of differentially expressed genes revealed that carbohydrate metabolism and phytohormone signaling pathways were differentially modulated. Eriodictyol treatment also promoted the biosynthesis of quercetin and dihydroquerectin in ovules and elongating fibres through enhanced expression of genes encoding chalcone isomerase, chalcone synthase and flavanone 3-hydroxylase. In addition, auxin biosynthesis and signaling pathway genes were differentially expressed in eriodictyol-driven in vitro fibre elongation. In absence of auxin, eriodictyol predominantly enhanced fibre growth when the localized auxin gradient was disrupted by the auxin transport inhibitor, triiodobenzoic acid. CONCLUSION Eriodictyol was found to significantly enhance fibre development through accumulating and maintaining the temporal auxin gradient in developing unicellular cotton fibres.
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Affiliation(s)
- Anam Qadir Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
| | - Zhonghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
| | - Muhammad Mahmood Ahmed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
- Institute of Plant Breeding & Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
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Chen Y, Chen B, Wang H, Hu W, Wang S, Zhou Z. Combined elevated temperature and soil waterlogging stresses limit fibre biomass accumulation and fibre quality formation by disrupting protein activity during cotton fibre development. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:715-724. [PMID: 31104693 DOI: 10.1071/fp18192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Soil waterlogging and high temperature conditions generally occur together, especially in the Yangtze River Valley, China, negatively affecting cotton (Gossypium hirsutum L.) fibre development. Therefore, combined elevated temperature (34.1/29.0°C) and soil waterlogging (6 days) were imposed to study their combined effects on fibre biomass and fibre qualities (length, strength and micronaire). The results showed that in the boll cohort exposed to waterlogging and/or elevated air temperature, combined elevated temperature and soil waterlogging decreased final fibre length (by 8.9-11.3%) and fibre biomass (by 25.8-33.9%) more than either stress individually. A total of 113, 263 and 290 differential abundance proteins were identified related to elevated temperature, waterlogging and the two treatments combined, respectively, in fibres at 15 days after anthesis via the isobaric tags for relative and absolute quantitation technique, which were classified as: carbohydrate and energy metabolism (21.7%), protein metabolism (16.6%), amino acid metabolism (12.8%), intracellular structural components (6.6%), transport (7.9%), oxidation-reduction process (7.9%), signal transduction (5.2%), lipid metabolism (5.2%), stress response (5.2%), nucleic acid metabolism (4.5%), organic acid metabolism (3.4%) and others (2.1%). Both vacuolar ATPase (V-ATPase) and plasma membrane H+-ATPase (PMH+-ATPase) were responsible for fibre length formation, although V-ATPase expression may play a major role in determining fibre cell elongation rather than PM H+-ATPase expression. It was concluded that fibre cell elongation and secondary wall thickening were inhibited mainly by reduced accumulation of osmolytes, blocked synthesis and transport of secondary wall components, and disruption of the cytoskeleton system under combined elevated temperature and soil waterlogging.
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Affiliation(s)
- Yinglong Chen
- College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, PR China; and College of Agriculture, Yangzhou University, Yangzhou 225009, PR China
| | - Binglin Chen
- College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, PR China
| | - Haimiao Wang
- College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, PR China
| | - Wei Hu
- College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, PR China
| | - Shanshan Wang
- College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, PR China
| | - Zhiguo Zhou
- College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, PR China; and Corresponding author.
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Naoumkina M, Thyssen GN, Fang DD, Jenkins JN, McCarty JC, Florane CB. Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population. BMC Genomics 2019; 20:112. [PMID: 30727946 DOI: 10.1186/s12864-019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/02/2019] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Improving cotton fiber length without reducing yield is one of the major goals of cotton breeding. However, genetic improvement of cotton fiber length by breeding has been a challenge due to the narrow genetic diversity of modern cotton cultivars and negative correlations between fiber quality and yield traits. A multi-parent advanced generation inter-cross (MAGIC) population developed through random mating provides an excellent genetic resource that allows quantitative trait loci (QTL) and causal genes to be identified. RESULTS An Upland cotton MAGIC population, consisting of 550 recombinant inbred lines (RILs) derived from eleven different cultivars, was used to identify fiber length QTLs and potential genes that contribute to longer fibers. A genome wide association study (GWAS) identified a cluster of single nucleotide polymorphisms (SNPs) on chromosome (Chr.) D11 that is significantly associated with fiber length. Further evaluation of the Chr. D11 genomic region among lines of the MAGIC population detected that 90% of RILs have a D11 haplotype similar to the reference TM-1 genome (D11-ref), whereas 10% of RILs inherited an alternative haplotype from one of the parents (D11-alt). The average length of fibers of D11-alt RILs was significantly shorter compared to D11-ref RILs, suggesting that alleles in the D11-alt haplotype contributed to the inferior fiber quality. RNAseq analysis of the longest and shortest fiber length RILs from D11-ref and D11-alt populations identified 949 significantly differentially expressed genes (DEGs). Gene set enrichment analysis revealed that different functional categories of genes were over-represented during fiber elongation between the four selected RILs. We found 12 genes possessing non-synonymous SNPs (nsSNPs) significantly associated with the fiber length, and three that were highly significant and were clustered at D11:24-Mb, including D11G1928, D11G1929 and D11G1931. CONCLUSION The results of this study provide insights into molecular aspects of genetic variation in fiber length and suggests candidate genes for genetic manipulation for cotton improvement.
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Affiliation(s)
- Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA.
| | - Gregory N Thyssen
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
- Cotton Chemistry and Utilization Research Unit, USDA-ARS-SRRC, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - Johnie N Jenkins
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, 810 Highway 12 East, Mississippi State, MS, 39762, USA
| | - Jack C McCarty
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, 810 Highway 12 East, Mississippi State, MS, 39762, USA
| | - Christopher B Florane
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
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Naoumkina M, Thyssen GN, Fang DD, Jenkins JN, McCarty JC, Florane CB. Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population. BMC Genomics 2019; 20:112. [PMID: 30727946 PMCID: PMC6366115 DOI: 10.1186/s12864-019-5427-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/02/2019] [Indexed: 11/10/2022] Open
Abstract
Background Improving cotton fiber length without reducing yield is one of the major goals of cotton breeding. However, genetic improvement of cotton fiber length by breeding has been a challenge due to the narrow genetic diversity of modern cotton cultivars and negative correlations between fiber quality and yield traits. A multi-parent advanced generation inter-cross (MAGIC) population developed through random mating provides an excellent genetic resource that allows quantitative trait loci (QTL) and causal genes to be identified. Results An Upland cotton MAGIC population, consisting of 550 recombinant inbred lines (RILs) derived from eleven different cultivars, was used to identify fiber length QTLs and potential genes that contribute to longer fibers. A genome wide association study (GWAS) identified a cluster of single nucleotide polymorphisms (SNPs) on chromosome (Chr.) D11 that is significantly associated with fiber length. Further evaluation of the Chr. D11 genomic region among lines of the MAGIC population detected that 90% of RILs have a D11 haplotype similar to the reference TM-1 genome (D11-ref), whereas 10% of RILs inherited an alternative haplotype from one of the parents (D11-alt). The average length of fibers of D11-alt RILs was significantly shorter compared to D11-ref RILs, suggesting that alleles in the D11-alt haplotype contributed to the inferior fiber quality. RNAseq analysis of the longest and shortest fiber length RILs from D11-ref and D11-alt populations identified 949 significantly differentially expressed genes (DEGs). Gene set enrichment analysis revealed that different functional categories of genes were over-represented during fiber elongation between the four selected RILs. We found 12 genes possessing non-synonymous SNPs (nsSNPs) significantly associated with the fiber length, and three that were highly significant and were clustered at D11:24-Mb, including D11G1928, D11G1929 and D11G1931. Conclusion The results of this study provide insights into molecular aspects of genetic variation in fiber length and suggests candidate genes for genetic manipulation for cotton improvement. Electronic supplementary material The online version of this article (10.1186/s12864-019-5427-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA.
| | - Gregory N Thyssen
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA.,Cotton Chemistry and Utilization Research Unit, USDA-ARS-SRRC, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - Johnie N Jenkins
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, 810 Highway 12 East, Mississippi State, MS, 39762, USA
| | - Jack C McCarty
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, 810 Highway 12 East, Mississippi State, MS, 39762, USA
| | - Christopher B Florane
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
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Zhang B. Transgenic Cotton: From Biotransformation Methods to Agricultural Application. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2018; 1902:3-16. [PMID: 30543057 DOI: 10.1007/978-1-4939-8952-2_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Transgenic cotton is among the first transgenic plants commercially adopted around the world. Since it was first introduced into the field in the middle of the 1990s, transgenic cotton has been quickly adopted by cotton farmers in many developed and developing countries. Transgenic cotton has offered many important environmental, social, and economic benefits, including reduced usage of pesticides, indirect increase of yield, minimizing environmental pollution, and reducing labor and cost. Agrobacterium-mediated genetic transformation method is the major method for obtaining transgenic cotton. However, pollen tube pathway-mediated method is also used, particularly by scientists in China, to breed commercial transgenic cotton. Although transgenic cotton plants with disease resistance, abiotic stress tolerance, and improved fiber quality have been developed in the past decades, insect-resistant and herbicide-tolerant cottons are the two dominant cottons in transgenic cotton market.
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Affiliation(s)
- Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, USA.
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Song L, Valliyodan B, Prince S, Wan J, Nguyen HT. Characterization of the XTH Gene Family: New Insight to the Roles in Soybean Flooding Tolerance. Int J Mol Sci 2018; 19:E2705. [PMID: 30208612 PMCID: PMC6164600 DOI: 10.3390/ijms19092705] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022] Open
Abstract
Xyloglucan endotransglycosylases/hydrolases (XTHs) are a class of enzymes involved in the construction and remodeling of cellulose/xyloglucan crosslinks and play an important role in regulating cell wall extensibility. However, little is known about this class of enzymes in soybean. Here, 61 soybean XTH genes (GmXTHs) were identified and classified into three subgroups through comparative phylogenetic analysis. Genome duplication greatly contributed to the expansion of GmXTH genes in soybean. A conserved amino acid motif responsible for the catalytic activity was identified in all GmXTHs. Further expression analysis revealed that most GmXTHs exhibited a distinct organ-specific expression pattern, and the expression level of many GmXTH genes was significantly associated with ethylene and flooding stress. To illustrate a possible role of XTH genes in regulating stress responses, the ArabidopsisAtXTH31 gene was overexpressed in soybean. The generated transgenic plants exhibited improved tolerance to flooding stress, with a higher germination rate and longer roots/hypocotyls during the seedling stage and vegetative growth stages. In summary, our combined bioinformatics and gene expression pattern analyses suggest that GmXTH genes play a role in regulating soybean stress responses. The enhanced soybean flooding tolerance resulting from the expression of an Arabidopsis XTH also supports the role of XTH genes in regulating plant flooding stress responses.
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Affiliation(s)
- Li Song
- Institutes of Agricultural Science and Technology Development, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Silvas Prince
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.
- Noble Research Institute, 2510 Sam noble Pkwy, Ardmore, OK 73401, USA.
| | - Jinrong Wan
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Henry T Nguyen
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.
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Genome-Wide Identification and Expression Profiling Analysis of the Xyloglucan Endotransglucosylase/Hydrolase Gene Family in Tobacco ( Nicotiana tabacum L.). Genes (Basel) 2018; 9:genes9060273. [PMID: 29795009 PMCID: PMC6027287 DOI: 10.3390/genes9060273] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/07/2018] [Accepted: 05/07/2018] [Indexed: 12/12/2022] Open
Abstract
Xyloglucan endotransglucosylase/hydrolase genes (XTHs) encode enzymes required for the reconstruction and modification of xyloglucan backbones, which will result in changes of cell wall extensibility during growth. A total of 56 NtXTH genes were identified from common tobacco, and 50 cDNA fragments were verified by PCR amplification. The 56 NtXTH genes could be classified into two subfamilies: Group I/II and Group III according to their phylogenetic relationships. The gene structure, chromosomal localization, conserved protein domains prediction, sub-cellular localization of NtXTH proteins and evolutionary relationships among Nicotiana tabacum, Nicotiana sylvestrisis, Nicotiana tomentosiformis, Arabidopsis, and rice were also analyzed. The NtXTHs expression profiles analyzed by the TobEA database and qRT-PCR revealed that NtXTHs display different expression patterns in different tissues. Notably, the expression patterns of 12 NtXTHs responding to environment stresses, including salinity, alkali, heat, chilling, and plant hormones, including IAA and brassinolide, were characterized. All the results would be useful for the function study of NtXTHs during different growth cycles and stresses.
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Ashraf J, Zuo D, Wang Q, Malik W, Zhang Y, Abid MA, Cheng H, Yang Q, Song G. Recent insights into cotton functional genomics: progress and future perspectives. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:699-713. [PMID: 29087016 PMCID: PMC5814580 DOI: 10.1111/pbi.12856] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/03/2017] [Accepted: 10/18/2017] [Indexed: 05/11/2023]
Abstract
Functional genomics has transformed from futuristic concept to well-established scientific discipline during the last decade. Cotton functional genomics promise to enhance the understanding of fundamental plant biology to systematically exploit genetic resources for the improvement of cotton fibre quality and yield, as well as utilization of genetic information for germplasm improvement. However, determining the cotton gene functions is a much more challenging task, which has not progressed at a rapid pace. This article presents a comprehensive overview of the recent tools and resources available with the major advances in cotton functional genomics to develop elite cotton genotypes. This effort ultimately helps to filter a subset of genes that can be used to assemble a final list of candidate genes that could be employed in future novel cotton breeding programme. We argue that next stage of cotton functional genomics requires the draft genomes refinement, re-sequencing broad diversity panels with the development of high-throughput functional genomics tools and integrating multidisciplinary approaches in upcoming cotton improvement programmes.
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Affiliation(s)
- Javaria Ashraf
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Dongyun Zuo
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Qiaolian Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Waqas Malik
- Genomics LabDepartment of Plant Breeding and GeneticsFaculty of Agricultural Sciences and TechnologyBahauddin Zakariya UniversityMultanPunjabPakistan
| | - Youping Zhang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Muhammad Ali Abid
- Genomics LabDepartment of Plant Breeding and GeneticsFaculty of Agricultural Sciences and TechnologyBahauddin Zakariya UniversityMultanPunjabPakistan
| | - Hailiang Cheng
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Qiuhong Yang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Guoli Song
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
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SSR-based association mapping of fiber quality in upland cotton using an eight-way MAGIC population. Mol Genet Genomics 2018; 293:793-805. [PMID: 29392407 DOI: 10.1007/s00438-018-1419-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/13/2018] [Indexed: 10/18/2022]
Abstract
The quality of fiber is significant in the upland cotton industry. As complex quantitative traits, fiber quality traits are worth studying at a genetic level. To investigate the genetic architecture of fiber quality traits, we conducted an association analysis using a multi-parent advanced generation inter-cross (MAGIC) population developed from eight parents and comprised of 960 lines. The reliable phenotypic data for six major fiber traits of the MAGIC population were collected from five environments in three locations. Phenotypic analysis showed that the MAGIC lines have a wider variation amplitude and coefficient than the founders. A total of 284 polymorphic SSR markers among eight parents screened from a high-density genetic map were used to genotype the MAGIC population. The MAGIC population showed abundant genetic variation and fast linkage disequilibrium (LD) decay (0.76 cM, r2 > 0.1), which revealed the advantages of high efficiency and power in QTL exploration. Association mapping via a mixed linear model identified 52 significant loci associated with six fiber quality traits; 14 of them were mapped in reported QTL regions with fiber-related or other agronomic traits. Nine markers demonstrated the pleiotropism that controls more than two fiber traits. Furthermore, two SSR markers, BNL1231 and BNL3452, were authenticated as hotspots that were mapped with multi-traits. In addition, we provided candidate regions and screened six candidate genes for identified loci according to the LD decay distance. Our results provide valuable QTL for further genetic mapping and will facilitate marker-based breeding for fiber quality in cotton.
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40
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Parekh MJ, Kumar S, Fougat RS, Zala HN, Pandit RJ. Transcriptomic profiling of developing fiber in levant cotton (Gossypium herbaceum L.). Funct Integr Genomics 2018; 18:211-223. [PMID: 29332190 DOI: 10.1007/s10142-017-0586-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 12/13/2017] [Accepted: 12/18/2017] [Indexed: 12/31/2022]
Abstract
Cotton (Gossypium spp.) is an imperative economic crop of the globe due to its natural textile fiber. Molecular mechanisms of fiber development have been greatly revealed in allotetraploid cotton but remained unexplored in Gossypium herbaceum. G. herbaceum can withstand the rigors of nature like drought and pests but produce coarse lint. This undesirable characteristic strongly needs the knowledge of fiber development at molecular basis. The present study reported the transcriptome sequence of the developing fiber of G. herbaceum on pyrosequencing and its analysis. About 1.38 million raw and 1.12 million quality trimmed reads were obtained followed by de novo assembly-generated 20,125 unigenes containing 14,882 coding sequences (CDs). BLASTx-based test of homology indicated that A1-derived transcripts shared a high similarity with Gossypium arboreum (A2). Functional annotation of the CDs using the UniProt categorized them into biological processes, cellular components, and molecular function, COG classification showed that a large number of CDs have significant homology in COG database (6215 CDs), and mapping of CDs with Kyoto Encyclopedia of Genes and Genomes (KEGG) database generated 200 pathways ultimately showing predominant engagement in the fiber development process. Transcription factors were predicted by comparison with Plant Transcription Factor Database, and their differential expression between stages exposed their important regulatory role in fiber development. Differential expression analysis based on reads per kilobase of transcript per million mapped reads (RPKM) value revealed activities of specific gene related to carbohydrate and lipid synthesis, carbon metabolism, energy metabolism, signal transduction, etc., at four stages of fiber development, and was validated by qPCR. Overall, this study will help as a valuable foundation for diploid cotton fiber improvement.
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Affiliation(s)
- Mithil J Parekh
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388 110, India
| | - Sushil Kumar
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388 110, India.
| | - Ranbir S Fougat
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388 110, India
| | - Harshvardhan N Zala
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388 110, India
| | - Ramesh J Pandit
- Department of Animal Biotechnology, Anand Agricultural University, Anand, 388 110, India
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Guo K, Tu L, He Y, Deng J, Wang M, Huang H, Li Z, Zhang X. Interaction between calcium and potassium modulates elongation rate in cotton fiber cells. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5161-5175. [PMID: 29045717 PMCID: PMC5853336 DOI: 10.1093/jxb/erx346] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/14/2017] [Indexed: 05/20/2023]
Abstract
Calcium (Ca2+) is necessary for fiber cell development in cotton (Gossypium hirsutum), both as a cell wall structural component and for environmental signaling responses. It is also known that potassium (K+) plays a critical role in cotton fiber cell elongation. However, it is unclear whether Ca2+ integrates its activities with K+ to regulate fiber elongation. Here, we report the novel discovery that Ca2+ deficiency, when integrated with K+ signaling, promotes fiber elongation. Using inductively coupled plasma-mass spectrometry (ICP-MS), we determined dynamic profiles of the ionome in ovules and fibers at different developmental stages, and found that a high accumulation of macro-elements, but not Ca2+, was associated with longer fibers. Using an in vitro ovule culture system, we found that under Ca2+-deficient conditions, sufficient K+ (52 mM) rapidly induced ovule and fiber browning, while reduced K+ (2 or 27 mM) not only suppressed tissue browning but also altered fiber elongation. Reduced K+ also enhanced reactive oxygen species scavenging ability and maintained abscisic acid and jasmonic acid levels, which in turn compensated for Ca2+ deficiency. Ca2+ deficiency combined with reduced K+ (0 mM Ca2+ and 27 mM K+) produced longer fibers in cultured ovules, due to cell wall loosening by phytosulfokine (PSK), expansin (EXP), and xyloglucan endotransglycosylase/hydrolase (XTH), and an increase of the K+ content of fiber cells. Using transgenic cotton, we showed that the CBL-INTERACTING PROTEIN KINASE 6 (GhCIPK6) gene mediates the uptake of K+ under Ca2+-deficient conditions. This study establishes a new link between Ca2+, K+, and fiber elongation.
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Affiliation(s)
- Kai Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- Correspondence:
| | - Yonghui He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinwu Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hui Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhonghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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Naoumkina M, Hinchliffe DJ, Fang DD, Florane CB, Thyssen GN. Role of xyloglucan in cotton (Gossypium hirsutum L.) fiber elongation of the short fiber mutant Ligon lintless-2 (Li 2). Gene 2017; 626:227-233. [PMID: 28546126 DOI: 10.1016/j.gene.2017.05.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 05/08/2017] [Accepted: 05/21/2017] [Indexed: 10/19/2022]
Abstract
Xyloglucan is a matrix polysaccharide found in the cell walls of all land plants. In growing cells, xyloglucan is thought to connect cellulose microfibrils and regulate their separation during wall extension. Ligon lintless-2 (Li2) is a monogenic dominant cotton fiber mutation that causes extreme reduction in lint fiber length with no pleiotropic effects on vegetative growth. Li2 represents an excellent model system to study fiber elongation. To understand the role of xyloglucan in cotton fiber elongation we used the short fiber mutant Li2 and its near isogenic wild type for analysis of xyloglucan content and expression of xyloglucan-related genes in developing fibers. Accumulation of xyloglucan was significantly higher in Li2 developing fibers than in wild type. Genes encoding enzymes for nine family members of xyloglucan biosynthesis were identified in the draft Gossypium hirsutum genome. RNAseq analysis revealed that most differentially expressed xyloglucan-related genes were down-regulated in Li2 fiber cells. RT-qPCR analysis revealed that the peak of expression for the majority of xyloglucan-related genes in wild type developing fibers was 5-16days post anthesis (DPA) compared to 1-3 DPA in Li2 fibers. Thus, our results suggest that early activation of xyloglucan-related genes and down regulation of xyloglucan degradation genes during the elongation phase lead to elevated accumulation of xyloglucan that restricts elongation of fiber cells in Li2.
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Affiliation(s)
- Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA.
| | - Doug J Hinchliffe
- Cotton Chemistry and Utilization Research Unit, USDA-ARS-SRRC, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Christopher B Florane
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Gregory N Thyssen
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA; Cotton Chemistry and Utilization Research Unit, USDA-ARS-SRRC, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
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43
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Dai Y, Yang J, Hu W, Zahoor R, Chen B, Zhao W, Meng Y, Zhou Z. Simulative Global Warming Negatively Affects Cotton Fiber Length through Shortening Fiber Rapid Elongation Duration. Sci Rep 2017; 7:9264. [PMID: 28835696 PMCID: PMC5569071 DOI: 10.1038/s41598-017-09545-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/25/2017] [Indexed: 02/04/2023] Open
Abstract
Global warming could possibly increase the air temperature by 1.8-4.0 °C in the coming decade. Cotton fiber is an essential raw material for the textile industry. Fiber length, which was found negatively related to the excessively high temperature, determines yarn quality to a great extent. To investigate the effects of global warming on cotton fiber length and its mechaism, cottons grown in artificially elevated temperature (34.6/30.5 °C, Tday/Tnight) and ambient temperature (31.6/27.3 °C) regions have been investigated. Becaused of the high sensitivities of enzymes V-ATPase, PEPC, and genes GhXTH1 and GhXTH2 during fiber elongation when responding to high temperature stress, the fiber rapid elongation duration (FRED) has been shortened, which led to a significant suppression on final fiber length. Through comprehensive analysis, Tnight had a great influence on fiber elongation, which means Tn could be deemed as an ideal index for forecasting the degree of high temperature stress would happen to cotton fiber property in future. Therefore, we speculate the global warming would bring unfavorable effects on cotton fiber length, which needs to take actions in advance for minimizing the loss in cotton production.
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Affiliation(s)
- Yanjiao Dai
- Key Laboratory of Crop Physiology & Ecology, Ministry of Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Jiashuo Yang
- Key Laboratory of Crop Physiology & Ecology, Ministry of Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Wei Hu
- Key Laboratory of Crop Physiology & Ecology, Ministry of Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Rizwan Zahoor
- Key Laboratory of Crop Physiology & Ecology, Ministry of Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Binglin Chen
- Key Laboratory of Crop Physiology & Ecology, Ministry of Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Wenqing Zhao
- Key Laboratory of Crop Physiology & Ecology, Ministry of Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Yali Meng
- Key Laboratory of Crop Physiology & Ecology, Ministry of Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Zhiguo Zhou
- Key Laboratory of Crop Physiology & Ecology, Ministry of Agriculture, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.
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Sun Z, Wang X, Liu Z, Gu Q, Zhang Y, Li Z, Ke H, Yang J, Wu J, Wu L, Zhang G, Zhang C, Ma Z. Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:982-996. [PMID: 28064470 PMCID: PMC5506648 DOI: 10.1111/pbi.12693] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 11/02/2016] [Accepted: 01/05/2017] [Indexed: 05/18/2023]
Abstract
Genetic improvement of fibre quality is one of the main breeding goals for the upland cotton, Gossypium hirsutum, but there are difficulties with precise selection of traits. Therefore, it is important to improve the understanding of the genetic basis of phenotypic variation. In this study, we conducted phenotyping and genetic variation analyses of 719 diverse accessions of upland cotton based on multiple environment tests and a recently developed Cotton 63K Illumina Infinium SNP array and performed a genome-wide association study (GWAS) of fibre quality traits. A total of 10 511 polymorphic SNPs distributed in 26 chromosomes were screened across the cotton germplasms, and forty-six significant SNPs associated with five fibre quality traits were detected. These significant SNPs were scattered over 15 chromosomes and were involved in 612 unique candidate genes, many related to polysaccharide biosynthesis, signal transduction and protein translocation. Two major haplotypes for fibre length and strength were identified on chromosomes Dt11 and At07. Furthermore, by combining GWAS and transcriptome analysis, we identified 163 and 120 fibre developmental genes related to length and strength, respectively, of which a number of novel genes and 19 promising genes were screened. These results provide new insight into the genetic basis of fibre quality in G. hirsutum and provide candidate SNPs and genes to accelerate the improvement of upland cotton.
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Affiliation(s)
- Zhengwen Sun
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Xingfen Wang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Zhengwen Liu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Qishen Gu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Yan Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Zhikun Li
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Huifeng Ke
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Jun Yang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Jinhua Wu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Liqiang Wu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Guiyin Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Caiying Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
| | - Zhiying Ma
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei ProvinceHebei Agricultural UniversityBaodingChina
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Genome-wide analysis of gene expression of EMS-induced short fiber mutant Ligon lintless-y (li y) in cotton (Gossypium hirsutum L.). Genomics 2017; 109:320-329. [PMID: 28577792 DOI: 10.1016/j.ygeno.2017.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/18/2017] [Accepted: 05/30/2017] [Indexed: 12/31/2022]
Abstract
In this work we describe a chemically-induced short fiber mutant cotton line, Ligon-lintless-y (liy), which is controlled by a single recessive locus and affects multiple traits, including height of the plant, and length and maturity of fiber. An RNAseq analysis was used to evaluate global transcriptional changes during cotton fiber development at 3, 8 and 16days post anthesis. We found that 613, 2629 and 3397 genes were significantly down-regulated, while 2700, 477 and 3260 were significantly up-regulated in liy at 3, 8 and 16 DPA. Gene set enrichment analysis revealed that many metabolic pathways, including carbohydrate, cell wall, hormone metabolism and transport were substantially altered in liy developing fibers. We discuss perturbed expression of genes involved in signal transduction and biosynthesis of phytohormones, such as auxin, abscisic acid, gibberellin and ethylene. The results of this study provide new insights into transcriptional regulation of cotton fiber development.
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Simmons TJ, Fry SC. Bonds broken and formed during the mixed-linkage glucan : xyloglucan endotransglucosylase reaction catalysed by Equisetum hetero-trans-β-glucanase. Biochem J 2017; 474:1055-1070. [PMID: 28108640 PMCID: PMC5341106 DOI: 10.1042/bcj20160935] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/12/2017] [Accepted: 01/19/2017] [Indexed: 11/17/2022]
Abstract
Mixed-linkage glucan∶xyloglucan endotransglucosylase (MXE) is one of the three activities of the recently characterised hetero-trans-β-glucanase (HTG), which among land plants is known only from Equisetum species. The biochemical details of the MXE reaction were incompletely understood - details that would promote understanding of MXE's role in vivo and enable its full technological exploitation. We investigated HTG's site of attack on one of its donor substrates, mixed-linkage (1→3),(1→4)-β-d-glucan (MLG), with radioactive oligosaccharides of xyloglucan as the acceptor substrate. Comparing three different MLG preparations, we showed that the enzyme favours those with a high content of cellotetraose blocks. The reaction products were analysed by enzymic digestion, thin-layer chromatography (TLC), high-pressure liquid chromatography (HPLC) and gel-permeation chromatography (GPC). Equisetum HTG consistently cleaved the MLG at the third consecutive β-(1→4)-bond following (towards the reducing terminus) a β-(1→3)-bond. It then formed a β-(1→4)-bond between the MLG and the non-reducing terminal glucose residue of the xyloglucan oligosaccharide, consistent with its xyloglucan endotransglucosylase/hydrolase subfamily membership. Using size-homogeneous barley MLG as the donor substrate, we showed that HTG does not favour any particular region of the MLG chain relative to the polysaccharide's reducing and non-reducing termini; rather, it selects its target cellotetraosyl unit stochastically along the MLG molecule. This work improves our understanding of how enzymes can exhibit promiscuous substrate specificities and provides the foundations to explore strategies for engineering novel substrate specificities into transglycanases.
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Affiliation(s)
- Thomas J Simmons
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3BF, U.K
| | - Stephen C Fry
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3BF, U.K.
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McGregor N, Yin V, Tung CC, Van Petegem F, Brumer H. Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:651-670. [PMID: 27859885 PMCID: PMC5315667 DOI: 10.1111/tpj.13421] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/14/2016] [Accepted: 11/04/2016] [Indexed: 05/22/2023]
Abstract
The xyloglucan endotransglycosylase/hydrolase (XTH) gene family encodes enzymes of central importance to plant cell wall remodeling. The evolutionary history of plant XTH gene products is incompletely understood vis-à-vis the larger body of bacterial endoglycanases in Glycoside Hydrolase Family 16 (GH16). To provide molecular insight into this issue, high-resolution X-ray crystal structures and detailed enzyme kinetics of an extant transitional plant endoglucanase (EG) were determined. Functionally intermediate between plant XTH gene products and bacterial licheninases of GH16, Vitis vinifera EG16 (VvEG16) effectively catalyzes the hydrolysis of the backbones of two dominant plant cell wall matrix glycans, xyloglucan (XyG) and β(1,3)/β(1,4)-mixed-linkage glucan (MLG). Crystallographic complexes with extended oligosaccharide substrates reveal the structural basis for the accommodation of both unbranched, mixed-linked (MLG) and highly decorated, linear (XyG) polysaccharide chains in a broad, extended active-site cleft. Structural comparison with representative bacterial licheninases, a xyloglucan endotranglycosylase (XET), and a xyloglucan endohydrolase (XEH) outline the functional ramifications of key sequence deletions and insertions across the phylogenetic landscape of GH16. Although the biological role(s) of EG16 orthologs remains to be fully resolved, the present biochemical and tertiary structural characterization provides key insight into plant cell wall enzyme evolution, which will continue to inform genomic analyses and functional studies across species.
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Affiliation(s)
- Nicholas McGregor
- Michael Smith Laboratories, University of British Columbia,
2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia,
2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Victor Yin
- Michael Smith Laboratories, University of British Columbia,
2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia,
2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ching-Chieh Tung
- Department of Biochemistry and Molecular Biology,
University of British Columbia, 2350 Health Sciences Mall, Vancouver, British
Columbia V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology,
University of British Columbia, 2350 Health Sciences Mall, Vancouver, British
Columbia V6T 1Z3, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia,
2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia,
2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Department of Biochemistry and Molecular Biology,
University of British Columbia, 2350 Health Sciences Mall, Vancouver, British
Columbia V6T 1Z3, Canada
- Department of Botany, University of British Columbia, 6270
University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
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48
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Liu D, Zhang J, Liu X, Wang W, Liu D, Teng Z, Fang X, Tan Z, Tang S, Yang J, Zhong J, Zhang Z. Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton. BMC Genomics 2016; 17:295. [PMID: 27094760 PMCID: PMC4837631 DOI: 10.1186/s12864-016-2605-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 03/28/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Improving fiber quality is a major challenge in cotton breeding, since the molecular basis of fiber quality traits is poorly understood. Fine mapping and candidate gene prediction of quantitative trait loci (QTL) controlling cotton fiber quality traits can help to elucidate the molecular basis of fiber quality. In our previous studies, one major QTL controlling multiple fiber quality traits was identified near the T1 locus on chromosome 6 in Upland cotton. RESULTS To finely map this major QTL, the F2 population with 6975 individuals was established from a cross between Yumian 1 and a recombinant inbred line (RIL118) selected from a recombinant inbred line population (T586 × Yumian 1). The QTL was mapped to a 0.28-cM interval between markers HAU2119 and SWU2302. The QTL explained 54.7 % (LOD = 222.3), 40.5 % (LOD = 145.0), 50.0 % (LOD = 194.3) and 30.1 % (LOD = 100.4) of phenotypic variation with additive effects of 2.78, -0.43, 2.92 and 1.90 units for fiber length, micronaire, strength and uniformity, respectively. The QTL region corresponded to a 2.7-Mb interval on chromosome 10 in the G. raimondii genome sequence and a 5.3-Mb interval on chromosome A06 in G. hirsutum. The fiber of Yumian 1 was much longer than that of RIL118 from 3 DPA to 7 DPA. RNA-Seq of ovules at 0 DPA and fibers at 5 DPA from Yumian 1 and RIL118 showed four genes in the QTL region of the G. raimondii genome to be extremely differentially expressed. RT-PCR analysis showed three genes in the QTL region of the G. hirsutum genome to behave similarly. CONCLUSIONS This study mapped a major QTL influencing four fiber quality traits to a 0.28-cM interval and identified three candidate genes by RNA-Seq and RT-PCR analysis. Integration of fine mapping and RNA-Seq is a powerful strategy to uncover candidates for QTL in large genomes.
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Affiliation(s)
- Dexin Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Jian Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Xueying Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Wenwen Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Dajun Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Zhonghua Teng
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Xiaomei Fang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Zhaoyun Tan
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Shiyi Tang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Jinghong Yang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Jianwei Zhong
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Zhengsheng Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
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49
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Li Y, Tu L, Pettolino FA, Ji S, Hao J, Yuan D, Deng F, Tan J, Hu H, Wang Q, Llewellyn DJ, Zhang X. GbEXPATR, a species-specific expansin, enhances cotton fibre elongation through cell wall restructuring. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:951-63. [PMID: 26269378 DOI: 10.1111/pbi.12450] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 05/08/2015] [Accepted: 05/26/2015] [Indexed: 05/18/2023]
Abstract
Cotton provides us the most important natural fibre. High fibre quality is the major goal of cotton breeding, and introducing genes conferring longer, finer and stronger fibre from Gossypium barbadense to Gossypium hirsutum is an important breeding strategy. We previously analysed the G. barbadense fibre development mechanism by gene expression profiling and found two homoeologous fibre-specific α-expansins from G. barbadense, GbEXPA2 and GbEXPATR. GbEXPA2 (from the DT genome) is a classical α-expansin, while its homoeolog, GbEXPATR (AT genome), encodes a truncated protein lacking the normal C-terminal polysaccharide-binding domain of other α-expansins and is specifically expressed in G. barbadense. Silencing EXPA in G. hirsutum induced shorter fibres with thicker cell walls. GbEXPA2 overexpression in G. hirsutum had no effect on mature fibre length, but produced fibres with a slightly thicker wall and increased crystalline cellulose content. Interestingly, GbEXPATR overexpression resulted in longer, finer and stronger fibres coupled with significantly thinner cell walls. The longer and thinner fibre was associated with lower expression of a number of secondary wall-associated genes, especially chitinase-like genes, and walls with lower cellulose levels but higher noncellulosic polysaccharides which advocated that a delay in the transition to secondary wall synthesis might be responsible for better fibre. In conclusion, we propose that α-expansins play a critical role in fibre development by loosening the cell wall; furthermore, a truncated form, GbEXPATR, has a more dramatic effect through reorganizing secondary wall synthesis and metabolism and should be a candidate gene for developing G. hirsutum cultivars with superior fibre quality.
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Affiliation(s)
- Yang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Filomena A Pettolino
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Plant Industry, Canberra, ACT, Australia
| | - Shengmei Ji
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Juan Hao
- 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
| | - Fenglin Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiafu Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Haiyan Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Danny J Llewellyn
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Plant Industry, Canberra, ACT, Australia
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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50
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Mujahid H, Pendarvis K, Reddy JS, Nallamilli BRR, Reddy KR, Nanduri B, Peng Z. Comparative Proteomic Analysis of Cotton Fiber Development and Protein Extraction Method Comparison in Late Stage Fibers. Proteomes 2016; 4:proteomes4010007. [PMID: 28248216 PMCID: PMC5217364 DOI: 10.3390/proteomes4010007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/19/2016] [Accepted: 01/28/2016] [Indexed: 12/21/2022] Open
Abstract
The distinct stages of cotton fiber development and maturation serve as a single-celled model for studying the molecular mechanisms of plant cell elongation, cell wall development and cellulose biosynthesis. However, this model system of plant cell development is compromised for proteomic studies due to a lack of an efficient protein extraction method during the later stages of fiber development, because of a recalcitrant cell wall and the presence of abundant phenolic compounds. Here, we compared the quality and quantities of proteins extracted from 25 dpa (days post anthesis) fiber with multiple protein extraction methods and present a comprehensive quantitative proteomic study of fiber development from 10 dpa to 25 dpa. Comparative analysis using a label-free quantification method revealed 287 differentially-expressed proteins in the 10 dpa to 25 dpa fiber developmental period. Proteins involved in cell wall metabolism and regulation, cytoskeleton development and carbohydrate metabolism among other functional categories in four fiber developmental stages were identified. Our studies provide protocols for protein extraction from maturing fiber tissues for mass spectrometry analysis and expand knowledge of the proteomic profile of cotton fiber development.
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Affiliation(s)
- Hana Mujahid
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Ken Pendarvis
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Joseph S Reddy
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Babi Ramesh Reddy Nallamilli
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
| | - K R Reddy
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Bindu Nanduri
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
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