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Luiza Atella A, Fatima Grossi-de-Sá M, Alves-Ferreira M. Cotton promoters for controlled gene expression. ELECTRON J BIOTECHN 2023. [DOI: 10.1016/j.ejbt.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Zhao N, Wang W, Grover CE, Jiang K, Pan Z, Guo B, Zhu J, Su Y, Wang M, Nie H, Xiao L, Guo A, Yang J, Cheng C, Ning X, Li B, Xu H, Adjibolosoo D, Aierxi A, Li P, Geng J, Wendel JF, Kong J, Hua J. Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fibre length, lint percentage and Fusarium wilt resistance. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:691-710. [PMID: 34800075 PMCID: PMC8989498 DOI: 10.1111/pbi.13747] [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: 07/01/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 05/04/2023]
Abstract
Sea Island cotton (Gossypium barbadense) is the source of the world's finest fibre quality cotton, yet relatively little is understood about genetic variations among diverse germplasms, genes underlying important traits and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fibre quality, yield, disease resistance, maturity and plant architecture. The highest number of associated loci was for fibre quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments, we confirmed the roles of five candidate genes regulating four key traits, that is disease resistance, fibre length, fibre strength and lint percentage. Geographical and temporal considerations demonstrated selection for the superior fibre quality (fibre length and fibre strength), and high lint percentage in improving G. barbadense in China. Pedigree selection breeding increased Fusarium wilt disease resistance and separately improved fibre quality and yield. Our work provides a foundation for understanding genomic variation and selective breeding of Sea Island cotton.
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Affiliation(s)
- Nan Zhao
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Weiran Wang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIAUSA
| | - Kaiyun Jiang
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Zhuanxia Pan
- Institute of Cotton ResearchShanxi Agricultural UniversityShanxiChina
| | - Baosheng Guo
- Cotton Research InstituteHebei Academy of Agriculture and Forestry SciencesHebeiChina
| | - Jiahui Zhu
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Ying Su
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Meng Wang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Hushuai Nie
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Li Xiao
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Anhui Guo
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jing Yang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Cheng Cheng
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xinmin Ning
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Bin Li
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Haijiang Xu
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Daniel Adjibolosoo
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Alifu Aierxi
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Pengbo Li
- Institute of Cotton ResearchShanxi Agricultural UniversityShanxiChina
| | - Junyi Geng
- Cotton Research InstituteHebei Academy of Agriculture and Forestry SciencesHebeiChina
| | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIAUSA
| | - Jie Kong
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Jinping Hua
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
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Ahmed MM, Huang C, Shen C, Khan AQ, Lin Z. Map-based cloning of qBWT-c12 discovered brassinosteroid-mediated control of organ size in cotton. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110315. [PMID: 31928681 DOI: 10.1016/j.plantsci.2019.110315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/14/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Assuring fiber yield stability is the primary objective for cotton breeders since the world population is on the rise, and the demand for cotton fiber is increasing every year. Thus, enhancing average cotton boll weight (BWT) could improve seed cotton production, and ultimately to increase cotton fiber yield. This study accomplished the map-based cloning of a novel boll weight regulating locus, qBWT-c12, in cotton. Bulk segregation analysis detected linked markers, aided in the detection of a stable BWT regulating locus, qBWT-c12, on Chr12 in a novel boll size mutant, BS41. Progeny evaluation confined the qBWT-c12 to a 0.89 cM interval between the AD-A12_07 and AD-FM_44 markers in recombinant derived F3 and F4 populations. Homology mapping detected a 40 bp insertion-deletion (InDel) site in the AD-FM_44 clone sequence situated +341 downstream of GhBRH1_A12, which showed complete linkage to the BWT phenotype. The suppressed expression of GhBRH1_A12 suggested its putative involvement during early boll development events in BS41. Although brassinosteroid (BR) biosynthesis and signaling pathway genes were up regulated in different tissues, but the organ growth was suppressed leading to dwarf plants, smaller leaves, and de-morphed smaller bolls in BS41. Thus, a disruption in the BR signal cascade is anticipated and could be related to lower GhBRH1_A12 expression in BS41.This study firstly reported the genetic dissection of boll size regulation of G. barbadense in G. hirsutum background using map-based cloning of a BWT regulating locus, qBWT-c12. Moreover, it also emphasized the putative role GhBRH1_A12 in regulating BR homeostasis and its potential to modulate plant growth and boll development in cotton.
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Affiliation(s)
- Muhammad Mahmood Ahmed
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Cong Huang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Anam Qadir Khan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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Salih H, Gong W, He S, Xia W, Odongo MR, Du X. Long non-coding RNAs and their potential functions in Ligon-lintless-1 mutant cotton during fiber development. BMC Genomics 2019; 20:661. [PMID: 31426741 PMCID: PMC6700839 DOI: 10.1186/s12864-019-5978-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 07/16/2019] [Indexed: 01/28/2023] Open
Abstract
Background Long non-coding RNAs (LncRNAs) are part of genes, which are not translated into proteins and play a vital role in plant growth and development. Nevertheless, the presence of LncRNAs and how they functions in Ligon-lintless-1 mutant during the early cessation of cotton fiber development are still not well understood. In order to investigate the function of LncRNAs in cotton fiber development, it is necessary and important to identify LncRNAs and their potential roles in fiber cell development. Results In this work, we identified 18,333 LncRNAs, with the proportion of long intergenic noncoding RNAs (LincRNAs) (91.5%) and anti-sense LncRNAs (8.5%), all transcribed from Ligon-lintless-1 (Li1) and wild-type (WT). Expression differences were detected between Ligon-lintless-1 and wild-type at 0 and 8 DPA (day post anthesis). Pathway analysis and Gene Ontology based on differentially expressed LncRNAs on target genes, indicated fatty acid biosynthesis and fatty acid elongation being integral to lack of fiber in mutant cotton. The result of RNA-seq and RT-qPCR clearly singles out two potential LncRNAs, LNC_001237 and LNC_017085, to be highly down-regulated in the mutant cotton. The two LncRNAs were found to be destabilized or repressed by ghr-miR2950. Both RNA-seq analysis and RT-qPCR results in Ligon-lintless-1 mutant and wild-type may provide strong evidence of LNC_001237, LNC_017085 and ghr-miR2950 being integral molecular elements participating in various pathways of cotton fiber development. Conclusion The results of this study provide fundamental evidence for the better understanding of LncRNAs regulatory role in the molecular pathways governing cotton fiber development. Further research on designing and transforming LncRNAs will help not only in the understanding of their functions but will also in the improvement of fiber quality. Electronic supplementary material The online version of this article (10.1186/s12864-019-5978-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haron Salih
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.,Zalingei University, Central Darfur, Sudan
| | - Wenfang Gong
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Shoupu He
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Wang Xia
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Magwanga Richard Odongo
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Xiongming Du
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.
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Feng H, Li X, Chen H, Deng J, Zhang C, Liu J, Wang T, Zhang X, Dong J. GhHUB2, a ubiquitin ligase, is involved in cotton fiber development via the ubiquitin-26S proteasome pathway. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5059-5075. [PMID: 30053051 PMCID: PMC6184758 DOI: 10.1093/jxb/ery269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/12/2018] [Indexed: 05/02/2023]
Abstract
Cotton fibers, which are extremely elongated single cells of epidermal seed trichomes and have highly thickened cell walls, constitute the most important natural textile material worldwide. However, the regulation of fiber development is not well understood. Here, we report that GhHUB2, a functional homolog of AtHUB2, controls fiber elongation and secondary cell wall (SCW) deposition. GhHUB2 is ubiquitously expressed, including within fibers. Overexpression of GhHUB2 in cotton increased fiber length and SCW thickness, while RNAi knockdown of GhHUB2 resulted in shortened fibers and thinner cell walls. We found that GhHUB2 interacted with GhKNL1, a transcriptional repressor predominantly expressed in developing fibers, and that GhHUB2 ubiquitinated and degraded GhKNL1 via the ubiquitin-26S proteasome pathway. GhHUB2 negatively regulated GhKNL1 protein levels and lead to the disinhibition of genes such as GhXTH1, Gh1,3-β-G, GhCesA4, GhAGP4, GhCTL1, and GhCOBL4, thus promoting fiber elongation and enhancing SCW biosynthesis. We found that GhREV-08, a transcription factor that participates in SCW deposition and auxin signaling pathway, was a direct target of GhKNL1. In conclusion, our study uncovers a novel function of HUB2 in plants in addition to its monoubiquitination of H2B. Moreover, we provide evidence for control of the fiber development by the ubiquitin-26S proteasome pathway.
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Affiliation(s)
- Hao Feng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xin Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hong Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jie Deng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chaojun Zhang
- 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
| | - Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Yadav VK, Yadav VK, Pant P, Singh SP, Maurya R, Sable A, Sawant SV. GhMYB1 regulates SCW stage-specific expression of the GhGDSL promoter in the fibres of Gossypium hirsutum L. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1163-1174. [PMID: 28182326 PMCID: PMC5552479 DOI: 10.1111/pbi.12706] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 02/03/2017] [Accepted: 02/04/2017] [Indexed: 05/19/2023]
Abstract
Secondary cell wall (SCW) biosynthesis is an important stage of the cotton fibre development, and its transcriptional regulation is poorly understood. We selected the Gossypium hirsutum GDSL (GhGDSL) lipase/hydrolase gene (CotAD_74480), which is expressed during SCW biosynthesis (19 through to 25 days postanthesis; DPA), for study. T1 -transgenic cotton lines expressing the β-glucuronidase (gus) reporter under the control of a 1026-bp promoter fragment of GhGDSL (PGhGDSL ) showed 19 DPA stage-specific increase in GUS expression. 5' deletion indicated that the 194-bp fragment between -788 and -594 relative to the transcription start site was essential for this stage-specific expression. Site-directed mutagenesis of eight transcription factor binding sites within PGhGDSL demonstrated that the MYB1AT motif (AAACCA) at -603/-598 was critical for the 19 DPA-specific reporter gene expressions. Yeast one-hybrid (Y1H) analysis identified nine proteins, including GhMYB1 (CotAD_64719) that bound to the PGhGDSL promoter. Further, Y1H experiments using the 5' promoter deletions and individually mutated promoter motifs indicated that GhMYB1 interacted with PGhGDSL at MYB1AT sequence. GhMYB1 was expressed specifically in fibre from 19 DPA, overlapping with the sharp rise in GhGDSL expression, indicating that it could regulate GhGDSL during fibre development. Analysis of genes co-expressed with GhMYB1 showed that it potentially regulates a number of other 19-25 DPA-specific genes in networks including those functioning in the cell wall and precursor synthesis, but not the major polysaccharide and protein components of the fibre SCW. GhGDSL and its promoter are therefore potential tools for the improvement of cotton fibre quality traits.
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Affiliation(s)
- Vrijesh Kumar Yadav
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
- Academy of Scientific and Innovative Research (AcSIR)CSIR‐National Botanical Research InstituteLucknowIndia
| | - Vikash Kumar Yadav
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
- Academy of Scientific and Innovative Research (AcSIR)CSIR‐National Botanical Research InstituteLucknowIndia
| | - Poonam Pant
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
- Academy of Scientific and Innovative Research (AcSIR)CSIR‐National Botanical Research InstituteLucknowIndia
| | - Surendra Pratap Singh
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
| | - Rashmi Maurya
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
| | - Anshulika Sable
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
| | - Samir V. Sawant
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
- Academy of Scientific and Innovative Research (AcSIR)CSIR‐National Botanical Research InstituteLucknowIndia
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Ma J, He X, Bai X, Niu Z, Duan B, Chen N, Shao X, Wan D. Genome-Wide Survey Reveals Transcriptional Differences Underlying the Contrasting Trichome Phenotypes of Two Sister Desert Poplars. Genes (Basel) 2016; 7:genes7120111. [PMID: 27916935 PMCID: PMC5192487 DOI: 10.3390/genes7120111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 11/24/2016] [Accepted: 11/24/2016] [Indexed: 11/16/2022] Open
Abstract
Trichomes, which are widely used as an important diagnostic characteristic in plant species delimitation, play important roles in plant defense and adaptation to adverse environments. In this study, we used two sister poplar species, Populus pruinosa and Populus euphratica—which have, respectively, dense and sparse trichomes—to examine the genetic differences associated with these contrasting phenotypes. The results showed that 42 and 45 genes could be identified as candidate genes related to trichomes in P. pruinosa and P. euphratica, respectively; most of these genes possessed high degrees of diversification in their coding sequences, but they were similar in intron/exon structure in the two species. We also found that most of the candidate trichome genes were expressed at higher levels in P. pruinosa, which has dense trichomes, than in P. euphratica, where there are few trichomes. Based on analyses of transcriptional profiles, a total of 195 genes, including many transcription factors, were found to show distinct differences in expression. The results of gene function annotation suggested that the genes identified as having contrasting levels of expression level are mainly associated with trichome elongation, ATPase activity, and hormone transduction. Changes in the expression of these and other related genes with high sequence diversification may have contributed to the contrast in the pattern of trichome phenotypes between the two species.
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Affiliation(s)
- Jianchao Ma
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Xiaodong He
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Xiaotao Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Zhimin Niu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Bingbing Duan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Ningning Chen
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Xuemin Shao
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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Liu Y, Zhang X, Zhu S, Zhang H, Li Y, Zhang T, Sun J. Overexpression of GhSARP1 encoding a E3 ligase from cotton reduce the tolerance to salt in transgenic Arabidopsis. Biochem Biophys Res Commun 2016; 478:1491-6. [PMID: 27402266 DOI: 10.1016/j.bbrc.2016.07.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 07/06/2016] [Indexed: 12/17/2022]
Abstract
Ubiquitination plays a very important role in the response to abiotic stresses of plant. To identify key regulators of salt stress, a gene GhSARP1(Salt-Associated Ring finger Protein)encoding C3H2C3-type E3 ligase, was cloned from cotton. Transcription level of GhSARP1 was high in leaf, flower and fiber of 24,27 and 27DPA (Days Post-Anthesis), but low in root and stem. Except PEG6000 treatment, the expression of GhSARP1 was down-regulated by NaCl, cold and ABA after being treated for 1 h. GhSARP1-GFP fusion protein located on the plasma membrane, which was dependent on trans-membrane motif. In vitro ubiquitination assay showed that GhSARP1 had E3 ligase activity. Heterogeneous overexpression of GhSARP1reduced salt tolerance of transgenic Arabidopsis in germination and post-germination stage. Our results suggested that the GhSARP1 might negatively regulate the response to salt stress mediated by the ubiquitination in cotton.
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Affiliation(s)
- Yongchang Liu
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi 832000, Xinjiang Province, China
| | - Xinyu Zhang
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi 832000, Xinjiang Province, China
| | - Shouhong Zhu
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi 832000, Xinjiang Province, China
| | - Hao Zhang
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi 832000, Xinjiang Province, China
| | - Yanjun Li
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi 832000, Xinjiang Province, China
| | - Tao Zhang
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi 832000, Xinjiang Province, China
| | - Jie Sun
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi 832000, Xinjiang Province, China.
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Detection and validation of one stable fiber strength QTL on c9 in tetraploid cotton. Mol Genet Genomics 2016; 291:1625-38. [PMID: 27119657 DOI: 10.1007/s00438-016-1206-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 04/08/2016] [Indexed: 10/21/2022]
Abstract
Fiber strength is an essential trait of fiber property in cotton, and it is quantitatively inherited. Identification of stable quantitative trait loci (QTL) contributing to fiber strength would provide the key basis for marker-assisted selection (MAS) in cotton breeding. In this study, four interspecific hybridization populations were established with a common G. barbadense parent Pima 90-53 and two G. hirsutum parents (CCRI 8 and Handan 208), each of which had fiber strength characteristic. Based on the phenotypic data of fiber strength from seven environments, a stable QTL, qFS-c9-1, was detected and validated on c9 in a marker interval between SSR markers NAU2395 and NAU1092. The QTL explaining 14.4-17.9 % of the phenotypic variation was firstly detected in two populations (CCRI 8 × Pima 90-53, BC1F1 and BC1F2) and its derived lines in four environments. And it accounting for 12.1-14.8 % of the phenotypic variation was further confirmed in two populations (Handan 208 × Pima 90-53, BC1F1, and F2) under one environment. In silico mapping using three sequenced cotton genomes indicated that homologous genes, anchored by NAU2395 and NAU1092, were aligned to the G. arboreum genome within a physical distance between 81.10 Mbps and 87.07 Mbps. In that interval, several genes were confirmed in literatures to associate with fiber development. Among these genes, seven genes were further selected for an expression analysis through fiber development transcriptome database, revealing unique expression patterns across different stages of fiber development between CCRI 8 and Pima 90-53. The genes underlying qFS-c9-1 were favorable to fine mapping and cloning. The current study results provided valuable evidence for mapping stable QTL of fiber strength utilizing multiple populations and environments, as well as map-based cloning the candidate gene underlying the QTL for future prospective research directions.
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10
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Ding M, Jiang Y, Cao Y, Lin L, He S, Zhou W, Rong J. Gene expression profile analysis of Ligon lintless-1 (Li1) mutant reveals important genes and pathways in cotton leaf and fiber development. Gene 2013; 535:273-85. [PMID: 24279997 DOI: 10.1016/j.gene.2013.11.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 11/02/2013] [Accepted: 11/13/2013] [Indexed: 12/14/2022]
Abstract
Ligon lintless-1 (Li1) is a monogenic dominant mutant of Gossypium hirsutum (upland cotton) with a phenotype of impaired vegetative growth and short lint fibers. Despite years of research involving genetic mapping and gene expression profile analysis of Li1 mutant ovule tissues, the gene remains uncloned and the underlying pathway of cotton fiber elongation is still unclear. In this study, we report the whole genome-level deep-sequencing analysis of leaf tissues of the Li1 mutant. Differentially expressed genes in leaf tissues of mutant versus wild-type (WT) plants are identified, and the underlying pathways and potential genes that control leaf and fiber development are inferred. The results show that transcription factors AS2, YABBY5, and KANDI-like are significantly differentially expressed in mutant tissues compared with WT ones. Interestingly, several fiber development-related genes are found in the downregulated gene list of the mutant leaf transcriptome. These genes include heat shock protein family, cytoskeleton arrangement, cell wall synthesis, energy, H2O2 metabolism-related genes, and WRKY transcription factors. This finding suggests that the genes are involved in leaf morphology determination and fiber elongation. The expression data are also compared with the previously published microarray data of Li1 ovule tissues. Comparative analysis of the ovule transcriptomes of Li1 and WT reveals that a number of pathways important for fiber elongation are enriched in the downregulated gene list at different fiber development stages (0, 6, 9, 12, 15, 18dpa). Differentially expressed genes identified in both leaf and fiber samples are aligned with cotton whole genome sequences and combined with the genetic fine mapping results to identify a list of candidate genes for Li1.
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Affiliation(s)
- Mingquan Ding
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Yurong Jiang
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Yuefen Cao
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Lifeng Lin
- Nanosphere Inc., 4088 Commercial Drive, Northbrook, IL 60062, USA
| | - Shae He
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Wei Zhou
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Junkang Rong
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China.
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