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Comparative Genomics and Functional Studies of Putative m 6A Methyltransferase (METTL) Genes in Cotton. Int J Mol Sci 2022; 23:ijms232214111. [PMID: 36430588 PMCID: PMC9694044 DOI: 10.3390/ijms232214111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022] Open
Abstract
N6-methyladenosine (m6A) RNA modification plays important regulatory roles in plant development and adapting to the environment, which requires methyltransferases to achieve the methylation process. However, there has been no research regarding m6A RNA methyltransferases in cotton. Here, a systematic analysis of the m6A methyltransferase (METTL) gene family was performed on twelve cotton species, resulting in six METTLs identified in five allotetraploid cottons, respectively, and three to four METTLs in the seven diploid species. Phylogenetic analysis of protein-coding sequences revealed that METTL genes from cottons, Arabidopsis thaliana, and Homo sapiens could be classified into three clades (METTL3, METTL14, and METTL-like clades). Cis-element analysis predicated the possible functions of METTL genes in G. hirsutum. RNA-seq data revealed that GhMETTL14 (GH_A07G0817/GH_D07G0819) and GhMETTL3 (GH_A12G2586/GH_D12G2605) had high expressions in root, stem, leaf, torus, petal, stamen, pistil, and calycle tissues. GhMETTL14 also had the highest expression in 20 and 25 dpa fiber cells, implying a potential role at the cell wall thickening stage. Suppressing GhMETTL3 and GhMETTL14 by VIGS caused growth arrest and even death in G. hirsutum, along with decreased m6A abundance from the leaf tissues of VIGS plants. Overexpression of GhMETTL3 and GhMETTL14 produced distinct differentially expressed genes (DEGs) in A. thaliana, indicating their possible divergent functions after gene duplication. Overall, GhMETTLs play indispensable but divergent roles during the growth of cotton plants, which provides the basis for the systematic investigation of m6A in subsequent studies to improve the agronomic traits in cotton.
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Cui W, Chen Z, Shangguan X, Li T, Wang L, Xue X, Cao J. TRY intron2 determined its expression in inflorescence activated by SPL9 and MADS-box genes in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111311. [PMID: 35696911 DOI: 10.1016/j.plantsci.2022.111311] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/24/2022] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
Plant trichomes are specialized epidermal cells that protect plants from insects and pathogens. In Arabidopsis, epidermal hairs decrease as internodes increase in height, with only few epidermal hairs produced on the sepals abaxial surface of the early flowers. TRIPTYCHON (TRY) is known to be a negative regulator of epidermal hair development in Arabidopsis, suppressing the formation of ectopic epidermal hairs in the inflorescence. Here, we reported that the second intron of TRY gene plays a critical role in trichome spatial distribution in Arabidopsis. The expression of TRY rises with the increasing stem nodes and reaches the peak in the inflorescence, while the trichomes distribution decrease. The transgenic plants showed that TRY promoter could only drive the genomic instead of coding sequences combined with GUS reporter gene, which indicates that the regulatory elements of TRY expression in inflorescence could be located in the intron regions. Multiple SPLs and MADS-box binding sites were found in the TRY intron2 sequence. Further genetic and biochemistry assays revealed that the flowering-related genes such as SPL9 could bind to these cis-elements directly, contributing to the TRY spatial expression. Since cotton fiber and Arabidopsis trichomes share similar regulatory mechanism, extended analysis showed that the intron2 of cotton TRY genes also contain the cis-elements. Thus, the introns harboring the transcription element may be the general way to regulate the gene expression in different plants and provides molecular clues for the related crops' traits design.
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Affiliation(s)
- Wenrui Cui
- National Key Laboratory of Plant Molecular genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Hainan Yazhou Bay Seed Laboratory, Sanya, China, 572025
| | - Xiaoxia Shangguan
- National Key Laboratory of Plant Molecular genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Taotao Li
- College of Agronomy, Nanjing Agriculture University, Nanjing 210095, China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xueyi Xue
- National Key Laboratory of Plant Molecular genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Junfeng Cao
- National Key Laboratory of Plant Molecular genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Shi Y, Wang X, Wang J, Niu J, Du R, Ji G, Zhu L, Zhang J, Lv P, Cao J. Systematical characterization of GRF gene family in sorghum, and their potential functions in aphid resistance. Gene 2022; 836:146669. [PMID: 35710084 DOI: 10.1016/j.gene.2022.146669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/19/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
Sorghum (Sorghum bicolor) is the fifth important cereal and an industrial energy crop in the world. Growth Regulation Factors (GRFs) play an important role in response to environmental stress, however, the knowledge of GRFs relating to the pest resistance is lacking. Here, we identified 8 GRF genes harboring the typical QLQ (glutamine, leucine, glutamine) and WRC (tryptophan, arginine, cysteine) domains in Sorghum, which could be classified into 4 clades through phylogenetic analysis. The SbGRF genes express in most tissues, while more than half of them express at the highest level in inflorescence. To further investigate their possible role in stress response, we analyzed the transcriptomics data. The results showed that SbGRFs could respond to the abiotic stresses including heat, salt and drought stress. Furthermore, combined the data with qRT-PCR, SbGRF1, 2, 4 and 7 were identified as dominant genes response to the aphid-induced stress. SSR markers close to these genes were also searched. Above all, we summarized the SbGRFs and provided their potential roles in aphid response.
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Affiliation(s)
- Yannan Shi
- Institute of Millet Crops, Hebei Academy of Agriculture & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang 050035, China
| | - Xinyu Wang
- Institute of Millet Crops, Hebei Academy of Agriculture & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang 050035, China
| | - Jinping Wang
- Institute of Millet Crops, Hebei Academy of Agriculture & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang 050035, China
| | - Jingtian Niu
- Institute of Millet Crops, Hebei Academy of Agriculture & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang 050035, China
| | - Ruiheng Du
- Institute of Millet Crops, Hebei Academy of Agriculture & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang 050035, China
| | - Guisu Ji
- Institute of Millet Crops, Hebei Academy of Agriculture & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang 050035, China
| | - Lining Zhu
- Hebei Nijiao Brewing Technology Innovation Center, Xingtai 054000, China
| | - Jing Zhang
- Hebei Seed Management Station, Shijiazhuang 050031, China
| | - Peng Lv
- Institute of Millet Crops, Hebei Academy of Agriculture & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang 050035, China.
| | - Junfeng Cao
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Huang C, Li P, Cao J, Zheng Z, Huang J, Zhang X, Shangguan X, Wang L, Chen Z. Comprehensive identification and expression analysis of CRY gene family in Gossypium. BMC Genomics 2022; 23:231. [PMID: 35331129 PMCID: PMC8952943 DOI: 10.1186/s12864-022-08440-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/03/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The cryptochromes (CRY) are specific blue light receptors of plants and animals, which play crucial roles in physiological processes of plant growth, development, and stress tolerance. RESULTS In the present work, a systematic analysis of the CRY gene family was performed on twelve cotton species, resulting in 18, 17, 17, 17, and 17 CRYs identified in five alloteraploid cottons (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum and G. darwinii), respectively, and five to nine CRY genes in the seven diploid species. Phylogenetic analysis of protein-coding sequences revealed that CRY genes from cottons and Arabidopsis thaliana could be classified into seven clades. Synteny analysis suggested that the homoeolog of G. hirsutum Gh_A02G0384 has undergone an evolutionary loss event in the other four allotetraploid cotton species. Cis-element analysis predicated the possible functions of CRY genes in G. hirsutum. RNA-seq data revealed that Gh_D09G2225, Gh_A09G2012 and Gh_A11G1040 had high expressions in fiber cells of different developmental states. In addition, the expression levels of one (Gh_A03G0120), 15 and nine GhCRY genes were down-regulated following the PEG, NaCl and high-temperature treatments, respectively. For the low-temperature treatment, five GhCRY genes were induced, and five were repressed. These results indicated that most GhCRY genes negatively regulate the abiotic stress treatments. CONCLUSION We report the structures, domains, divergence, synteny, and cis-elements analyses systematically of G. hirsutum CRY genes. Possible biological functions of GhCRY genes in differential tissues as well as in response to abiotic stress during the cotton plant life cycle were predicted.
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Affiliation(s)
- Chaochen Huang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Pengbo Li
- Shanxi Key Laboratory of Cotton Germplasm Resources Utilization and Molecular Design Breeding, Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, 044099, China.
| | - Junfeng Cao
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zishou Zheng
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.,University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jinquan Huang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiufang Zhang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaoxia Shangguan
- Shanxi Key Laboratory of Cotton Germplasm Resources Utilization and Molecular Design Breeding, Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, 044099, China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. .,Institute of Carbon Materials Science, Shanxi Datong University, Datong, 037009, China.
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Zhu L, Wang X, Tian J, Zhang X, Yu T, Li Y, Li D. Genome-wide analysis of VPE family in four Gossypium species and transcriptional expression of VPEs in the upland cotton seedlings under abiotic stresses. Funct Integr Genomics 2022; 22:179-192. [DOI: 10.1007/s10142-021-00818-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 01/21/2023]
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Mehari TG, Xu Y, Magwanga RO, Umer MJ, Shiraku ML, Hou Y, Wang Y, Wang K, Cai X, Zhou Z, Liu F. Identification and functional characterization of Gh_D01G0514 (GhNAC072) transcription factor in response to drought stress tolerance in cotton. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:361-375. [PMID: 34153881 DOI: 10.1016/j.plaphy.2021.05.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/31/2021] [Indexed: 05/10/2023]
Abstract
Cotton encounters long-term drought stress problems resulting in major yield losses. Transcription factors (TFs) plays an important role in response to biotic and abiotic stresses. The coexpression patterns of gene networks associated with drought stress tolerance were investigated using transcriptome profiles. Applying a weighted gene coexpression network analysis, we discovered a salmon module with 144 genes strongly linked to drought stress tolerance. Based on coexpression and RT-qPCR analysis GH_D01G0514 was selected as the candidate gene, as it was also identified as a hub gene in both roots and leaves with a consistent expression in response to drought stress in both tissues. For validation of GH_D01G0514, Virus Induced Gene Silencing was performed and VIGS plants showed significantly higher excised leaf water loss and ion leakage, while lower relative water and chlorophyll contents as compared to WT (Wild type) and positive control plants. Furthermore, the WT and positive control seedlings showed higher CAT and SOD activities, and lower activities of hydrogen peroxide and MDA enzymes as compared to the VIGS plants. Gh_D01G0514 (GhNAC072) was localized in the nucleus and cytoplasm. Y2H assay demonstrates that Gh_D01G0514 has a potential of auto activation. It was observed that the Gh_D01G0514 was highly upregulated in both tissues based on RNA Seq and RT-qPCR analysis. Thus, we inferred that, this candidate gene might be responsible for drought stress tolerance in cotton. This finding adds significantly to the existing knowledge of drought stress tolerance in cotton and deep molecular analysis are required to understand the molecular mechanisms underlying drought stress tolerance in cotton.
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Affiliation(s)
- Teame Gereziher Mehari
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China; Ethiopian Institute of Agricultural Research, Mekhoni Agricultural Research Center, P.O Box 47, Mekhoni, Tigray, Ethiopia
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China; School of Biological and Physical Sciences (SBPS), Main Campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Main Campus, P.O. Box 210-40601, Bondo, Kenya
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Margaret Linyerera Shiraku
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China.
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, Henan, 455000, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, PR China.
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Zhang X, Cao J, Huang C, Zheng Z, Liu X, Shangguan X, Wang L, Zhang Y, Chen Z. Characterization of cotton ARF factors and the role of GhARF2b in fiber development. BMC Genomics 2021; 22:202. [PMID: 33752589 PMCID: PMC7986310 DOI: 10.1186/s12864-021-07504-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/02/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Cotton fiber is a model system for studying plant cell development. At present, the functions of many transcription factors in cotton fiber development have been elucidated, however, the roles of auxin response factor (ARF) genes in cotton fiber development need be further explored. RESULTS Here, we identify auxin response factor (ARF) genes in three cotton species: the tetraploid upland cotton G. hirsutum, which has 73 ARF genes, and its putative extent parental diploids G. arboreum and G. raimondii, which have 36 and 35 ARFs, respectively. Ka and Ks analyses revealed that in G. hirsutum ARF genes have undergone asymmetric evolution in the two subgenomes. The cotton ARFs can be classified into four phylogenetic clades and are actively expressed in young tissues. We demonstrate that GhARF2b, a homolog of the Arabidopsis AtARF2, was preferentially expressed in developing ovules and fibers. Overexpression of GhARF2b by a fiber specific promoter inhibited fiber cell elongation but promoted initiation and, conversely, its downregulation by RNAi resulted in fewer but longer fiber. We show that GhARF2b directly interacts with GhHOX3 and represses the transcriptional activity of GhHOX3 on target genes. CONCLUSION Our results uncover an important role of the ARF factor in modulating cotton fiber development at the early stage.
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Affiliation(s)
- Xiufang Zhang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Junfeng Cao
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- Plant Stress Biology Center, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Shanghai, 200032 China
| | - Chaochen Huang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China
| | - Zishou Zheng
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Shanghai, 200032 China
| | - Xia Liu
- Esquel Group, 25 Harbour Road, Wanchai, Hong Kong, China
| | - Xiaoxia Shangguan
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Yugao Zhang
- Esquel Group, 25 Harbour Road, Wanchai, Hong Kong, China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, 037009 China
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Zhang S, Cai Y, Guo J, Li K, Peng R, Liu F, Roberts JA, Miao Y, Zhang X. Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints. Evol Bioinform Online 2019; 15:1176934319889948. [PMID: 31798299 PMCID: PMC6868568 DOI: 10.1177/1176934319889948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/30/2019] [Indexed: 11/16/2022] Open
Abstract
Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.
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Affiliation(s)
- Shulin Zhang
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Yaling Cai
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Jinggong Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Kun Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Renhai Peng
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, China
| | - Jeremy A Roberts
- School of Biological and Marine Sciences, Faculty of Science and Engineering, University of Plymouth, Devon, UK
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Xuebin Zhang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
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