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Wang H, Cai X, Umer MJ, Xu Y, Hou Y, Zheng J, Liu F, Wang K, Chen M, Ma S, Yu J, Zhou Z. Genetic Analysis of Cotton Fiber Traits in Gossypium Hybrid Lines. PHYSIOLOGIA PLANTARUM 2024; 176:e14442. [PMID: 39030776 DOI: 10.1111/ppl.14442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/25/2024] [Indexed: 07/22/2024]
Abstract
Cotton plays a crucial role in the progress of the textile industry and the betterment of human life by providing natural fibers. In our study, we explored the genetic determinants of cotton architecture and fiber yield and quality by crossbreeding Gossypium hirsutum and Gossypium barbadense, creating a recombinant inbred line (RIL) population. Utilizing SNP markers, we constructed an extensive genetic map encompassing 7,730 markers over 2,784.2 cM. We appraised two architectural and seven fiber traits within six environments, identifying 58 QTLs, of which 49 demonstrated stability across these environments. These encompassed QTLs for traits such as lint percentage (LP), boll weight (BW), fiber strength (STRENGTH), seed index (SI), and micronaire (MIC), primarily located on chromosomes chr-A07, chr-D06, and chr-D07. Notably, chr-D07 houses a QTL region affecting SI, corroborated by multiple studies. Within this region, the genes BZIP043 and SEP2 were identified as pivotal, with SEP2 particularly showing augmented expression in developing ovules. These discoveries contribute significantly to marker-assisted selection, potentially elevating both the yield and quality of cotton fiber production. These findings provide valuable insights into marker-assisted breeding strategies, offering crucial information to enhance fiber yield and quality in cotton production.
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Affiliation(s)
- Heng Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China/ National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China
- Henan International Joint Laboratory of Cotton Biology, Anyang, Henan, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
- Henan International Joint Laboratory of Cotton Biology, Anyang, Henan, China
| | - Jie Zheng
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China/ National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China
- Henan International Joint Laboratory of Cotton Biology, Anyang, Henan, China
| | - Fang Liu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China/ National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Cotton Biology, Anyang, Henan, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
| | - Mengshan Chen
- Chinese Academy of Agricultural Science, Beijing, China
| | | | - Jingzhong Yu
- Standing Committee of the People's Congress of Jiangsu Province, Nanjing, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
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Abdelraheem A, Zhu Y, Zeng L, Stetina S, Zhang J. A genome-wide association study for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in diploid cotton (Gossypium arboreum) and resistance transfer to tetraploid Gossypium hirsutum. Mol Genet Genomics 2024; 299:30. [PMID: 38472439 DOI: 10.1007/s00438-024-02130-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024]
Abstract
Fusarium wilt, caused by the soilborne fungus Fusarium oxysporum f. sp. vasinfectum (FOV), is a devastating disease affecting cotton (Gossypium spp.) worldwide. Understanding the genetic basis of resistance in diploid cotton and successfully transferring the resistance to tetraploid Upland cotton (G. hirsutum) are crucial for developing resistant cotton cultivars. Although numerous studies have been conducted to investigate the genetic basis of Fusarium wilt in tetraploid cotton, little research has been conducted on diploid species. In this study, an association mapping panel consisting of 246 accessions of G. arboreum, was used to identify chromosomal regions for FOV race 4 (FOV4) resistance based on foliar disease severity ratings in four greenhouse tests. Through a genome-wide association study (GWAS) based on 7,009 single nucleotide polymorphic (SNP) markers, 24 FOV4 resistance QTLs, including three major QTLs on chromosomes A04, A06, and A11, were detected. A validation panel consisting of 97 diploid cotton accessions was employed, confirming the presence of several QTLs. Evaluation of an introgressed BC2F7 population derived from G. hirsutum/G. aridum/G. arboreum showed significant differences in disease incidence and mortality rate, as compared to susceptible and resistant controls, suggesting that the resistance in G. arboreum and/or G. aridum was transferred into Upland cotton for the first time. The identification of novel major resistance QTLs, along with the transfer of resistance from the diploid species, expands our understanding of the genomic regions involved in conferring resistance to FOV4 and contributes to the development of resilient Upland cotton cultivars.
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Affiliation(s)
- Abdelraheem Abdelraheem
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Yi Zhu
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Linghe Zeng
- USDA Agricultural Research Service Crop Genetics Research Unit, Stoneville, MS, 38776, USA
| | - Salliana Stetina
- USDA Agricultural Research Service Crop Genetics Research Unit, Stoneville, MS, 38776, USA
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
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Yang Z, Gao C, Zhang Y, Yan Q, Hu W, Yang L, Wang Z, Li F. Recent progression and future perspectives in cotton genomic breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:548-569. [PMID: 36226594 DOI: 10.1111/jipb.13388] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/11/2022] [Indexed: 05/26/2023]
Abstract
Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate "super cotton", synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.
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Affiliation(s)
- Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chenxu Gao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Yihao Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Qingdi Yan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Lan Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572000, China
- Sanya Institute, Zhengzhou University, Sanya, 572000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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Li C, Dong C, Zhao H, Wang J, Du L, Ai N. Identification of superior parents with high fiber quality using molecular markers and phenotypes based on a core collection of upland cotton ( Gossypium hirsutum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:30. [PMID: 37312963 PMCID: PMC10248707 DOI: 10.1007/s11032-022-01300-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
The combination of molecular markers and phenotypes to select superior parents has become the goal of modern breeders. In this study, 491 upland cotton (Gossypium hirsutum L.) accessions were genotyped using the CottonSNP80K array and then a core collection (CC) was constructed. Superior parents with high fiber quality were identified using molecular markers and phenotypes based on the CC. The Nei diversity index, Shannon's diversity index, and polymorphism information content among chromosomes for 491 accessions ranged from 0.307 to 0.402, 0.467 to 0.587, and 0.246 to 0.316, with mean values of 0.365, 0.542, and 0.291, respectively. A CC containing 122 accessions was established and was categorized into eight clusters based on the K2P genetic distances. From the CC, 36 superior parents (including duplicates) were selected, which contained the elite alleles of markers and ranked in the top 10% of phenotypic values for each fiber quality trait. Among the 36 materials, eight were for fiber length, four were for fiber strength, nine were for fiber micronaire, five were for fiber uniformity, and ten were for fiber elongation. In particular, the nine materials, 348 (Xinluzhong34), 319 (Xinluzhong3), 325 (Xinluzhong9), 397 (L1-14), 205 (XianIII9704), 258 (9D208), 464 (DP201), 467 (DP150), and 465 (DP208), possessed the elite alleles of markers for at least two traits and could be given priority in breeding applications for a more synchronous improvement of fiber quality. The work provides an efficient method for superior parent selection and will facilitate the application of molecular design breeding to cotton fiber quality. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01300-0.
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Affiliation(s)
- Chengqi Li
- Life Science College, Yuncheng University, Yuncheng, 044000 China
| | - Chengguang Dong
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture, Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000 China
| | - Haihong Zhao
- Life Science College, Yuncheng University, Yuncheng, 044000 China
| | - Juan Wang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture, Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000 China
| | - Lei Du
- Life Science College, Yuncheng University, Yuncheng, 044000 China
| | - Nijiang Ai
- Shihezi Agricultural Science Research Institute, Shihezi, 832000 China
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Dadjo C, Nyende AB, Yao N, Kiplangat N, Assogbadjo AE. Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology. PLoS One 2020; 15:e0238984. [PMID: 32966312 PMCID: PMC7511007 DOI: 10.1371/journal.pone.0238984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 08/27/2020] [Indexed: 11/18/2022] Open
Abstract
Garcinia kola (Heckel) is a versatile tree indigenous to West and Central Africa. All parts of the tree have value in traditional medicine. Natural populations of the species have declined over the years due to overexploitation. Assessment of genetic diversity and population structure of G. kola is important for its management and conservation. The present study investigates the genetic diversity and population structure of G. kola populations in Benin using ultra-high-throughput diversity array technology (DArT) single nucleotide polymorphism (SNP) markers. From the 102 accessions sampled, two were excluded from the final dataset owing to poor genotyping coverage. A total of 43,736 SNPs were reported, of which 12,585 were used for analyses after screening with quality control parameters including Minor allele frequency (≥ 0.05), call rate (≥ 80%), reproducibility (≥ 95%), and polymorphic information content (≥ 1%). Analysis revealed low genetic diversity with expected heterozygosity per population ranging from 0.196 to 0.228. Pairwise F-statistics (FST) revealed low levels of genetic differentiation between populations while an Analysis of molecular variance (AMOVA) indicated that the majority of variation (97.86%) was within populations. Population structure analysis through clustering and discriminant analysis on principal component revealed two admixed clusters, implying little genetic structure. However, the model-based maximum likelihood in Admixture indicated only one genetic cluster. The present study indicated low genetic diversity of G. kola, and interventions are needed to be tailored towards its conservation.
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Affiliation(s)
- Colombe Dadjo
- Institute of Basic Sciences, Technology and Innovation, Pan African University, Nairobi, Kenya
- Laboratory of Applied Ecology, Faculty Agronomic Sciences, University of Abomey-Calavi, Cotonou, Rep. Benin
- * E-mail:
| | - Aggrey B. Nyende
- Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Nasser Yao
- Bioscience Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - Ngeno Kiplangat
- Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | - Achille E. Assogbadjo
- Laboratory of Applied Ecology, Faculty Agronomic Sciences, University of Abomey-Calavi, Cotonou, Rep. Benin
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Genetic Identification and Transcriptome Analysis of Lintless and Fuzzless Traits in Gossypium arboreum L. Int J Mol Sci 2020; 21:ijms21051675. [PMID: 32121400 PMCID: PMC7084617 DOI: 10.3390/ijms21051675] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 11/17/2022] Open
Abstract
Cotton fibres, as single cells arising from the seed coat, can be classified as lint and fuzz according to their final length. Gossypium arboreum is a cultivated diploid cotton species and a potential donor of the A subgenome of the more widely grown tetraploid cottons. In this study, we performed genetic studies on one lintless and seven fuzzless G. arboreum accessions. Through association and genetic linkage analyses, a recessive locus on Chr06 containing GaHD-1 was found to be the likely gene underlying the lintless trait. GaHD-1 carried a mutation at a splicing acceptor site that resulted in alternative splicing and a deletion of 247 amino acid from the protein. The regions containing GaGIR1 and GaMYB25-like were found to be associated with fuzz development in G. arboreum, with the former being the major contributor. Comparative transcriptome analyses using 0-5 days post-anthesis (dpa) ovules from lintless, fuzzless, and normal fuzzy seed G. arboreum accessions revealed gene modules and hub genes potentially important for lint and fuzz initiation and development. Three significant modules and 26 hub genes associated with lint fibre initiation were detected by weighted gene co-expression network analysis. Similar analyses identified three vital modules and 10 hub genes to be associated with fuzz development. The findings in this study contribute to understanding the complex molecular mechanism(s) regulating fibre initiation and development and indicate that G. arboreum may have fibre developmental pathways different from tetraploid cotton. It also provides candidate genes for further investigation into modifying fibre development in G. arboreum.
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Transcriptomic analysis of root specific drought mediated response of G. arboreum and G. hirsutum. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00382-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ma X, Wang Z, Li W, Zhang Y, Zhou X, Liu Y, Ren Z, Pei X, Zhou K, Zhang W, He K, Zhang F, Liu J, Ma W, Xiao G, Yang D. Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:762-775. [PMID: 30220108 PMCID: PMC6419577 DOI: 10.1111/pbi.13013] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 05/21/2023]
Abstract
Upland cotton (Gossypium hirsutum) is the world's largest source of natural fibre and dominates the global textile industry. Hybrid cotton varieties exhibit strong heterosis that confers high fibre yields, yet the genome-wide effects of artificial selection that have influenced Upland cotton during its breeding history are poorly understood. Here, we resequenced Upland cotton genomes and constructed a variation map of an intact breeding pedigree comprising seven elite and 19 backbone parents. Compared to wild accessions, the 26 pedigree accessions underwent strong artificial selection during domestication that has resulted in reduced genetic diversity but stronger linkage disequilibrium and higher extents of selective sweeps. In contrast to the backbone parents, the elite parents have acquired significantly improved agronomic traits, with an especially pronounced increase in the lint percentage. Notably, identify by descent (IBD) tracking revealed that the elite parents inherited abundant beneficial trait segments and loci from the backbone parents and our combined analyses led to the identification of a core genomic segment which was inherited in the elite lines from the parents Zhong 7263 and Ejing 1 and that was strongly associated with lint percentage. Additionally, SNP correlation analysis of this core segment showed that a non-synonymous SNP (A-to-G) site in a gene encoding the cell wall-associated receptor-like kinase 3 (GhWAKL3) protein was highly correlated with increased lint percentage. Our results substantially increase the valuable genomics resources available for future genetic and functional genomics studies of cotton and reveal insights that will facilitate yield increases in the molecular breeding of cotton.
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Affiliation(s)
- Xiongfeng Ma
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhenyu Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Wei Li
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Yuzhou Zhang
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical ChemistryNational Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of ChinaCollege of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Xiaojian Zhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Yangai Liu
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhongying Ren
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Xiaoyu Pei
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Kehai Zhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Wensheng Zhang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Kunlun He
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Fei Zhang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Junfang Liu
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Wenyu Ma
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Guanghui Xiao
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical ChemistryNational Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of ChinaCollege of Life SciencesShaanxi Normal UniversityXi'anChina
- Present address:
College of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Daigang Yang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
- Present address:
Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
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Li C, Wang Y, Ai N, Li Y, Song J. A genome-wide association study of early-maturation traits in upland cotton based on the CottonSNP80K array. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:970-985. [PMID: 29877621 DOI: 10.1111/jipb.12673] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/31/2018] [Indexed: 05/18/2023]
Abstract
Genome-wide association studies (GWASs) efficiently identify genetic loci controlling traits at a relatively high resolution. In this study, variations in major early-maturation traits, including seedling period (SP), bud period (BP), flower and boll period (FBP), and growth period (GP), of 169 upland cotton accessions were investigated, and a GWAS of early maturation was performed based on a CottonSNP80K array. A total of 49,650 high-quality single-nucleotide polymorphisms (SNPs) were screened, and 29 significant SNPs located on chromosomes A6, A7, A8, D1, D2, and D9, were repeatedly identified as associated with early-maturation traits, in at least two environments or two algorithms. Of these 29 significant SNPs, 1, 12, 11, and 5 were related to SP, BP, FBP, and GP, respectively. Six peak SNPs, TM47967, TM13732, TM20937, TM28428, TM50283, and TM72552, exhibited phenotypic contributions of approximately 10%, which could allow them to be used for marker-assisted selection. One of these, TM72552, as well as four other SNPs, TM72554, TM72555, TM72558, and TM72559, corresponded to the quantitative trait loci previously reported. In total, 274 candidate genes were identified from the genome sequences of upland cotton and were categorized based on their functional annotations. Finally, our studies identified Gh_D01G0340 and Gh_D01G0341 as potential candidate genes for improving cotton early maturity.
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Affiliation(s)
- Chengqi Li
- Collaborative Innovation Center of Modern Biological Breeding, Henan Province/Cotton Research Institute, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yuanyuan Wang
- Collaborative Innovation Center of Modern Biological Breeding, Henan Province/Cotton Research Institute, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Nijiang Ai
- Shihezi Agricultural Science Research Institute, Shihezi 832000, China
| | - Yue Li
- Collaborative Innovation Center of Modern Biological Breeding, Henan Province/Cotton Research Institute, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Jiafeng Song
- Collaborative Innovation Center of Modern Biological Breeding, Henan Province/Cotton Research Institute, Henan Institute of Science and Technology, Xinxiang 453003, China
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Li R, Erpelding JE, Stetina SR. Genome-wide association study of Gossypium arboreum resistance to reniform nematode. BMC Genet 2018; 19:52. [PMID: 30075700 PMCID: PMC6091029 DOI: 10.1186/s12863-018-0662-3] [Citation(s) in RCA: 4] [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: 09/01/2017] [Accepted: 07/26/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reniform nematode (Rotylenchulus reniformis) has emerged as one of the most destructive root pathogens of upland cotton (Gossypium hirsutum) in the United States. Management of R. reniformis has been hindered by the lack of resistant G. hirsutum cultivars; however, resistance has been frequently identified in germplasm accessions from the G. arboreum collection. To determine the genetic basis of reniform nematode resistance, a genome-wide association study (GWAS) was performed using 246 G. arboreum germplasm accessions that were genotyped with 7220 single nucleotide polymorphic (SNP) sequence markers generated from genotyping-by-sequencing. RESULTS Fifteen SNPs representing 12 genomic loci distributed over eight chromosomes showed association with reniform nematode resistance. For 14 SNPs, major alleles were shown to be associated with resistance. From the 15 significantly associated SNPs, 146 genes containing or physically close to these loci were identified as putative reniform nematode resistance candidate genes. These genes are involved in a broad range of biological pathways, including plant innate immunity, transcriptional regulation, and redox reaction that may have a role in the expression of resistance. Eighteen of these genes corresponded to differentially expressed genes identified from G. hirsutum in response to reniform nematode infection. CONCLUSIONS The identification of multiple genomic loci associated with reniform nematode resistance would indicate that the G. arboreum collection is a significant resource of novel resistance genes. The significantly associated markers identified from this GWAS can be used for the development of molecular tools for breeding improved reniform nematode resistant upland cotton with resistance introgressed from G. arboreum. Additionally, a greater understanding of the molecular mechanisms of reniform nematode resistance can be determined through genetic structure and functional analyses of candidate genes, which will aid in the pyramiding of multiple resistance genes.
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Affiliation(s)
- Ruijuan Li
- Present address: Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616 USA
| | - John E. Erpelding
- USDA-ARS, Crop Genetics Research Unit, 141 Experiment Station Road, PO Box 345, Stoneville, MS 38776 USA
| | - Salliana R. Stetina
- USDA-ARS, Crop Genetics Research Unit, 141 Experiment Station Road, PO Box 345, Stoneville, MS 38776 USA
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Yuan C, Wang M, Skinner DZ, See DR, Xia C, Guo X, Chen X. Inheritance of Virulence, Construction of a Linkage Map, and Mapping Dominant Virulence Genes in Puccinia striiformis f. sp. tritici Through Characterization of a Sexual Population with Genotyping-by-Sequencing. PHYTOPATHOLOGY 2018; 108:133-141. [PMID: 28876207 DOI: 10.1094/phyto-04-17-0139-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Puccinia striiformis f. sp. tritici, the wheat stripe rust pathogen, is a dikaryotic, biotrophic, and macrocyclic fungus. Genetic study of P. striiformis f. sp. tritici virulence was not possible until the recent discovery of Berberis spp. and Mahonia spp. as alternate hosts. To determine inheritance of virulence and map virulence genes, a segregating population of 119 isolates was developed by self-fertilizing P. striiformis f. sp. tritici isolate 08-220 (race PSTv-11) on barberry leaves under controlled greenhouse conditions. The progeny isolates were phenotyped on a set of 29 wheat lines with single genes for race-specific resistance and genotyped with simple sequence repeat (SSR) markers, single nucleotide polymorphism (SNP) markers derived from secreted protein genes, and SNP markers from genotyping-by-sequencing (GBS). Using the GBS technique, 10,163 polymorphic GBS-SNP markers were identified. Clustering and principal component analysis grouped these markers into six genetic groups, and a genetic map, consisting of six linkage groups, was constructed with 805 markers. The six clusters or linkage groups resulting from these analyses indicated a haploid chromosome number of six in P. striiformis f. sp. tritici. Through virulence testing of the progeny isolates, the parental isolate was found to be homozygous for the avirulence loci corresponding to resistance genes Yr5, Yr10, Yr15, Yr24, Yr32, YrSP, YrTr1, Yr45, and Yr53 and homozygous for the virulence locus corresponding to resistance gene Yr41. Segregation was observed for virulence phenotypes in response to the remaining 19 single-gene lines. A single dominant gene or two dominant genes with different nonallelic gene interactions were identified for each of the segregating virulence phenotypes. Of 27 dominant virulence genes identified, 17 were mapped to two chromosomes. Markers tightly linked to some of the virulence loci may facilitate further studies to clone these genes. The virulence genes and their inheritance information are useful for understanding the host-pathogen interactions and for selecting effective resistance genes or gene combinations for developing stripe rust resistant wheat cultivars.
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Affiliation(s)
- Congying Yuan
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Meinan Wang
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Danniel Z Skinner
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Deven R See
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Chongjing Xia
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Xinhong Guo
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Xianming Chen
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
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Naqvi RZ, Zaidi SSEA, Akhtar KP, Strickler S, Woldemariam M, Mishra B, Mukhtar MS, Scheffler BE, Scheffler JA, Jander G, Mueller LA, Asif M, Mansoor S. Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum. Sci Rep 2017; 7:15880. [PMID: 29162860 PMCID: PMC5698292 DOI: 10.1038/s41598-017-15963-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/03/2017] [Indexed: 12/13/2022] Open
Abstract
Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton. While the widely cultivated cotton species Gossypium hirsutum is generally susceptible, the diploid species G. arboreum is a natural source for resistance against CLCuD. However, the influence of CLCuD on the G. arboreum transcriptome and the interaction of CLCuD with G. arboreum remains to be elucidated. Here we have used an RNA-Seq based study to analyze differential gene expression in G. arboreum under CLCuD infestation. G. arboreum plants were infested by graft inoculation using a CLCuD infected scion of G. hirsutum. CLCuD infested asymptomatic and symptomatic plants were analyzed with RNA-seq using an Illumina HiSeq. 2500. Data analysis revealed 1062 differentially expressed genes (DEGs) in G. arboreum. We selected 17 genes for qPCR to validate RNA-Seq data. We identified several genes involved in disease resistance and pathogen defense. Furthermore, a weighted gene co-expression network was constructed from the RNA-Seq dataset that indicated 50 hub genes, most of which are involved in transport processes and might have a role in the defense response of G. arboreum against CLCuD. This fundamental study will improve the understanding of virus-host interaction and identification of important genes involved in G. arboreum tolerance against CLCuD.
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Affiliation(s)
- Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Syed Shan-E-Ali Zaidi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
- AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
| | - Khalid Pervaiz Akhtar
- Nuclear Institute for Agriculture & Biology (NIAB), Jhang Road, Faisalabad, Punjab, Pakistan
| | - Susan Strickler
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Melkamu Woldemariam
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Bharat Mishra
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit (USDA-ARS), Stoneville, MS, USA
| | - Jodi A Scheffler
- Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, MS, USA
| | - Georg Jander
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Lukas A Mueller
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan.
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