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Zhang B, Huang Y, Zhang L, Zhou Z, Zhou S, Duan W, Yang C, Gao Y, Li S, Chen M, Li Y, Yang X, Zhang G, Huang D. Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane. J Agric Food Chem 2023; 71:16815-16826. [PMID: 37856846 DOI: 10.1021/acs.jafc.3c02935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Sugarcane, a major sugar and energy crop worldwide faces an increasing demand for higher yields. Identifying yield-related markers and candidate genes is valuable for breeding high-yield varieties using molecular techniques. In this work, seven yield-related traits were evaluated in a diversity panel of 159 genotypes, derived from Tripidium arundinaceum, Saccharum spontaneum, and modern sugarcane genotypes. All traits exhibited significant genetic variance with high heritability and high correlations. Genetic diversity analysis reveals a genomic decay of 23 kb and an average single nucleotide polymorphism (SNP) number of 25,429 per genotype. These 159 genotypes were divided into 4 subgroups. Genome-wide association analysis identified 47 SNPs associated with brix, spanning 36 quantitative trait loci (QTLs), and 138 SNPs for other traits across 104 QTLs, covering all 32 chromosomes. Interestingly, 12 stable QTLs associated with yield-related traits were identified, which contained 35 candidate genes. This work provides markers and candidate genes for marker-assisted breeding to improve sugarcane yields.
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Affiliation(s)
- Baoqing Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Yuxin Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Lijun Zhang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Zhongfeng Zhou
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Shan Zhou
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Weixing Duan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Cuifang Yang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Yijing Gao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Sicheng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Meiyan Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Yangrui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Gemin Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
| | - Dongliang Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
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Han Z, Ke H, Li X, Peng R, Zhai D, Xu Y, Wu L, Wang W, Cui Y. Detection of epistasis interaction loci for fiber quality-related trait via 3VmrMLM in upland cotton. Front Plant Sci 2023; 14:1250161. [PMID: 37841603 PMCID: PMC10568130 DOI: 10.3389/fpls.2023.1250161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023]
Abstract
Cotton fiber quality-related traits, such as fiber length, fiber strength, and fiber elongation, are affected by complex mechanisms controlled by multiple genes. Determining the QTN-by-QTN interactions (QQIs) associated with fiber quality-related traits is therefore essential for accelerating the genetic enhancement of cotton breeding. In this study, a natural population of 1,245 upland cotton varieties with 1,122,352 SNPs was used for detecting the main-effect QTNs and QQIs using the 3V multi-locus random-SNP-effect mixed linear model (3VmrMLM) method. A total of 171 significant main-effect QTNs and 42 QQIs were detected, of which 22 were both main-effect QTNs and QQIs. Of the detected 42 QQIs, a total of 13 significant loci and 5 candidate genes were reported in previous studies. Among the three interaction types, the AD interaction type has a preference for the trait of FE. Additionally, the QQIs have a substantial impact on the enhancement predictability for fiber quality-related traits. The study of QQIs is crucial for elucidating the genetic mechanism of cotton fiber quality and enhancing breeding efficiency.
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Affiliation(s)
- Zhimin Han
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Xiaoyu Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Ruoxuan Peng
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Dongdong Zhai
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Wensheng Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
| | - Yanru Cui
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
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Qin G, Zhao N, Wang W, Wang M, Zhu J, Yang J, Lin F, Huang X, Zhang Y, Min L, Chen G, Kong J. Glyphosate-Induced Abscisic Acid Accumulation Causes Male Sterility in Sea Island Cotton. Plants (Basel) 2023; 12:1058. [PMID: 36903918 PMCID: PMC10005681 DOI: 10.3390/plants12051058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Sea Island cotton is the best quality tetraploid cultivated cotton in the world, in terms of fiber quality. Glyphosate is a widely used herbicide in cotton production, and the improper use of herbicides has led to pollen abortion in sea island cotton and, consequently, to a dramatic decrease in yield; however, the mechanism remains unclear. In this study, different concentrations (0, 3.75, 7.5, 15, and 30 g/L) of glyphosate were applied to CP4-EPSPS transgenic sea island cotton Xinchang 5 in 2021 and 2022 at Korla, with 15 g/L glyphosate chosen as the suitable concentration. By comparing the paraffin sections of 2-24 mm anthers in the 15 g/L glyphosate treatment group with those in the water control group, we showed that the key period of anther abortion after glyphosate treatment was the formation and development of tetrads, which corresponded to 8-9 mm buds. Transcriptome sequencing analysis of the treated and control anthers revealed a significant enrichment of differentially expressed genes in phytohormone-related pathways, in particular abscisic acid response and regulation pathways. Additionally, after treatment with 15 g/L of glyphosate, there was a significant increase in the amount of abscisic acid in the anthers in the 8-9 mm buds. Further analysis of the differential expression of abscisic acid response and regulatory genes, an abscisic acid response gene GbTCP14 (Gbar_A11G003090) was identified, which was significantly upregulated in buds with 15 g/L glyphosate treatment than the control, and it could be a key candidate gene for the subsequent research involving male sterility induced by glyphosate in sea island cotton.
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Affiliation(s)
- Guoli Qin
- College of Agriculture, Tarim University, Alar 843300, China
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Nan Zhao
- College of Agronomy and Biotechnology, China Agricultusral University, Beijing 100000, China
| | - Weiran Wang
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Meng Wang
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Jiahui Zhu
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Jing Yang
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng Lin
- College of Agriculture, Tarim University, Alar 843300, China
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Xinglei Huang
- College of Agriculture, Tarim University, Alar 843300, China
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Yanhui Zhang
- College of Grassland Sciences, Xinjiang Agricultural University, Urumqi 830052, China
| | - Ling Min
- Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guodong Chen
- College of Agriculture, Tarim University, Alar 843300, China
| | - Jie Kong
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830052, China
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Duan Y, Chen Q, Chen Q, Zheng K, Cai Y, Long Y, Zhao J, Guo Y, Sun F, Qu Y. Analysis of transcriptome data and quantitative trait loci enables the identification of candidate genes responsible for fiber strength in Gossypium barbadense. G3 Genes|Genomes|Genetics 2022; 12:6650278. [PMID: 35881688 PMCID: PMC9434320 DOI: 10.1093/g3journal/jkac167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022]
Abstract
Gossypium barbadense possesses a superior fiber quality because of its fiber length and strength. An in-depth analysis of the underlying genetic mechanism could aid in filling the gap in research regarding fiber strength and could provide helpful information for Gossypium barbadense breeding. Three quantitative trait loci related to fiber strength were identified from a Gossypium barbadense recombinant inbred line (PimaS-7 × 5917) for further analysis. RNA sequencing was performed in the fiber tissues of PimaS-7 × 5917 0–35 days postanthesis. Four specific modules closely related to the secondary wall-thickening stage were obtained using the weighted gene coexpression network analysis. In total, 55 genes were identified as differentially expressed from 4 specific modules. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for enrichment analysis, and Gbar_D11G032910, Gbar_D08G020540, Gbar_D08G013370, Gbar_D11G033670, and Gbar_D11G029020 were found to regulate fiber strength by playing a role in the composition of structural constituents of cytoskeleton and microtubules during fiber development. Quantitative real-time PCR results confirmed the accuracy of the transcriptome data. This study provides a quick strategy for exploring candidate genes and provides new insights for improving fiber strength in cotton.
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Affiliation(s)
- Yajie Duan
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Qin Chen
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Quanjia Chen
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Kai Zheng
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yongsheng Cai
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yilei Long
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Jieyin Zhao
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yaping Guo
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Fenglei Sun
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yanying Qu
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
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Feng Z, Li L, Tang M, Liu Q, Ji Z, Sun D, Liu G, Zhao S, Huang C, Zhang Y, Zhang G, Yu S. Detection of Stable Elite Haplotypes and Potential Candidate Genes of Boll Weight Across Multiple Environments via GWAS in Upland Cotton. Front Plant Sci 2022; 13:929168. [PMID: 35769298 PMCID: PMC9234699 DOI: 10.3389/fpls.2022.929168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/17/2022] [Indexed: 05/02/2023]
Abstract
Boll weight (BW) is a key determinant of yield component traits in cotton, and understanding the genetic mechanism of BW could contribute to the progress of cotton fiber yield. Although many yield-related quantitative trait loci (QTLs) responsible for BW have been determined, knowledge of the genes controlling cotton yield remains limited. Here, association mapping based on 25,169 single-nucleotide polymorphisms (SNPs) and 2,315 insertions/deletions (InDels) was conducted to identify high-quality QTLs responsible for BW in a global collection of 290 diverse accessions, and BW was measured in nine different environments. A total of 19 significant markers were detected, and 225 candidate genes within a 400 kb region (± 200 kb surrounding each locus) were predicted. Of them, two major QTLs with highly phenotypic variation explanation on chromosomes A08 and D13 were identified among multiple environments. Furthermore, we found that two novel candidate genes (Ghir_A08G009110 and Ghir_D13G023010) were associated with BW and that Ghir_D13G023010 was involved in artificial selection during cotton breeding by population genetic analysis. The transcription level analyses showed that these two genes were significantly differentially expressed between high-BW accession and low-BW accession during the ovule development stage. Thus, these results reveal valuable information for clarifying the genetic basics of the control of BW, which are useful for increasing yield by molecular marker-assisted selection (MAS) breeding in cotton.
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Affiliation(s)
- Zhen Feng
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Libei Li
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Minqiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou, China
| | - Qibao Liu
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Zihan Ji
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Dongli Sun
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Guodong Liu
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shuqi Zhao
- Huanggang Academy of Agricultural Sciences, Huanggang, China
| | - Chenjue Huang
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Yanan Zhang
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Guizhi Zhang
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shuxun Yu
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
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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 Biotechnol J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Zhao N, Wang W, Jiang K, Grover CE, Cheng C, Pan Z, Zhao C, Zhu J, Li D, Wang M, Xiao L, Yang J, Ning X, Li B, Xu H, Su Y, Aierxi A, Li P, Guo B, Wendel JF, Kong J, Hua J. A Calmodulin-Like Gene ( GbCML7) for Fiber Strength and Yield Improvement Identified by Resequencing Core Accessions of a Pedigree in Gossypium barbadense. Front Plant Sci 2022; 12:815648. [PMID: 35185964 PMCID: PMC8850914 DOI: 10.3389/fpls.2021.815648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/29/2021] [Indexed: 05/23/2023]
Abstract
Sea Island cotton (Gossypium barbadense) is world-renowned for its superior natural fiber. Although fiber strength is one of the most important fiber quality traits, genes contributing to fiber strength are poorly understood. Production of sea island cotton also is inextricably linked to improving its relatively low yield, thus enhancing the importance of joint improvement of both fiber quality and yield. We used genomic variation to uncover the genetic evidence of trait improvement resulting from pedigree breeding of Sea Island cotton. This pedigree was aimed at improving fiber strength and yielded an elite cultivar, XH35. Using a combination of genome-wide association study (GWAS) and selection screens, we detected 82 putative fiber-strength-related genes. Expression analysis confirmed a calmodulin-like gene, GbCML7, which enhanced fiber strength in a specific haplotype. This gene is a major-effect gene, which interacts with a minor-effect gene, GbTUA3, facilitating the enhancement of fiber strength in a synergistic fashion. Moreover, GbCML7 participates in the cooperative improvement of fiber strength, fiber length, and fiber uniformity, though a slight compromise exists between the first two of these traits and the latter. Importantly, GbCML7 is shown to boost yield in some backgrounds by increasing multiple yield components to varying degrees, especially boll number. Our work provides valuable genomic evidence and a key genetic factor for the joint improvement of fiber quality and yield in Sea Island cotton.
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Affiliation(s)
- Nan Zhao
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Weiran Wang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Kaiyun Jiang
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Cheng Cheng
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhuanxia Pan
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
| | - Cunpeng Zhao
- Cotton Research Institute, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Jiahui Zhu
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Dan Li
- Cotton Research Institute, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Meng Wang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Li Xiao
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Jing Yang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Xinmin Ning
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Bin Li
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Haijiang Xu
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Ying Su
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Alifu Aierxi
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Pengbo Li
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
| | - Baosheng Guo
- Cotton Research Institute, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Jinping Hua
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Yu J, Hui Y, Chen J, Yu H, Gao X, Zhang Z, Li Q, Zhu S, Zhao T. Whole-genome resequencing of 240 Gossypium barbadense accessions reveals genetic variation and genes associated with fiber strength and lint percentage. Theor Appl Genet 2021; 134:3249-3261. [PMID: 34240238 DOI: 10.1007/s00122-021-03889-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/08/2021] [Indexed: 05/26/2023]
Abstract
KEY MESSAGE Genetic variation in a G. barbadense population was revealed using resquencing. GWAS on G.barbadense population identified several candidate genes associated with fiber strength and lint percentage. Gossypium barbadense is the second-largest cultivated cotton species planted in the world, which is characterized by high fiber quality. Here, we described the global pattern of genetic polymorphisms for 240 G. barbadense accessions based on the whole-genome resequencing. A total of 3,632,231 qualified single-nucleotide polymorphisms (SNPs) and 221,354 insertion-deletions (indels) were obtained. We conducted a genome-wide association study (GWAS) on 12 traits under four environments. Two traits with more stable associated variants, fiber strength and lint percentage, were chosen for further analysis. Three putative candidate genes, HD16 orthology (GB_D11G3437), WDL2 orthology (GB_D11G3460) and TUBA1 orthology (GB_D11G3471), on chromosome D11 were found to be associated with fiber strength, and one gene orthologous to Arabidopsis Receptor-like protein kinase HERK 1 (GB_A07G1034) was predicated to be the candidate gene for the lint percentage improvement. The identified genes may serve as promising targets for genetic engineering to accelerate the breeding process for G. barbadense and the high-density genome variation map constructed in this work may facilitate our understanding of the genetic architecture of cotton traits.
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Affiliation(s)
- Jingwen Yu
- Institute of Crop Science, College of Agriculture, Zhejiang University, Hangzhou, 310058, China
| | - Yixuan Hui
- Institute of Crop Science, College of Agriculture, Zhejiang University, Hangzhou, 310058, China
| | - Jinhong Chen
- Institute of Crop Science, College of Agriculture, Zhejiang University, Hangzhou, 310058, China
| | - Hurong Yu
- Institute of Crop Science, College of Agriculture, Zhejiang University, Hangzhou, 310058, China
| | - Xinpeng Gao
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Zhaohui Zhang
- Hainan Institute, Zhejiang University, Sanya, 572025, China
| | - Qin Li
- Hainan Institute, Zhejiang University, Sanya, 572025, China
| | - Shuijin Zhu
- Institute of Crop Science, College of Agriculture, Zhejiang University, Hangzhou, 310058, China.
- Hainan Institute, Zhejiang University, Sanya, 572025, China.
| | - Tianlun Zhao
- Institute of Crop Science, College of Agriculture, Zhejiang University, Hangzhou, 310058, China.
- Hainan Institute, Zhejiang University, Sanya, 572025, China.
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Huang C, Shen C, Wen T, Gao B, Zhu D, Li D, Lin Z. Genome-wide association mapping for agronomic traits in an 8-way Upland cotton MAGIC population by SLAF-seq. Theor Appl Genet 2021; 134:2459-2468. [PMID: 33912997 DOI: 10.1007/s00122-021-03835-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
One sub-MAGIC population was genotyped using SLAF-seq, and QTLs and candidate genes for agronomic traits were identified in Upland cotton. The agronomic traits of Upland cotton have serious impacts on cotton production, as well as economic benefits. To discover the genetic basis of important agronomic traits in Upland cotton, a subset MAGIC (multi-parent advanced generation inter-cross) population containing 372 lines (SMLs) was selected from an 8-way MAGIC population with 960 lines. The 372 lines and 8 parents were phenotyped in six environments and deeply genotyped by SLAF-seq with 60,495 polymorphic SNPs. The genetic diversity indexes of all SNPs were 0.324 and 0.362 for the parents and MAGIC lines, respectively. The LD decay distance of the SMLs was 600 kb (r2 = 0.1). Genome-wide association mapping was performed using 60,495 SNPs and the phenotypic data of the SMLs, and 177 SNPs were identified to be significantly associated with 9 stable agronomic traits in multiple environments. The identified SNPs were divided into 117 QTLs (quantitative trait loci) by LD decay distance, explaining 5.44% to 31.64% of the phenotypic variation. Among the 117 QTLs, 3 QTLs were stable in multiple environments, and 11 QTL regions were proven to have pleiotropism associated with multiple traits. Within QTL regions, 154 genes were preferentially expressed in correlated tissues, and 8 genes with known functions were identified as priori candidate genes. Two genes, GhACT1 and GhGASL3, reported to have clear functions, were, respectively, located in qFE-A05-4 and qFE-D04-3, two stable QTLs for FE. This study revealed the genetic basis of important agronomic traits of Upland cotton, and the results will facilitate molecular breeding in cotton.
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Affiliation(s)
- 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
| | - Tianwang Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Bin Gao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - De Zhu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dingguo Li
- Institute of Crop Genetic and Breeding, Yangtze University, Jingzhou, 434025, 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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Song X, Zhu G, Hou S, Ren Y, Amjid MW, Li W, Guo W. Genome-Wide Association Analysis Reveals Loci and Candidate Genes Involved in Fiber Quality Traits Under Multiple Field Environments in Cotton ( Gossypium hirsutum). Front Plant Sci 2021; 12:695503. [PMID: 34421946 PMCID: PMC8374309 DOI: 10.3389/fpls.2021.695503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/16/2021] [Indexed: 05/17/2023]
Abstract
Fiber length, fiber strength, and fiber micronaire are the main fiber quality parameters in cotton. Thus, mining the elite and stable loci/alleles related to fiber quality traits and elucidating the relationship between the two may accelerate genetic improvement of fiber quality in cotton. Here, genome-wide association analysis (GWAS) was performed for fiber quality parameters based on phenotypic data, and 56,010 high-quality single nucleotide polymorphisms (SNPs) using 242 upland cotton accessions under 12 field environments were obtained. Phenotypic analysis exhibited that fiber length (FL) had a positive correlation with fiber strength (FS) and had a negative correlation with fiber micronaire (Mic). Genetic analysis also indicated that FL, FS, and Mic had high heritability of more than 80%. A total of 67 stable quantitative trait loci (QTLs) were identified through GWAS analysis, including 31 for FL, 21 for FS, and 22 for Mic. Of them, three pairs homologous QTLs were detected between A and D subgenomes, and seven co-located QTLs with two fiber quality parameters were found. Compared with the reported QTLs, 34 co-located with previous studies, and 33 were newly revealed. Integrated with transcriptome analysis, we selected 256, 244, and 149 candidate genes for FL, FS, and Mic, respectively. Gene Ontology (GO) analysis showed that most of the genes located in QTLs interval of the three fiber quality traits were involved in sugar biosynthesis, sugar metabolism, microtubule, and cytoskeleton organization, which played crucial roles in fiber development. Through correlation analysis between haplotypes and phenotypes, three genes (GH_A05G1494, GH_D11G3097, and GH_A05G1082) predominately expressed in fiber development stages were indicated to be potentially responsible for FL, FS, and Mic, respectively. The GH_A05G1494 encoded a protein containing SGS-domain, which is related to tubulin-binding and ubiquitin-protein ligase binding. The GH_D11G3097 encoded 20S proteasome beta subunit G1, and was involved in the ubiquitin-dependent protein catabolic process. The GH_A05G1082 encoded RAN binding protein 1 with a molecular function of GTPase activator activity. These results provide new insights and candidate loci/genes for the improvement of fiber quality in cotton.
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Khanbo S, Tangphatsornruang S, Piriyapongsa J, Wirojsirasak W, Punpee P, Klomsa-Ard P, Ukoskit K. Candidate gene association of gene expression data in sugarcane contrasting for sucrose content. Genomics 2020; 113:229-237. [PMID: 33321201 DOI: 10.1016/j.ygeno.2020.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022]
Abstract
Association mapping of gene expression data, generated from transcriptome and proteome studies, provides a means of understanding the functional significance and trait association potential of candidate genes. In this study, we applied candidate gene association mapping to validate sugarcane genes, using data from the starch and sucrose metabolism pathway, transcriptome, and proteome. We performed multiplex PCR targeted amplicon sequencing of 109 candidate genes, using NGS technology. A range of statistical models, both single-locus and multi-locus, were compared for minimization of false positives in association mapping of four sugar-related traits with different heritability. The Fixed and random model Circulating Probability Unification model effectively suppressed false positives for both low- and high-heritability traits. We identified favorable alleles of the candidate genes involved in signalling and transcriptional regulation. The results will support genetic improvement of sugarcane and may help clarify the genetic architecture of sugar-related traits.
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Affiliation(s)
- Supaporn Khanbo
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand
| | - Sithichoke Tangphatsornruang
- National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jittima Piriyapongsa
- National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Warodom Wirojsirasak
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Prapat Punpee
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Peeraya Klomsa-Ard
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand.
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