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陆地棉纤维长度和强度的优异位点挖掘及其候选基因预测
史春辉1, 张爱1, 马麒2, 谢晓宇1, 刘娟娟1, 李美丽1, 李朝周1, 王彩香1, 宿俊吉1
0
(1.甘肃农业大学生命科学技术学院;2.新疆农垦科学院棉花研究所)
摘要:
纤维长度和强度是陆地棉(Gossypium hirsutum L.)纤维品质性状中的两个关键性状,其遗传基础的解析对优质棉品种培育具有重要意义。本研究以315个陆地棉品种系为关联分析群体,利用混合线性模型(MLM,mixed linear model)对来自五个环境的纤维长度和强度进行全基因组关联分析(GWAS,genome-wide association study)。结果表明,五个环境下纤维长度和强度的表型值均呈现出一定的差异,且广义遗传力较高,纤维长度变异系数为3.97%~8.44%,纤维强度变异系数为7.85%~11.26%。方差分析表明,基因型、环境型和基因型×环境型互作对纤维长度和强度均有极显著影响(P<0.001)。聚类分析和群体结构分析表明,315份材料可分为2个类群。GWAS共检测到5个与纤维长度和强度显著关联的SNP,其中位点D12_57032285与纤维长度和强度均显著关联。与纤维长度显著关联3个SNP位点,分别位于A05、D11和D12染色体上,解释8.05%、12.47%和8.79%的表型变异,优异等位变异类型分别为A05_15144433(AA)、D11_24483544(TT)和D12_57032285(CC);与纤维强度显著关联3个SNP位点,分别位于A08、D09和D12染色体上,解释9.03%、7.94%和7.90%的表型变异,优异等位变异类型分别为A08_84604654(TT)、D09_43463271(TT)和D12_57032285(CC)。通过两组不同转录组数据的基因表达模式分析,筛选出30个可能与纤维发育相关的候选基因。通过GO富集分析和KEGG代谢途径分析发现,候选基因主要参与蛋白质或蛋白质复合物及5''-三磷酸腺苷(ATP)选择性且非共价地相互作用,代谢途径主要为核糖体代谢途径。本研究结果可为棉花纤维品质性状的分子遗传改良提供理论依据。
关键词:  陆地棉  纤维长度  纤维强度  全基因组关联分析  优异等位变异  候选基因
DOI:10.13430/j.cnki.jpgr.20210118002
投稿时间:2021-01-18修订日期:2021-02-22
基金项目:国家自然科学基金项目(31971986);甘肃省自然科学基金项目(20JR10RA520);甘肃省陇原青年创新创业人才项目(2020RCXM182);新疆石河子市现代农业科技攻关与成果转化计划(2017HZ02)
Exploration of Elite Loci for Fiber Length and Strength in Upland Cotton and Prediction of Their Candidate Genes
SHI Chun-hui1, ZHANG Ai1, MA Qi2, XIE Xiao-yu1, LIU Juan-juan1, LI Mei-li1, LI Chao-zhou1, WANG Cai-xiang1, SU Jun-ji1
(1.College of Life Science and Technology, Gansu Agricultural University;2.Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi)
Abstract:
Fiber length and strength are the two most important traits in fiber quality of upland cotton (Gossypium hirsutum L.), and the understanding of their genetic basis is significant for breeding cultivars with high-quality cotton. We performed the genome-wide association study (GWAS) for fiber length and strength of association analysis group which comprises 315 upland cotton accessions grown in five different environments, through the mixed linear model (MLM). The results showed the presence of some differences in the phenotypic values of fiber length and strength, of high generalized heritability, with the fiber length variation coefficient ranging from 3.97% to 8.44%, and the fiber strength variation coefficient ranging from 7.85% to 11.26%. The analysis of variance for fiber length and strength showed highly significant effects of the genotype, environment, and genotype-environment interaction (P<0.001). Cluster analysis and population structure analysis showed that the 315 accessions could be divided into 2 groups. A total of 5 SNPs significantly associated with fiber length and/or strength were detected by GWAS, among which the locus D12_57032285 was significantly associated with both the fiber length and strength. The three loci significantly associated with fiber length were located on chromosomes A05, D11, and D12, respectively, which could explain 8.05%, 12.47% and 8.79% of the phenotypic variation, the elite allele types being A05_15144433 (AA), D11_24483544 (TT) and D12_57032285 (CC). The three loci significantly associated with fiber strength were located on chromosomes A08, D09 and D12, respectively, which could explain 9.03%, 7.94% and 7.90% of the phenotypic variation, the elite allele types being A08_84604654 (TT), D09_43463271 (TT) and D12_57032285 (CC). Through the analysis of gene expression patterns of two sets of different transcriptome data, 30 candidate genes that might be related to fiber development were selected. Through GO enrichment analysis and KEGG metabolic pathway analysis, it was found that the candidate genes mainly involved proteins or protein complexes and selectively and non-covalently interact with adenosine 5''-triphosphate (ATP), and the metabolic pathway was mainly the ribosomal metabolic pathway. The results can provide a theoretical basis for molecular genetic improvement of cotton fiber quality traits.
Key words:  SHI Chun-hui1, ZHANG Ai1 MA Qi2, XIE Xiao-yu1, LIU Juan-juan1, LI Mei-li1, LI Chao-zhou1, WANG Cai-xiang1, SU Jun-ji1

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