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Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

文献类型： 外文期刊

作者： Su, Xiujuan 1 ; Zhu, Guozhong 1 ; Song, Xiaohui 1 ; Xu, Haijiang 3 ; Li, Weixi 1 ; Ning, Xinzhu 4 ; Chen, Quanjia 2 ; Guo 1 ;

作者机构： 1.Nanjing Agr Univ, Minist Educ, State Key Lab Crop Genet & Germplasm Enhancement, Engn Res Ctr Hybrid Cotton Dev, Nanjing 210095, Peoples R China

2.Xinjiang Agr Univ, Minist Educ, Engn Res Ctr Cotton, Urumqi 830052, Peoples R China

3.Xinjiang Acad Agr Sci, Inst Ind Crops, Urumqi 830091, Peoples R China

4.Xinjiang Acad Agr & Reclamat Sci, Cotton Res Inst, Shihezi 832000, Peoples R China

关键词： Gossypium barbadense; Genetic diversity; Genome-wide association study; Fiber quality; Quantitative trait loci; Salt stress

期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）

ISSN： 1471-2229

年卷期： 2020 年 20 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundSea island cotton (Gossypium barbadense) has markedly superior high quality fibers, which plays an important role in the textile industry and acts as a donor for upland cotton (G. hirsutum) fiber quality improvement. The genetic characteristics analysis and the identification of key genes will be helpful to understand the mechanism of fiber development and breeding utilization in sea island cotton.ResultsIn this study, 279 sea island cotton accessions were collected from different origins for genotyping and phenotyping fiber quality traits. A set of 6303 high quality single nucleotide polymorphisms (SNPs) were obtained by high-density CottonSNP80K array. The population characteristics showed that the sea island cotton accessions had wide genetic diversity and were clustered into three groups, with Group1 closely related to Menoufi, an original sea island cotton landrace, and Group2 and Group3 related to widely introduced accessions from Egypt, USA and Former Soviet Union. Further, we used 249 accessions and evaluated five fiber quality traits under normal and salt environments over 2 years. Except for fiber uniformity (FU), fiber length (FL) and fiber elongation (FE) were significantly decreased in salt conditions, while fiber strength (FS) and fiber micronaire (MIC) were increased. Based on 6303 SNPs and genome-wide association study (GWAS) analysis, a total of 34 stable quantitative trait loci (QTLs) were identified for the five fiber quality traits with 25 detected simultaneously under normal and salt environments. Gene Ontology (GO) analysis indicated that candidate genes in the 25 overlapped QTLs were enriched mostly in "cellular and biological process". In addition, "xylem development" and "response to hormone" pathways were also found. Haplotype analyses found that GB_A03G0335 encoding an E3 ubiquitin-protein ligase in QTL TM6004 had SNP variation (A/C) in gene region, was significantly correlated with FL, FS, FU, and FE, implying a crucial role in fiber quality.ConclusionsThe present study provides a foundation for genetic diversity of sea island cotton accessions and will contribute to fiber quality improvement in breeding practice.

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