Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL, significant SNP and transcriptomic data
文献类型： 外文期刊
作者： Xu Shudi 1 ; Pan Zhenyuan 1 ; Yin Feifan 2 ; Yang Qingyong 1 ; Lin Zhongxu 1 ; Wen Tianwang 3 ; Zhu Longfu 1 ; Zhang Dawei 4 ; Nie Xinhui 1 ;
作者机构： 1.Shihezi Univ, Agr Coll, Key Lab Oasis Ecol Agr Xinjiang Prod & Construct, Shihezi 832000, Peoples R China
2.Huazhong Agr Univ, Coll Informat, Hubei Key Lab Agr Bioinformat, Wuhan 430070, Hubei, Peoples R China
3.Huazhong Agr Univ, Coll Plant Sci & Technol, Natl Key Lab Crop Genet Improvement, Wuhan 430070, Hubei, Peoples R China
4.Xinjiang Acad Agr Sci, Res Inst Econ Crops, Urumqi 830091, Peoples R China
关键词： Fiber quality traits; Meta-QTL; Significant SNPs; Candidate genes; Transcriptomic data
期刊名称：JOURNAL OF COTTON RESEARCH （ 影响因子：2.6； 五年影响因子：2.8 ）
ISSN： 2096-5044
年卷期： 2020 年 3 卷
页码：
收录情况： SCI
摘要： Background: Meta-analysis of quantitative trait locus (QTL) is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies. The combination of meta-QTL intervals, significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants. Results: In our study, 884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1, as a result, 74 meta-QTLs were identified, including 19 meta-QTLs for fiber length; 18 meta-QTLs for fiber strength; 11 meta-QTLs for fiber uniformity; 11 meta-QTLs for fiber elongation; and 15 meta-QTLs for micronaire. Combined with 8 589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies, 297 candidate genes were identified in the meta-QTL intervals, 20 of which showed high expression levels specifically in the developing fibers. According to the function annotations, some of the 20 key candidate genes are associated with the fiber development. Conclusions: This study provides not only stable QTLs used for marker-assisted selection, but also candidate genes to uncover the molecular mechanisms for cotton fiber development.
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