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Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

文献类型： 外文期刊

作者： Zhang, Zhen 1 ; Shang, Haihong 1 ; Shi, Yuzhen 1 ; Huang, Long 1 ; Li, Junwen 1 ; Ge, Qun 1 ; Gong, Juwu 1 ; Liu, Aiying 1 ; Chen, Tingting 1 ; Wang, Dan 1 ; Wang, Yanling 1 ; Palanga, Koffi Kibalou 1 ; Muhammad, Jamshed 1 ; Li, Weijie 1 ; Lu, Quanwei 1 ; Deng, Xiaoying 1 ; Tan, Yunna 1 ; Song, Weiwu 1 ; Cai, Juan 1 ; Li, Pengtao 1 ; Rashid, Harun Or 1 ; Gong, Wankui 1 ; Yuan, Youlu 1 ;

作者机构： 1.State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China

2.Biomarker Technologies Corporation, Beijing 103100, China

3.Anyang Institute of Technology, Anyang 455000, Henan, China

关键词： Upland cotton (Gossypium hirsutum L.);Quantitative trait loci mapping;Specific locus amplified fragment sequencing;Boll weight;Single nucleotide polymorphism marker

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： 2016 年 16 卷

页码：

收录情况： SCI

摘要： Background: Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. Results: In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. Conclusions: This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.

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