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.)

被引：115

作者：

Zhang, Zhen ^{[1
]}

Shang, Haihong ^{[1
]}

Shi, Yuzhen ^{[1
]}

Huang, Long ^{[2
]}

Li, Junwen ^{[1
]}

Ge, Qun ^{[1
]}

Gong, Juwu ^{[1
]}

Liu, Aiying ^{[1
]}

Chen, Tingting ^{[1
]}

Wang, Dan ^{[2
]}

Wang, Yanling ^{[1
]}

Palanga, Koffi Kibalou ^{[1
]}

Muhammad, Jamshed ^{[1
]}

Li, Weijie ^{[1
]}

Lu, Quanwei ^{[3
]}

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
]}

机构：

[1] Chinese Acad Agr Sci, Key Lab Biol & Genet Breeding Cotton, Inst Cotton Res, State Key Lab Cotton Biol,Minist Agr, Anyang 455000, Peoples R China

[2] Biomarker Technol Corp, Beijing 103100, Peoples R China

[3] Anyang Inst Technol, Anyang 455000, Henan, Peoples R China

来源：

BMC PLANT BIOLOGY | 2016年 / 16卷

基金：

国家高技术研究发展计划(863计划);

关键词：

Upland cotton (Gossypium hirsutum L.); Quantitative trait loci mapping; Specific locus amplified fragment sequencing; Boll weight; Single nucleotide polymorphism marker; FIBER QUALITY; MARKER DEVELOPMENT; GENOME SEQUENCE; YIELD; IDENTIFICATION;

D O I：

10.1186/s12870-016-0741-4

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

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.

引用

页数：18

共 43 条

[41] Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement [J].

Zhang, Tianzhen ;

Hu, Yan ;

Jiang, Wenkai ;

Fang, Lei ;

Guan, Xueying ;

Chen, Jiedan ;

Zhang, Jinbo ;

Saski, Christopher A. ;

Scheffler, Brian E. ;

Stelly, David M. ;

Hulse-Kemp, Amanda M. ;

Wan, Qun ;

Liu, Bingliang ;

Liu, Chunxiao ;

Wang, Sen ;

Pan, Mengqiao ;

Wang, Yangkun ;

Wang, Dawei ;

Ye, Wenxue ;

Chang, Lijing ;

Zhang, Wenpan ;

Song, Qingxin ;

Kirkbride, Ryan C. ;

Chen, Xiaoya ;

Dennis, Elizabeth ;

Llewellyn, Danny J. ;

Peterson, Daniel G. ;

Thaxton, Peggy ;

Jones, Don C. ;

Wang, Qiong ;

Xu, Xiaoyang ;

Zhang, Hua ;

Wu, Huaitong ;

Zhou, Lei ;

Mei, Gaofu ;

Chen, Shuqi ;

Tian, Yue ;

Xiang, Dan ;

Li, Xinghe ;

Ding, Jian ;

Zuo, Qiyang ;

Tao, Linna ;

Liu, Yunchao ;

Li, Ji ;

Lin, Yu ;

Hui, Yuanyuan ;

Cao, Zhisheng ;

Cai, Caiping ;

Zhu, Xiefei ;

Jiang, Zhi .

NATURE BIOTECHNOLOGY, 2015, 33 (05) :531-U252

[42] Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing [J].

Zhang, Yanxin ;

Wang, Linhai ;

Xin, Huaigen ;

Li, Donghua ;

Ma, Chouxian ;

Ding, Xia ;

Hong, Weiguo ;

Zhang, Xiurong .

BMC PLANT BIOLOGY, 2013, 13

[43] High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength, Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L.) [J].

Zhang, Zhen ;

Li, Junwen ;

Muhammad, Jamshed ;

Cai, Juan ;

Jia, Fei ;

Shi, Yuzhen ;

Gong, Juwu ;

Shang, Haihong ;

Liu, Aiying ;

Chen, Tingting ;

Ge, Qun ;

Palanga, Koffi Kibalou ;

Lu, Quanwei ;

Deng, Xiaoying ;

Tan, Yunna ;

Li, Wei ;

Sun, Linyang ;

Gong, Wankui ;

Yuan, Youlu .

PLOS ONE, 2015, 10 (08)

← 1 2 3 4 5 →