title: 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.).
abstract: 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.
authors.affiliation: 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.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: Haihong
authors.initials: H
authors.lastname: Shang
authors.affiliation: 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.
authors.forename: Yuzhen
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Biomarker Technologies Corporation, Beijing, 103100, China.
authors.forename: Long
authors.initials: L
authors.lastname: Huang
authors.affiliation: 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.
authors.forename: Junwen
authors.initials: J
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Qun
authors.initials: Q
authors.lastname: Ge
authors.affiliation: 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.
authors.forename: Juwu
authors.initials: J
authors.lastname: Gong
authors.affiliation: 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.
authors.forename: Aiying
authors.initials: A
authors.lastname: Liu
authors.affiliation: 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.
authors.forename: Tingting
authors.initials: T
authors.lastname: Chen
authors.affiliation: Biomarker Technologies Corporation, Beijing, 103100, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Yanling
authors.initials: Y
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Koffi Kibalou
authors.initials: KK
authors.lastname: Palanga
authors.affiliation: 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.
authors.forename: Jamshed
authors.initials: J
authors.lastname: Muhammad
authors.affiliation: 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.
authors.forename: Weijie
authors.initials: W
authors.lastname: Li
authors.affiliation: Anyang Institute of Technology, Anyang, 455000, Henan, China.
authors.forename: Quanwei
authors.initials: Q
authors.lastname: Lu
authors.affiliation: 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.
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Deng
authors.affiliation: 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.
authors.forename: Yunna
authors.initials: Y
authors.lastname: Tan
authors.affiliation: 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.
authors.forename: Weiwu
authors.initials: W
authors.lastname: Song
authors.affiliation: 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.
authors.forename: Juan
authors.initials: J
authors.lastname: Cai
authors.affiliation: 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.
authors.forename: Pengtao
authors.initials: P
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Harun or
authors.initials: Ho
authors.lastname: Rashid
authors.affiliation: 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. wkgong@aliyun.com.
authors.forename: Wankui
authors.initials: W
authors.lastname: Gong
authors.affiliation: 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. youluyuan@hotmail.com.
authors.forename: Youlu
authors.initials: Y
authors.lastname: Yuan
mesh_terms: D000704:Analysis of Variance; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics*; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics; D005838:Genotype; D003368:Gossypium / Q000145:classification / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D013045:Species Specificity
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers
keywords: Boll weight; Quantitative trait loci mapping; Single nucleotide polymorphism marker; Specific locus amplified fragment sequencing; Upland cotton (Gossypium hirsutum L.)