title: Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing.
abstract: Using bulked segregant analysis based on next-generation sequencing, the recessive nulliplex-branch gene was mapped between two SNP markers ~600 kb apart. In a "nulliplex-branch" cotton mutant, most of the flowers arise directly from leaf axils on the main shoot, which usually does not have a fruiting branch. A nulliplex-branch is a useful trait by which to study cotton architecture; however, the genetic basis of this mutant has remained elusive. In this study, bulked segregant analysis combined with next-generation sequencing technology was used to finely map the underlying genes that result in a nulliplex-branch plant. The nulliplex-branch Pima cotton variety, Xinhai-18, was crossed with the normal branch upland cotton line, TM-1, resulting in an F2 population. The nulliplex-branch trait was found to be controlled by the recessive gene gb_nb1. Allelic single-nucleotide polymorphisms (SNPs) were discovered by reduced-representation sequencing between the parents, and their profiles were also characterized in the nulliplex-branch and normal branch bulks constructed using the F2 plants. A candidate ~9.0 Mb-long region comprising 42 SNP markers was found to be associated with gb_nb1, which helped localize it at the ~600-kb interval on Chr 16 by segregation analysis in the F2 population. The closely linked markers with gb_nb1 developed in this study will facilitate the marker-assisted selection of the nulliplex-branch trait, and the fine map constructed will accelerate map-based cloning of gb_nb1.
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research, The Chinese Academy of Agricultural Sciences, Anyang, 455004, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.forename: Jinbo
authors.initials: J
authors.lastname: Yao
authors.forename: Li
authors.initials: L
authors.lastname: Chu
authors.forename: Zhengwen
authors.initials: Z
authors.lastname: Yuan
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.forename: Yongshan
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D002874:Chromosome Mapping; D017343:Genes, Plant; D005808:Genes, Recessive; D056726:Genetic Association Studies; D008040:Genetic Linkage; D005819:Genetic Markers; D003368:Gossypium / Q000235:genetics* / Q000254:growth & development; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers