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Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing

Chen, Wei, Yao, Jinbo, Chu, Li, Yuan, Zhengwen, Li, Yan, Zhang, Yongshan
Theoretical and applied genetics 2015 v.128 no.3 pp. 539-547
Gossypium hirsutum, branches, chromosome mapping, cotton, flowers, fruiting, genetic markers, high-throughput nucleotide sequencing, leaves, marker-assisted selection, molecular cloning, mutants, parents, recessive genes, shoots, single nucleotide polymorphism
KEY MESSAGE : 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 F₂population. 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 F₂plants. 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 F₂population. 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.