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

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Using bulked segregant analysis based on next-generation sequencing, the recessive nulliplex-branch gene was mapped between two SNP markers ~600 kb apart.

Abstract

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.

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Acknowledgments

This work was financially supported by grants from the National Natural Science Foundation of China (No. 31101187) and the National High-Tech Research and Development Program of China (2012AA101108).

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The authors declare that they have no conflict of interest.

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The authors declare that the study complies with the current laws of the countries in which the experiments were performed.

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Correspondence to Yongshan Zhang.

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Communicated by Michael Gore.

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Chen, W., Yao, J., Chu, L. et al. Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing. Theor Appl Genet 128, 539–547 (2015). https://doi.org/10.1007/s00122-014-2452-2

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