The development of specific SNP markers for chromosome 14 in cotton using next-generation sequencing.

摘要

Lacking of reference genome sequence for the development of stable molecular markers for specific chromosomes (intervals) remains to be a challenge in cotton, which was a necessary step in fine mapping of gene (QTL). In this study, the feasibility of development of single-nucleotide polymorphism (SNP) markers between CS-B14Sh (a substitution line for short arm of Chromosome 14) and TM-1 (the recurrent parent) was explored using next-generation sequencing (NGS) based on reduced representation libraries (RRLs). High-quality genome sequences, representing about 7.1%, 8.8% and 10.4% of the tetraploid cotton genome, were generated for TM-1, 3-79 (the donor parent) and CS-B14Sh, respectively. A total of 397 putative SNP markers were detected between CS-B14Sh and TM-1, and most (358) of them were also detected between TM-1 and 3-79. Allele-specific PCR method was used for validation of 40 SNP markers, and 27 of them showed polymorphism between TM-1 and CS-B14Sh, and a linkage group comprising of 25 SNP markers and five SSR markers was constructed. The order of SNP markers agreed well with the position of them on Chr05 of D genome, which further approved the truth of SNPs detected. The results suggested that the development of SNP markers in specific genome region using NGS was efficient in substitution or near-isogenic lines.