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

Abstract

AbstractLacking 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.