Increasing Gossypium hirsutum Intraspecific SNPs via Genomic Sequencing

SNP-based genetic analysis, manipulation and improvement of Gossypium hirsutum are limited by the lack of large numbers of SNPs.  Large numbers of intraspecific SNPs are also key to community-wide enthusiasm for large-scale cotton SNP genotyping platforms.  SNP development via NGS assemblies from normalized transcriptomes was quite successful for wild species, but less so for intraspecific SNPs (Ashrafi et al. 2012).  Previous research revealed only limited intraspecific polymorphism between lines and cultivars, even when genotype-by-sequencing (GBS) and RAD technologies were used.  The efficacy of RNAseq approaches was further constrained by conservation of the exon sequences, and so the yields of SNPs were relatively low and insufficient in number.  Although a reference genome assembly does not yet exist for G. hirsutum, the high output and low run costs on the Illumina HiSeq, genomic sequencing offers a useful approach for intraspecific SNP discovery in this species.  We sequenced 11 diverse G. hirsutum lines and cultivars to increase the number of putative intraspecific SNPs and a single G. barbadense line. A de novo assembly of TM-1 was created to map SNPs back to yield well over 1 million intraspecific SNPs with high validation rates. These SNPs made a significant contribution to the Illumina 70K Infinium Chip for cotton improvement.