Working group session:
Comparative Genomics and Bioinformatics
Presentation type:
oral
Authors:
Udall, Joshua A.; Page, Justin T.; Ashrafi, Harmid; Van Deynze, Allen; Stelly, David
Presenter:
Udall, Joshua A.
Correspondent:
Udall, Joshua A.
Abstract:
The cotton tetraploid genome contains two types of SNPs: SNPs between alleles (allele-SNPs) and SNPs between genomes (homoeo-SNPs). These two types of SNPs represent different levels of DNA variation and discrimination between these two types has been a serious obstacle for plant improvement programs that use molecular markers. In this project, we have identified a robust set of putative homoeo-SNPs by re-sequencing 5 A and 5 D diploid, cotton genomes. By aligning these reads to the D-reference genome, we were able to identify numerous SNPs between the A and D genomes that were consistent within both sets of diploids (homoeo-SNPs). We were also able to identify homozygous and heterozygous SNPs within subsets of accessions (allele-SNPs). Because of the related genomes within tetraploid cotton, many of these homoeo-SNPs are also found between the AT and DT genomes of cultivated cotton. This SNP collection will allow researchers to discriminate homoeo-SNPs from allele-SNPs during sequence and genetic analyses of tetraploid cotton.