Localization of Allotetraploid Gossypium SNPs Using Physical Mapping Resources

Recent efforts in Gossypium SNP development have produced thousands of putative SNPs for G. barbadense, G. mustelinum, and G. tomentosum relative to G. hirsutum. Here we report our current efforts to localize putative SNPs using physical mapping resources. Recent advances in cotton genomics have generated a BAC physical map with BAC end sequences, the genomic sequence of D5-genome diploid species relative, Gossypium raimondii, a BIBAC physical map of G. hirsutum with BIBAC end sequences, interspecific F1 cytogenetic hypo-aneuploids, and populations of whole-genome radiation hybrids. SNP sequences were aligned to the D5-genome to separate the D-subgenome sequences from the A-subgenome sequences and produce a tentative order for D-subgenome loci. Using the D5-genome sequence based physical alignment as a guide, SNPs were grouped by relative position on chromosomes. Subsets of SNPs were tested with Kbioscience KASPar assay from chromosomes which were represented by cytogenetic aneuploid stocks. Putative SNPs that were amenable to KASPar assays were used to genotype a whole-genome radiation hybrid population. BAC and BIBAC end sequences were blasted with putative SNP sequences to determine which SNPs were represented on the BAC and BIBAC physical maps. A random subset of BAC-associated SNPs was also tested using KASPar assays. A finalized AD-genome SNP localization resource will be beneficial for high density physical and linkage mapping, assisting AD-genome sequence generation, fine mapping traits of interest, and various kinds of marker-assisted selection (MAS).