Alien Chromosome-Specific SNP Discovery for Monitoring Alien Chromosome Introgression in Wheat

Wild crop relatives are an indispensable source of genes for widening the gene pool of crop plants. However, monitoring of alien introgression during wide hybridization and recurrent breeding is hampered by lack of readily available molecular markers because of limited information about the genome structure of the wild crop relative. In a complex polyploid genome like wheat, flow sorting of single chromosome or chromosome arms offers excellent opportunity to reduce the complexity of the genome and to generate genome or chromosome-specific markers.  Here we report development of SNP markers specific to telosomic chromosome t5M^gS introgressed as a telosomic addition line into wheat from Ae. geniculata. The SNP markers were mapped on wheat-Ae. geniculata recombinant mapping population segregating for leaf rust resistant gene Lr57, and strip rust resistant gene Yr40. We flow sorted ditelosomic 5M (TA7670), performed whole genome amplification followed by Illumina HiSeq with coverage of over 15x. Sequenced data generated from short arm of 5M of Ae. geniculata chromosome was used for SNP discovery. The progress in development, validation and mapping of genome specific SNPs will be presented.