A Comparative Genomics Based Approach to Target Alien Chromosome Specific Genes in Wheat

The tertiary gene pool of wheat represents an excellent resource for agronomically important genes against biotic and abiotic stress that can be used in wheat improvement. Aegilops geniculata is an important species from tertiary gene pool of common wheat and holds tremendous potential for wheat improvement against biotic and abiotic stresses. Chromosome 5M^g from Ae. geniculata TA10437 has been identified as a source of important resistance genes such as Lr57, Yr40 and Sr53. Beside these genes, our results have indicated that this chromosome plays an important role in  inducing homoeologous pairing even in presence of the Ph1 gene of hexaploid bread wheat. To facilitate genomic analysis of this chromosome, we flow-sorted chromosome 5M^g from a wheat/Aegilops geniculata disomic substitution line [DS5M^g (5D)] and sequenced it using an Illumina HiSeq 2000 system at approximately 50x coverage. Paired-end sequences were assembled and used for structural and functional annotation. Comparative genomics based approaches were used to anchor and order 5M^g genes. Generated genomic resources were used to develop SNP markers and these SNPs helped us to delineate the Lr57 and Yr40 region on rice and Ae. tauschii (5D) genomes. Using GenomeZipper based comparative genomics approach we were able to delineate the Lr57 and Yr40 region to a rice BAC on chromosome 12, work is in progress towards identification of candidate genes and their evaluations.