Genomic-Specific Single Nucleotide Polymorphism (SNP) Markers for Monitoring Introgression from Tall-Wheatgrass, Lophorpyrum elongatum, into Wheat

Background: Tall wheatgrasses (genus Lophorpyrum) are close relatives of wheat and exceptional sources of germplasm for breeding of wheat for diseases resistance and tolerance of abiotic stresses. The utility of these wheat relatives for wheat improvement is currently limited by the absence of basic genetic sources, such as genetic markers and maps. Here we report the development of SNP markers for the detection of tall wheatgrass germplasm in the wheat genetic background.

Results: The genome (designated as E) of diploid L. elongatum was sequenced with the Illumina Hiseq 2000 platform to ~10X coverage. To discover SNPs between L. elongatum and wheat, the reads were aligned against reference genome sequence of Aegilops. tauschii, the diploid progenitor for the D genome of wheat. About 160k SNPs were called. L. elongatum SNPs along with 100bp of flanking sequence were used as queries in blast against IWGSC chromosome survey assemblies. Of the 160K SNPs, 92,647 were E-genome specific and 27K were in exon regions. All 92,647 SNPs were classified into four different types based on the genome location of mismatches of flanking sequences. For majority (92.3%), the 100bp flanking sequence showed 100% identity to one wheat subgenome and less than 100% sequence identity the other two wheat subgenomes (henceforth type III SNPs). For most type III SNPs, the genome with 100% sequence identity was the D subgenome. Primers for the detection of these E-/D-genome specific SNPs with the Sequenom genotyping platform are being designed and validated.

Conclusion: The use of an annotated Ae. tauschii genome sequence in the selection of L. elongatum reads for SNP discovery resulted in the of thousands of SNP markers that specifically detect L. elongatum germplasm in the wheat genetic background with predicted genomic locations. We are exploiting these attributes in SNP marker development and deployment in monitoring introgression from L. elongatum into the wheat.