New tools for wheat genetics and breeding: Genome-wide analysis of SNP variation

Eduard Akhunov

Department of Plant Pathology, Kansas State University, USA

S. Chao, V. Catana, D. See, G. Brown-Guedira, A. Akhunova, J. Dubcovsky, C. Cavanagh, and M. Hayden


Single nucleotide polymorphism (SNP) is one of the most broadly distributed types of molecular variation in a genome which, along with the availability of costand labor-effective genotyping platforms, make it the marker of choice for many crops. Our work is aimed at the development of a dense set of genetically mapped SNP markers for low-cost high-throughput genotyping of wheat germplasm. Next generation sequencing of normalized cDNA libraries was used for developing gene-associated SNPs in polyploid wheat. A total of 7.5 million 454 reads were generated from cDNA libraries of 10 wheat cultivars from US and Australia and processed for discovering SNPs using a bioinformatical pipeline specifically designed for variant discovery in polyploid transcriptomes. A total of 25,000 high-quality SNPs distributed among 14,500 EST contigs were identified. All these SNPs were validated by comparison with RNAseq data generated from an additional set of 17 U.S. and Australian cultivars. A total of 9,000 genome-wide common SNPs were selected for designing an Illumina iSelect assay. Preliminary testing showed that more than 95% of SNPs produce high-quality genotype calls with up to 70% being polymorphic in a diverse sample of U.S. and Australian cultivars with a minor allele frequency >0.05. The assay is currently being used for studying patterns of genetic diversity in a worldwide collection of wheat cultivars and for developing a high-density SNP map. A long term goal of this initiative is to advance wheat research and breeding by developing genetic and genomic tools for efficient analysis of agronomic traits using high-resolution linkage and association mapping and deploying SNP markers in breeding programs