Effective Single Nucleotide Polymorphism Discovery in Common Wheat Transcriptome Using Haplotypes Information and Draft Genome Sequence of Aegilops tauschii and Triticum urartu

Wheat is one of the three most important crops for human and livestock feed and the most widely grown crop. However, the amount of molecular markers available in the application of marker-assisted selection is limited due to the declined genetic diversity in elite cultivars and complex nature of the wheat genome. Though single nucleotide polymorphisms (SNPs) are the most abundant type of molecular genetic marker and becoming the dominant form for genetic and genomic analysis, identification and application of SNP markers in wheat breeding program is difficult as the large and polypoid genome features, especially in the transcriptome. We have tried a new SNP discovery method to distinct inter-homoeologue SNPs and varietal SNPs in four common wheat transcriptome making use of the information of Haplotypes in high similar transcripts coupled with the available draft genome sequence of Aegilops tauschii and Triticum urartu. More than ten thousands of high quality SNPs are discovered in this pilot experiment and more than 45% SNPs are validated utilizing the draft assembly of whole chromosome shotgun sequencing data of 7A/7B/7D. Based on this promising result, the approach established in this pilot experiment is valuable in SNPs discovery in large and complex genomes.