Mining homologues of rice domestication genes in an Australian wild grass species

Abstract

Extensive sequencing and comparative mapping has established a high degree of conservation between rice and other grasses, allowing the isolation of the corresponding homologues of important rice genes in other grasses. In this study, a number of known rice domestication genes are being used as references to characterize homologues in a wild rice relative, Microlaena stipoides, also known as weeping grass. Whole genome sequence data for M. stipoides was generated by Illumina GAII and assembled by reference to the genome sequence of domesticated rice to generate species specific PCR primers for putative BADH2, GW2 and Hd6 homologues in M. stipoides. Pooled PCR amplicons for these homologues generated from both chemically induced mutant and naturally occurring populations were then screened using the Illumina GAII platform to discover single nucleotide polymorphisms (SNPs). We present a new method of SNPs discovery using the Illumina GAII as a quick and efficient method comparable to Sanger sequencing. We will report the SNPs frequency of putative homologues of BADH2, GW2 and Hd6 in M. stipoides. Potentially useful SNP can be used in establishing new breeding lines of M. stipoides suitable for domestication. Once domesticated, M. stipoides will become a new crop for commercial food production