Development and Applications of Genome Wide High Density Snp Genotyping Assays for the Characterization of Indian Wild Rice Germplasm

Abstract

Rice (Oryza sativa L.) is one of the most important cereal crops that serves as a staple food source worldwide. Cultivated rice varieties have a narrow genetic base because of under utilization of wild rice species as breeding resource. Use of single nucleotide polymorphism (SNP) genotyping assays is promising for dissecting genetic variability in cultivated and wild rice germplasm to identify agronomically important abiotic and biotic stress tolerance genes. As genetic markers, SNPs are the most abundant DNA sequence variation, which are stable, amenable to automation, efficient, and increasingly cost-effective. After the publication of rice genome reference sequence in 2005, several re-sequencing projects have contributed enormously to the information on the genome wide structural variations and genetic diversity of rice. Several genotyping assays have been developed for medium to high throughput SNP genotyping in rice using different platforms, including Sequenom, Illumina and Affymetrix SNP chips. Low-multiplexing with high sample throughput assays is useful for population structure analysis, foreground selection, fine mapping, diagnostics, and seed quality control. Whereas, high-multiplexing assays is necessary for association mapping, background selection, genomic selection, and evolutionary studies. Several rice SNP assays and chips have been designed on different SNP genotyping platforms for varied applications, such as Infinium 6K rice chip used for genome-wide scan, 44K Affymetrix SNP chip for dissecting phenotype-genotype associations in rice. Similarly, RiceSNP50 Infinium chip and 700K Affymetrix chip have been used for Genome-wide association studies (GWAS) and evolutionary studies. A GWAS for salinity stress tolerance in rice has been reported using a custom designed 6K Infinium SNP array based on stress-responsive genes. The gene-based SNP array was found cost-effective and efficient in unveiling candidate genes regulating particular trait in rice. newline