Genotyping-By-Sequencing in Rice Molecular Breeding: From Genome-wide Association Analysis to SNP Marker Development

Next generation sequencing (NGS) is a powerful tool to identify SNPs and unravel functional variations underlying a target trait. The development of genotyping-by-sequencing (GBS) that involves multiplexed sequencing has reduced the cost per sample and has provided high-resolution scans for genome-wide association studies (GWAS). The aim of this study is to demonstrate the power of SNPs derived from GBS to identify loci associated with bacterial blight resistance in rice and to develop SNP markers that can be used for developing “breeder’s chips” useful in marker-aided selection to accelerate rice breeding. Genome-wide association study of bacterial blight resistance was performed using a panel of 198 indica and aus rice accessions to identify loci that are highly associated to bacterial blight resistance. Five representative strains of Xanthomonas oryzae pv. oryzae (Xoo) from the Philippines were used to screen for bacterial blight resistance. From 245,669 high quality SNPs from GBS, 40,840 SNPs were used after filtering (>0.05 minimum allele frequency and 90% allele calling).  A number of SNPs highly associated with differential resistance to specific Xoo strains that are potentially novel loci were found on chromosomes 5, 9, 11 and 12. In addition, some significant SNPs overlapping and flanking known resistance genes such as Xa4, xa5, Xa7, xa13 and Xa21 were identified and were used to design Fluidigm SNPtype assays. Results of this study will facilitate SNP marker development for marker-aided selection and demonstrates the usefulness of GBS on molecular breeding applications.