Core single-nucleotide polymorphisms—a tool for genetic analysis of the Japanese rice population

Abstract

To analyze genetic features in the Japanese rice population, which is mainly composed of closely related accessions, a core set of single-nucleotide polymorphisms (SNPs) was selected from SNP resources based on Japanese rice cultivars. A total of 25,199 SNPs were newly detected from the comparison of genomic sequences between two cultivars (Eiko and Rikuu132) and Nipponbare as a reference. A total of 81,499 non-redundant SNPs, including 67,051 SNPs of Koshihikari detected in a previous study, were used as candidates to select the core SNPs. Across the entire genome, 3379 SNPs were selected based on the chromosomal position of each SNP and were investigated each allele of 92 Japanese rice accessions and 3 from outside of Japan. As a result, 2551 SNPs were found to be informative for at least 91 cultivars for reducing the potential risks of genotyping error. The Japanese rice accessions were classified into three groups (upland, lowland Hokkaido, and other lowland) using all 2551 SNPs. In addition, a core set of 768 SNPs was selected to provide an even distribution among the chromosomes. Comparison of dendrograms generated by all 2551 SNPs and the core set of 768 SNPs demonstrated that the core SNPs could be used efficiently and reliably in the classification of the Japanese rice population. The core SNPs can be used for diversity analysis and for genetic analysis of the biparental populations of Japanese rice accessions.