Investigation of the genetic diversity of a core collection of japanese rice landraces (JRC) using whole-genome sequencing.

The Rice Core Collection of Japanese Landraces (JRC) consisting of 50 accessions was developed by the genebank at the National Agriculture and Food Research Organization (NARO) in 2008. As a Japanese landrace core collection, the JRC has been used for many research projects, including screening for different phenotypes and allele mining for target genes. To understand the genetic diversity of Japanese Landraces, we performed whole genome re-sequencing of these 50 accessions, and obtained a total of 2,145,095 SNPs and 317,832 insertion-deletions (indels) by mapping against the Oryza sativa ssp. japonica Nipponbare genome. A JRC phylogenetic tree based on 1,394 representative SNPs showed that JRC accessions were divided into two major groups and one small group. We used the multiple genome browser, TASUKE+ to examine haplotypes of flowering genes and detected new mutations in these genes. Finally, we performed GWAS for agronomical traits using the JRC and another core collection, the world rice core collection (WRC), comprising of 69 accessions also provided by the NARO genebank. In leaf blade width a strong peak close to NAL1, a key gene for the regulation of leaf width, and in heading date, a peak near HESO1, involved in flowering regulation were observed in GWAS using the JRC. They were also detected in GWAS using the combined JRC+WRC. Thus, JRC and JRC+WRC are suitable populations for GWAS in particular traits.