Development of mini core collection of Japanese rice landrace

Abstract

A mini core collection of Japanese rice landrace was developed based on a genome-wide SSR polymorphism survey of 236 accessions. The accessions used in the initial survey were selected based on the historical record and passport data from the collection maintained at the Genebank of the National Institute of Agrobiological Sciences (NIAS). These accessions were analyzed using 32 SSR markers. A total of 247 alleles were detected and the number of alleles per locus ranged from 3 to 15 (mean 7.7). Principal coordinate analysis using SSR data enabled classification of the accessions into three major groups, two Japonica groups and one Indica group. To develop a Japanese landrace mini core collection, the SSR data on the 236 accessions were subjected to cluster analysis and 50 groups were recognized at a similarity index of 0.88. A single accession from each of the 50 groups was selected. These 50 accessions retained 87.5% of the alleles detected in the original 236 accessions, and covered the variation of the initial set of accessions in terms of several agro-morphological traits.