Population structure in Japanese rice population

Abstract

It is essential to elucidate genetic diversity and relationships among even related individuals and populations for plant breeding and genetic analysis. Since Japanese rice breeding has improved agronomic traits such as yield and eating quality, modern Japanese rice cultivars originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in Japanese rice population, we used a total of 706 alleles detected by 134 simple sequence repeat markers in a total of 114 cultivars composed of 94 improved varieties and 20 landraces, which are representative and important for Japanese rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Model-based Bayesian clustering analysis revealed six subgroups and admixture situation in the cultivars, showing good agreement with pedigree information. This method could be superior to phylogenetic method in classifying a related population. The leading Japanese rice cultivar, Koshihikari is unique due to the specific genome constitution. We defined Japanese rice diverse sets that capture the maximum number of alleles for given sample sizes. These sets are useful for a variety of genetic application in Japanese rice cultivars.

Keywords: Japanese rice cultivars; Japanese rice diverse cultivars; genetic diversity; pedigree; population structure; simple sequence repeat.

Fig. 1

Model-based clustering (K = 6) in 114 Japanese rice cultivars with 134 SSR markers. Color codes indicate typical genotypes of the inferred subgroups: Kirara 397, red; Reimei, green; Nipponbare, blue; Koshihikari, black; Asahi, yellow; Kamenoo, pink. The numbers and cultivar names in Supplemental Table 1 are indicated above the color code. The order of the cultivars is based on the highest membership coefficient. The squared numbers show representatives in the subgroups and also members in 24 Japanese rice diverse cultivars. The cultivars pointed by black triangles indicate members in 24 Japanese rice diverse cultivars.

Fig. 2

The pedigree and admixture situation in Koshihikari, the sister cultivars and the progenitorial cultivars.