Genetic Diversity Analysis of Japanese Champa Rice on The Basis of Whole genome Sequence Data

Abstract

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This study investigates the genetic diversity, population structure, and relationships among Japanese red rice accessions, as well as their counterparts from China and Vietnam, with a specific focus on Champa rice. The dataset included six Japanese landraces, seven Vietnamese rice varieties associated with the Champa Kingdom, and accessions from the 3K-RP and WRC collections. A substantial level of genetic diversity such as with 6,956,304 SNP variants was detected in the dataset. Population structure analysis using various methods revealed distinct clustering patterns and three major clusters were observed: Japonica, Indica, and Aus. Within Japonica group, the red rice DRR240845_Akamai was close to Chinese accessions, and DRR240846_Akamai was close to Vietnamese accessions. Among the Indica group, both red rice varieties, DRR240828_Akamai and DRR240848_Akamai, as well as the Japanese Champa rice varieties Touboshi and Karahoushi showed a closer genetic relationship to some Chinese accessions. By incorporating some more new Vietnamese accessions into the initial dataset, this study achieved a more comprehensive representation of subpopulations. Consistent results were observed across multiple analyses. However, apparent differences were found between the Vietnamese accessions and the Japanese accessions classified as Champa rice, suggesting a potential discrepancy between them. It is speculated that the rice accessions currently recognized as Champa rice might have been derived from multiple sources. Overall, this study provides valuable insights into the genetic diversity, population structure, and potential of Champa rice in modern rice research.