Cluster Analysis on Japonica Rice (Oryza sativa L.) with Good Eating Quality Based on SSR Markers and Phenotypic Traits

Abstract Diversity of 60 conventional japonica rice accessions with good eating quality at home and abroad was analyzed using SSR molecular markers, agronomic traits and taste characteristics. A total of 290 alleles were detected in the 60 accessions at 72 SSR loci with the high similarity coefficients varying between 0.600 and 0.924. The loci on chromosome 5 showed the greatest value in average allele number. Additionally, most of the SSR loci could detect 3 to 4 alleles. An UPGMA dendrogram based on the cluster analysis of the genetic similarity coefficients showed that the grouping trend of part of the rice accessions was geographic-related and most of the rice accessions in Jiangsu Province, China were clustered together. Furthermore, many domestic accessions from south and north origins in China were close to the foreign japonica rice varieties, as proved by their pedigree origin from the foreign high-quality sources. For taste characteristics, part of the accessions with excellent taste were clearly clustered into one category though they came from different geographical regions, which indicates that taste characteristics of some varieties were mainly genetically determined. In addition, the agronomic traits of japonica rice with good taste might be closely related with their geographical origins, but the relationship between superior taste characteristics and agronomic traits should be further clarified.