Population Structure of a Worldwide Collection of Tropical Japonica Rice Indicates Limited Geographic Differentiation and Shows Promising Genetic Variability Associated with New Plant Type

Abstract

Abating the approaching yield plateau in rice requires taking advantage of potential technologies that requires knowledge on genetic diversity. Hybrid breeding, particularly in indica rice, requires the recruitment of large genetic variability from outside because the available genetic diversity of the cultivated pool has already been utilized to a great extent. In this study, we examined an assembly of 200 tropical japonica lines collected worldwide for population genetic structure and variability in yield-associated traits. Tested along with 30 indica and six wild rice lines belonging to India, the tropical japonica lines indicated great phenotypic variability, particularly related to new plant type (NPT) phenology, and formed six clusters. Furthermore, a marker-based characterization using a universal diversity marker panel classified the genotype assembly into four clusters, of which three encompassed tropical japonica lines, while the last cluster included mostly indica lines. The population structure of the panel also revealed a similar pattern, with tropical japonica lines forming three subpopulations. Remarkable variation in the allelic distribution was observed between the subpopulations. Superimposing the geographical sources of the genotypes over the population structure did not reveal any pattern. The genotypes sourced closer to the center of origin of rice showed relatively little diversity compared with the ones obtained from other parts of the world, suggesting migration from a common region of origin. The tropical japonica lines can be a great source of parental diversification for hybrid development after confirming the presence of widely compatible genes.

Keywords: genetic diversity; genetic variability; interspecific hybridization; new plant type; population structure; rice.

Figure 1

Box plots of agro-morphologic traits among the tropical japonica lines. Originating from 43 countries, the genetic variability among the lines was relatively low.

Figure 2

PCA based on agronomic data. Panicle length, grain number, plant height, and spikelet fertility accounted for the maximum variability along with the first principal component, while grain yield and tiller number accounted for the variation along the second principal component axis. The grouping of the genotypes showed at least five clusters with maximum concentration in one cluster. The geographical distribution across clusters showed no definite pattern, indicating that the tropical japonica genotypes had a common origin and were distributed across the globe through domestication activities.

Figure 3

Principal coordinate analysis of 200 tropical japonica lines and 36 check lines based on 46 SSR markers.

Figure 4

Estimated population structure of 236 rice accessions, which included 200 tropical japonica lines.

Figure 5

Distribution of sources of origin of germplasm lines among the four sub-populations.

Figure 6

Pairwise FST matrix of tropical japonica lines based on their countries of origin. The population showed greater differentiation among 19 countries, while the rest of the population showed relatively little genetic difference.

Figure 7

Chromosome-wise allele distribution among the genotypes of four subpopulations sourced from different countries.