Genetic Diversity and Population Structure of the Parental lines of Hybrid Japonica Rice in Northern China Revealed by 8K SNP-Chips

Abstract BackgroundThe hybrid rice varieties have made a significant contribution to food security. Although there has been rapid development of hybrid indica rice variety, the development of hybrid japonica rice has been relatively slow. This study aimed to understand the genetic background of representative parental lines of hybrid japonica rice in northern China that were beneficial for increasing efficiency to find a superior breeding combination using a restorer line and a sterile line. ResultsWe selected 137 parental lines of hybrid japonica rice, including 90 restorer lines, 47 sterile lines, which broadly represented the recent rice breeding trends in China. These lines were genotyped using 8K SNP-Chips (China Golden Marker Biotechnology Co. Ltd.) to understand the genetic diversity, population structure, phylogenetic evolution, and indica blood content. The genetic diversity of total parental lines averaged 0.264, with values for the restorer line and sterility line as 0.287 and 0.148, respectively. Based on the model-based population structure analysis and distance-based clustering, these 137 lines were divided into 14 groups, including seven independent restorer lines groups and seven mixture groups. There were 70% restorer lines in the above-mentioned seven independent restorer lines groups, and the indica blood content was 0.348, while 30% restorer lines were genetically similar to the sterile lines and constituted the other seven mixture groups, where the indica blood content in the restorer lines and the sterility lines was 0.142 and 0.121, respectively. The results of distance-based clustering revealed that the restorer lines, Group 1 and Group 2 (containing only restorer lines), had longer genetic distances with groups containing mainly sterile lines (the genetic distance ranged from 0.672 to 0.788), which served as a potential heterotic for hybrid rice breeding. This observation was consistent with the breeding strategy of high yield hybrid japonica rice.ConclusionsThe typical japonica sterile lines were crossed with the restorer lines containing high indica components indicating a strong heterosis pattern was a feasible scheme for heterosis utilization of indica-japonica subspecies. Thus, the effective ways to further improve the rice quality of hybrid japonica rice in northern China included maintaining moderate genetic distance and indica components between the parental lines along with the excellent quality of both the parental lines.