Analysis of parental genetic diversity and its impact on grain yield and quality of japonica hybrid rice in northern China

The relationship between parental genetic differences and the quality and yield of japonica hybrid rice strongly influences japonica hybrid rice breeding. In this study, 137 parental lines of japonica hybrid rice were genotyped using 8K rice SNP-Chips to characterize their genetic diversity, population structure, and indica-genotype proportion. The genetic diversity of total parental lines averaged 0.264, with values of 0.287 for restorer lines and 0.148 for the sterile lines. The introduction of indica lineage increased the genetic diversity of restorer lines relative to that of sterile lines. By model-based population structure analysis, the 137 lines were divided into 14 groups. According to the grouping results, eight restorer lines and five sterile lines were selected from different groups for cross breeding, yielding 40 japonica hybrid rice combinations (F1). Investigation of the yield and quality of these combinations showed that high-yield combinations could be obtained by increasing parental genetic distance to 0.8–0.9, a result accomplished largely by the introduction of indica genomic components of restorer lines. To further improve grain quality, the genetic distance between parents should be reduced to 0.4–0.5, suggesting an indica-genotype proportion of 30%–40% for restorer lines. This study may provide a reference for breeding of japonica hybrid rice.