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To make advances in rice molecular design breeding, it is important to understand the genetic background and phenotypes of the parental lines, to known superior allele of the breeding material. In this study, 34 pairs of insertion-deletion (InDel) markers were used to analyze the differentiation of – properties in 277 primal parental lines of hybrid rice that are used in China and abroad. The genetic diversity and population structure were assessed with simple sequence repeat (SSR) markers. We also evaluated the association between SSR markers and seven yield traits and four grain-quality traits of 256  rice lines. The main results are as follows. (1) Within the 277 lines there were two subgroups:  and . The 256 lines of the -subgroup were further divided into four sub–sub-groups: landrace, maintainer, restorer, and rice lines from the International Rice Research Institute. (2) We identified 29 loci associated with 11 agronomic traits, including one for plant height, two for tiller number, one for panicle length, three for grain length, eight for grain width, eight for grain length/width ratio, one for thousand grain weight, one for amylose content, two for gel consistency, one for gelatinization temperature and one for total protein content. (3) Among those loci, 16 markers were closely linked to previously identified genes. Superior allele carrier lines and allele effects were also analyzed. Our results provided the population structure and – properties for parent matching, and the marker–trait association will also be useful for molecular design breeding.

Population structure and association analysis of yield and grain quality traits in hybrid rice primal parental lines