No abstract

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 indica-japonica 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 grainquality traits of 256 indica rice lines. The main results are as follows. (1) Euphytica (2016) 212:261-273 DOI 10.1007/s10681-016-1766 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 indica-japonica properties for parent matching, and the marker-trait association will also be useful for molecular design breeding.