Comparison of DNA-based and pedigree-based genetic similarity among Korean rice cultivars

A comprehensive knowledge of the genetic diversity in parental cultivars could improve the effectiveness of breeding programs. The objectives of this study were to assess the level of genetic similarity among the Korean-bred rice cultivars and to investigate the relation between two methods of measuring genetic similarity (GS): the DNA-based genetic similarity (GS_DNA) and pedigree-based genetic similarity (GS_ped). Polymerase chain reaction (PCR) with fifteen simple sequence repeat (SSR) markers was used for estimation of GS_DNA among a group of one hundred and nine Korean-bred rice cultivars. GS_ped was estimated from coefficients of parentage (CP) for the same set of cultivars used for estimation of GS_DNA. The mean of the 5886 GS_ped pairwise comparisons was 0.13, with the range from 0.000 to 0.751, with higher distribution in the region of GS < 0.20. In contrast, GS_DNA were normally distributed (mean = 0.79), mostly distributed to GS > 0.5. In spite of substantially different means and distributions of the two diversity measures, a correlation (r = 0.266, P < 0.05) was detected between the two GS matrix, indicating the DNA data may help to more-accurately quantify the degree of relationship among rice cultivars. Conclusively, although GS_ped was not effective for identifying degree of relatedness among individual cultivars, combining of the information from GS_ped and GS_DNA may be adequate for assessing overall patterns of genetic variation among rice germplasm.