Pedigree and RAPD‐Based DNA Analysis of Commercial U.S. Rice Cultivars

Abstract

Pedigree information has traditionally been used to obtain estimates of genetic variation, predict hybrid performance, and select parents for crossing in crop improvement programs. We have generated and compared pedigree and randomly amplified polymorphic DNA (RAPD) data obtained from 26 elite cultivars and lines rice ( Oryza sativa L.) recommended for commercial production in Louisiana and elsewhere in the USA. For the RAPD analysis, 220 commercially available primers (10‐mers) were evaluated for their ability to distinguish pairwise combinations of the cultivars‐lines that included four sets of full sibs. A total of 69 primers produced 92 polymorphic bands, 0.25 to 3.5 kb in size. Seven primers were identified that could differentiate all cultivars‐lines. Genetic distances obtained from RAPD data were correlated with estimated kinship coefficients. Within the RAPD or pedigree method, similar mean genetic distances were detected for long‐ and medium‐grain cultivars. However, mean genetic distances based on pedigrees were significantly greater than those based on RAPD data for both grains types. Cultivars with the same maturity group or grain type were generally placed together in cluster analyses based on either RAPD or known pedigree data. RAPD information can be used to establish genetic relationships among commercial U.S. rice cultivars with unknown or unrelated pedigrees.