MOLECULAR MAPPING AT QUANTITATIVE TRAIT LOCI IN JAPONICA RICE

Rice (Oryza sativa L.) molecular maps have previously been constructed using interspecific crosses or crosses between the two major subspeci es: indica and japonica. For japonica breeding programs, however, it w ould be more suitable to use intrasubspecific crosses. A linkage map o f 129 random amplified polymorphic DNA (RAPD) and 18 restriction fragm ent length polymorphism (RFLP) markers was developed using 118 F-2 pla nts derived from a cross between two japonica cultivars with high and low seedling vigor, Italica Livorno (IL) and Labelle (LBL), respective ly. The map spanned 980.5 cM (Kosambi function) with markers on all 12 rice chromosomes and an average distance of 7.6 cM between markers. C odominant (RFLP) and coupling phase linkages (among RAPDs) accounted f or 79% of total map length and 71% of all intervals. This map containe d a greater percentage of markers on chromosome 10, the least marked o f the 12 rice chromosomes, than other rice molecular maps, but had rel atively fewer markers on chromosomes 1 and 2. We used this map to dete ct quantitative trait loci (QTL) for four seedling vigor related trait s Scored on 113 F-3 families in a growth chamber slantboard test at 18 degrees C. Two coleoptile, five root, and five mesocotyl length QTLs, each accounting for 9-50% of the phenotypic variation, were identifie d by interval analysis. Single-point analysis confirmed interval mappi ng results and detected additional markers significantly influencing e ach trait. About two-thirds of alleles positive for the putative QTLs were from the high-vigor parent, LL. One RAPD marker (OPAD13(720)) was associated with a IL allele that accounted for 18.5% of the phenotypi c variation for shoot length, the most important determinant of seedli ng vigor in water-seeded rice. Results indicate that RAPDs are useful for map development and QTL mapping in rice populations with narrow ge netic base, such as those derived from crosses among japonica cultivar s. Other potential uses of the map are discussed.