Co-dominant RAPD markers closely linked with two morphological genes in rice (Oryza sativa L.)

Abstract

By bulked segregant analysis, we screened for markers linked to two morphological genes, brittle culm (bc-1) and lazy (la). We identified four dominant and two co-dominant RAPD (randomly amplified polymorphic DNA) markers for bc-1 and eleven dominant and six co-dominant RAPD markers for la. One of the co-dominant RAPD markers, located 1.4cM from bc-1, was converted into co-dominant SCAR (sequence characterized amplified region). The six co-dominant markers were linked to la at various distances; two of which spanned a region with many RAPD markers. These co-dominant RAPD markers were detected by size and were a result of sequence modification between, not within, the priming sites. Non-parental bands were observed when the F1 and the heterozygous F2 RAPD and SCAR products were analyzed electrophorectically. Possible reasons for these non-parental bands were examined by sequence analysis, DNA annealing experiments, and Southern hybridization. The results indicated they were heteroduplex DNA formed by identical fragments amplified from allelic sequences. The presence of non-parental bands is further evidence of the co-dominance of the markers of interest. The co-dominant RAPD markers developed in this study overcome many of the limitations of RAPDs, and are readily verifiable and applicable. With these and additional PCR based markers, gene mapping or marker aided selection can be made more efficient.