Screening of RAPD markers linked to the photoperiod-sensitivity gene in rice chromosome 6 using bulked segregant analysis.

Bulked segregant analysis was used to determine randomly amplified polymorphic DNA (RAPD) markers in a specific interval in the middle of chromosome 6 of rice for tagging the photoperiod sensitivity gene. Two pools of F2 individuals (japonica cv. Nipponbare and indica cv. Kasalath) were constructed according to the genotypes of three restriction fragment length polymorphism (RFLP) markers located at both ends and the middle of the targeted interval. Then another pair of pools were constructed based on the "graphical genotype," which was made with our high density linkage map. RAPD analysis was performed using these DNA pools as templates, and polymorphic fragments were detected and mapped. Using 80 primers, either singly or pairwise, we tested 2,404 primer pairs and established 14 markers tightly linked to the photoperiod sensitivity gene. The obtained RAPD markers were converted into sequence-tagged sites by cloning and sequencing of the polymorphic fragments and they can be used directly for construction of physical maps. This bulked segregant method can be applied for any species and any region of interest in which detailed linkage maps or physical maps are needed.