Screening of RAPD Markers Linked to the Photoperiod-Sensitivity Gene in Rice Chromosome 6 Using Bulked Segregant Analysis

摘要

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 sensitivitygene. 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 singlyor pairwise, we tested 2,404 primer pairs and established 14 markers tightly linked to the photoperiod sensitivitygene. The obtained RAPD markers were converted into sequence-tagged sites bycloning and sequencing of the polymorphic fragments and they can be used directlyfor 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.