Genetic diversity of rice germplasm used in Taiwan breeding programs

Abstract

Rice is one of the most important cereal crops in the world and is the major crop in Taiwan. Assessment of genetic diversity of rice germplasm is imperative for conservation and breeding. We used 114 simple sequence repeat (SSR) and 5 sequence tagged site (STS) markers with 80 common rice varieties, including 52 japonica and 28 indica varieties used in Taiwan breeding programs, and detected 395 alleles. The mean number of alleles per marker was 3.5, range 2 to 7. The mean polymorphism information content (PIC) for each marker was 0.43 (range 0.04-0.76). The japonica and indica varieties were obviously separated into clusters by the distance-based unweighted pair-group method with averages (UPGMA) and principal coordinate analysis (PCoA). Taiwan and Japanese japonica varieties aggregated in the same clusters because of their highly similar genetic background. The genetic diversity was greater for indica than japonica varieties. The genetic diversity of Taiwan cultivars was relatively narrow, specifically in japonica varieties, and introduced exotic elite cultivars exhibited enriched alleles. The differentiation of domestic and introduced indica cultivars was moderate (F-ST =0.25), which was the same revealed japonica cultivars (F-ST =0.15). However, there was no significant differentiation between Taiwan and Japanese japonica cultivars as supported by the small F-ST (0.05); thus, introducing exotic germplasm other than from Japan should enlarge the gene pool of Taiwan cultivars. This DNA polymorphism analysis revealed genomic relationships in Taiwan rice germplasm, and the database on 'The Resource of Rice Genetic Markers in Taiwan' is useful for cultivar identification, local germplasm conservation and breeding programs.