Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats

Short mononucleotide repeats analogous to nuclear microsatellites or simple sequence repeats (SSRs) have been identified in chloroplast genomes. Primers flanking mononucleotide repeats in the fully sequenced rice chloroplast genome have been used in conjunction with PCR to amplify genomic DNA from 42 wild rice accessions. The amplification products exhibited length polymorphism, which allowed the levels of chloroplast variability detected to be quantified. Seven primer pairs that amplified products from different regions of the rice chloroplast were used, five of which also amplified polymorphic products in cultivated rice (Oryza sativa). Diversity values ranged from 0.5224 ± 0.0845 (SE) to 0.8298 ± 0.0085 in the wild accessions, which was higher than that detected in the O. sativa accessions. Both intra- and inter-specific polymorphism was detected, and the extent of chloroplast genomic differentiation based on chloroplast simple sequence repeat (cpSSR) assays was quantified using the R(ST) statistic. Primers designed to amplify cpSSRs in O. sativa can also be used to generate polymorphic chloroplast markers in related taxa. The potential of using cpSSR to trace the origin of rice polyploid species is discussed.