Temporal changes in SSR allelic diversity of major rice cultivars in China

Forty simple sequence repeats (SSRs) were used to assess the changes of diversity in 310 major Chinese rice cultivars grown during the 1950s–1990s. Of the 40 SSR loci, 39 were polymorphic. A total of 221 alleles were detected with an average of 5.7 alleles per locus (Na). The Nei's genetic diversity index (He) varied drastically among the loci (0.207 to 0.874, mean 0.625). Comparing the temporal changes in Na and He, the cultivars from the 1950s had more alleles and higher He scores than the cultivars from the other four decades. Analysis of molecular variance (AMOVA) indicated that the genetic differentiation among the five decades was not significant in the whole set, but significant within indica and japonica. More changes among the decades were revealed in indica cultivars than in japonica cultivars. Some alleles had been lost in current rice cultivars in the 1990s, occurring more frequently in indica. These results suggest that more elite alien genetic resources should be explored to widen the genetic backgrounds of rice cultivars currently grown in China.