SSR analysis of genetic variation in Chinese major inbred rice varieties.

A total of 40 SSR markers were used to assess the genetic variation in 329 Chinese major inbred rice varieties planted during the past 50 years.Of the 40 SSR loci,39 were polymorphic while one locus(RM479) was monomorphic.All the 39 polymorphic loci revealed a total of 223 alleles.The mean number of alleles per locus(Na) was 5.7 with a range from 2 to 11.Total genetic diversity index of Nei(He) varied greatly among loci from 0.221 at RM174 to 0.873 at RM418,with an average value of 0.632.There existed visible difference in SSR allelic diversity between indica and japonica subspecies.Indica showed more variation than japonica both for Na(indica: 5.4;japonica: 4.4) and He(indica: 0.440;japonica: 0.397).The whole set of Chinese major rice varieties had smaller genetic identity(I = 0.366) than that of indica(I=0.558) and japonica rice(I=0.600).The narrow genetic base within subspecies was mainly due to the close relationship among primary parents in breeding programs.The differences among three season types were obvious in Nei′s genetic identity indexes,of which late-season indica rice and early-season japonica rice had higher genetic variation.Cluster analysis indicated that the genetic distances between Chinese major rice varieties were season type-and rice region-dependant,especially in japonica rice.Therefore,it is suggested that more alien elite genetic resources should be exploited in the rice breeding for broadening the genetic base of Chinese rice varieties.