SSR analysis on japonica rice landraces from the Taihu Lake Region, China.

Forty-five SSR markers were used to study the genetic diversity in 224 japonica rice landraces from the Taihu Lake Region,China. There were 162 alleles at the 45 loci investigated. The number of alleles per locus (Na) ranged from 2 to 7,with a mean value of 3.6. The Nei's genetic diversity index (He) varied widely from 0.009 (RM169) to 0.663 (RM444) with an average value of 0.197. The genetic diversity of all the traditional eco-types (green rice,yellow rice,red rice and white rice) was low. Analysis of molecular variance (AMOVA) indicated that most of the genetic variation was from differences among traditional eco-types. The pairwise comparison of F-statistics(Fst) revealed a significant genetic differentiation in the four pairs (green rice vs red rice; green rice vs white rice; red rice vs white rice; red rice vs yellow rice),whereas no significant differentiation was found between other types. The results showed that more rare alleles and low genetic diversity were detected in japonica rice landraces from the Taihu Lake Region,China. This will be helpful to conserve and exploit Taihu japonica rice landraces.