Genetic Diversity Revealed by SSR Markers and Temporal Trends of Major Commercial Inbred Indica Rice Cultivars in South China in 1949–2005

The genetic diversity of 95 major commercial inbred rice cultivars (Oryza sativa L. subsp. indica) released in South China from 1949 to 2005 were evaluated using 300 simple sequence repeat (SSR) markers distributing evenly on the whole rice genome. A total of 236 polymorphic loci were detected with 776 alleles. The number of allele per locus ranged from 2 to 12 with an average of 3.29. Only 2–4 alleles were found at 206 loci, which accounted for 87.3%. The average polymorphism information content (PIC) value of polymorphic loci was 0.42, which varied with chromosomes. Chromosome 10 had the greatest values in allele number per locus and PIC, and chromosome 5 had the lowest values. The allele number per locus showed an increase trend in the cultivars released from the 1950s to the 1970s and declined afterwards. Analysis of molecular variance (AMOVA) disclosed the significant genetic variation (P < 0.001) among cultivars from different decades, although it only explained 3.77% of the total genetic variation. The genetic distance among cultivars was decreased from the 1950s to the 2000s. According to clustering analysis with COMPLETE method, the 95 cultivars were grouped into 5 clusters at genetic similarity coefficient of 0.685, and several core parents were found in the cultivars released in each decade. The results indicate that the genetic diversity of indica rice cultivars in South China is in a low level and even narrowing after the 1970s. Thus, the genetic basis of indica rice cultivars should be broadened through incorporating new variability into existing rice germplasm in breeding programs.