Genetic diversity analysis within a species is vital for understanding evolutionary processes at the population and genomic levels. We report a detailed study of molecular diversity, polymorphism and linkage disequilibrium in three groups of rice (Oryza) germplasm accessions based on 176 SSR markers. The first group included 65 rice (O. sativa L.) accessions introduced from seven countries, including five regions of China. The second group included 58 US rice varieties released in the past 25 years. The third group consisted of 54 accessions of rice wild relatives represented by ten different species. The number of alleles per SSR marker ranged from 4 to 32 with a mean of 16 alleles and the polymorphism information content values ranged from 0.43 to 0.91 with a mean of 0.70. The variation in SSR alleles was a significant contribution to the genetic discrimination of the 177 accessions within the three Oryza groups. Analysis of molecular variance identified deviation from Hardy-Weinberg equilibrium. Principal coordinates analysis clearly separated the accessions into their respective three groups. Neighbor-joining phylogenetic cluster reflects the ordination of each accession. Linkage disequilibrium (D′) averaged 0.75 in wild Oryza spp., and about 0.5 in both US and international O. sativa accessions. Our results showed that LD among adjacent loci in both O. sativa and Oryza spp. accessions is strong enough to be detecting marker-trait association via genome-wide scans.
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