Population structure analysis reveals the maintenance of isolated sub-populations of weedy rice

P>This study was conducted to assess the genetic diversity, population structure and linkage disequilibrium (LD) of weedy rice in Korea using 73 weedy rice, 24 landrace lines, 12 breeding lines and 24 international varieties. In total, 772 alleles were detected in 63 microsatellite loci. The number of alleles per marker locus ranged from two to 40, with an average of 12.3. The gene diversity and polymorphism information content value averaged 0.694 and 0.668, with a range of 0.016-0.941 and 0.016-0.946 respectively. In a model-based analysis of population structure, Korean rice germplasm was classified into four subpopulations, designated 'cultivated indica', 'cultivated japonica', 'weedy indica', 'weedy japonica.' Pair-wise estimates of F-ST indicated different degrees of differentiation between the four model-based populations, with values ranging from 0.073 (between cultivated and weedy japonica) to 0.474 (between weedy japonica and weedy indica). The weedy indica population appeared to be highly differentiated, compared with the other populations. The cultivated indica lines had the highest gene diversity (0.58), followed by cultivated japonica (0.50), weedy japonica (0.42) and weedy indica (0.35). The total number of private alleles in weedy indica and japonica populations was 39 (23 markers) and 55 (22 markers) respectively. The average of LD (r2) of weedy indica and japonica types was higher than that of the two cultivated populations, both for inter- and intrachromosome values, indicating the possible reproductive and geographical isolation of sub-populations in cultivated rice fields.