3. Results
3.1. Genetic diversity
A total of 220 alleles were detected using 58 SSR markers randomly distributed on rice 12 chromosomes and 8 STS markers (Table S2). The average major allele frequency was 0.61, ranging from 0.35 to 0.92, indicating that 61% of loci shared a common major allele at any given locus. The average number of alleles per locus was 3.33, ranging from 2 to 7. The average gene diversity was 0.51, ranging from 0.15 to 0.73 and the average PIC value was 0.44, ranging from 0.14 to 0.68.
3.2. Population structure
The ln P(D) value increased with K from 1 to 10, but showed a large increase at K = 2 ( Fig. 1), suggesting two distinct groups. There was also a sharp peak of Evanno's ΔK at K = 2 ( Fig. 1). A neighbor-joining tree was constructed based on Nei's genetic distance ( Fig. 2). The same result was revealed based on STRUCTURE membership assignment for the 96 accessions ( Fig. 3). The majority of accessions, including 58 landraces, 9 varieties/lines and Nona Bokra were assigned to Group 1 and 21 landraces comprised Group 2 (Table S1). Seven landraces with membership probabilities ranging from 0.56 to 0.79 were classified as an admixed group. Nine indica genotypes, as well as Nona Bokra, were all in Group 1, indicating that Group 1 corresponds to ssp. indica.