SSR variation
Fifty-one (71.8%) and 53 (74.6%) out of 71 azuki bean SSR markers were able to amplify DNA of V. exilis and V. grandiflora, respectively. Forty-seven of the 51 amplifiable SSRs in V. exilis showed polymorphism, while 38 of the 53 amplifiable SSRs in V. grandiflora showed polymorphism. Twenty-one SSRs showing clear and polymorphic bands in both V. exilis and V. grandiflora were further used to analyze the populations. Thesemarkers came from 11 linkage groups of azuki bean (2n = 2x = 22) (Table 2), which corresponded to the haploid chromosome number of both V. exilis and V. grandiflora. In both species, most of the SSR markers showed high discriminating power, with the PIC value of each marker always higher than 0.70. In total, the 21 loci detected 196 alleles for V. exilis and 219 alleles for V. grandiflora (Table 2). The average number of alleles and average allelic richness detected by the SSRs were comparable among the two species (9.3 vs. 10.4 and 5.70 vs. 4.55, respectively) (Table 2). Null alleles were present in both V. exilis (3.87% of the data) and V. grandiflora (4.65% of the data) (data not shown). A pairwise linkage disequilibrium (LD) test revealed that 44 and 11 out of 210 marker combinations show significant LD (P < 0.05) in V. exilis and V. grandiflora, respectively.
The average of the FST value, an index of genetic differentiation, in V. exilis (0.512) was much higher than that in V. grandiflora (0.193)