Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple-sequence repeats (SSRs)

Fifty one clones isolated from a size-fractionated genomic DNA library of S orghum bicolor (L.) Moench, that had been probed with four radiolabeled di- and tri-nucleotide oligomers, were sequenced. Fifty of the clones contained one or more simple-sequence repeats (SSRs) [72% of which were (AG/TC)(n) S SRs] and, following analysis of the clones, polymerase-chain-reaction prime r sets that amplify 38 unique SSR loci were developed. Genotyping of the 38 loci in 18 sorghum accessions, including the parents of a recombinant inbr ed (RI) mapping population, revealed polymorphism at 36 of the loci among t he 18 accessions and at 31 of the loci (not including null alleles at two l oci) between the parents of the RI population. All of the latter 31 loci we re mapped. The genotypes at 17-mapped SSR loci were assayed in 190 S. bicol or accessions in order to determine delta(T)*, the estimated level of allel ic differentiation (the estimated probability that two members of a populat ion, chosen at random and without replacement, differ in allelic compositio n), at each of the loci. The mean delta(T)* value determined for S. bicolor overall was 0.89, the range of mean delta(T)* values for ten S. bicolor ra ces was from 0.88 to 0.83, and the range of mean delta(T)* values for ten w orking groups (= sub-races) of the race caudatum, with only two exceptions, was from 0.87 to 0.79. The lowest delta(T)* values for six of the loci amo ng the ten race-caudatum working groups ranged from 0.86 to 0.70; thus, the probability that different alleles will be present at one or more of these loci in two accessions chosen at random from a working group is > 0.996 wh en three of the loci are genotyped, and >0.9999 when all six of the loci ar e genotyped. The results of this study confirm that most S. bicolor SSR loc i are sufficiently polymorphic to be useful in marker-assisted selection pr ograms and they indicate that the levels of polymorphism at some loci are h igh enough to allow the vast majority of S. bicolor accessions, even access ions within working groups, to be distinguished from one another by determi ning the genotypes at a small number, perhaps as few as a half-dozen, SSR l oci.