An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench

We report the development, testing, and use (for genetic mapping) of a larg e number of polymerase chain reaction (PCR) primer sets that amplify DNA si mple sequence repeat (SSR) loci of Sorghum bicolor (L.) Moench. Most of the primer sets were developed from clones isolated from two sorghum bacterial artificial chromosome (BAC) libraries and three enriched sorghum genomic-D NA (gDNA) libraries. A few were developed from sorghum DNA sequences presen t in public databases. The libraries were probed with radiolabeled di- and trinucleotide oligomers, the BAC libraries with four and six oligomers, res pectively, and the enriched gDNA libraries with four and three oligomers, r espectively. Both types of libraries were markedly enriched for SSRs relati ve to a size-fractionated gDNA library studied earlier. However, only 2% of the sequenced clones obtained from the size-fractionated gDNA library lack ed a SSR, whereas 13% and 17% of the sequenced clones obtained from the BAC and enriched gDNA libraries, respectively, lacked a SSR. Primer sets were produced for 313 SSR loci. Two-hundred sixty-six (85%) of the loci were amp lified and 165 (53%) of the loci were found to be polymorphic in a populati on composed of 18 diverse sorghum lines. (AG/TC)(n) and (AC/TG)(n) repeats comprised 91% of the dinucleotide SSRs and 52% of all of the SSRs at the po lymorphic loci, whereas four types of repeats comprised 66% of the trinucle otide SSRs at the loci. Primer sequences are reported for the 165 polymorph ic loci and for eight monomorphic loci that have a high degree of homology to genes. Also reported are the genetic map locations of 113 novel SSR loci (including four SSR-containing gene loci) and a linkage map composed of 14 7 SSR loci and 323 RFLP (restriction fragment length polymorphism) loci. Th e number of SSR loci per linkage group ranges from 8 to 30. The SSR loci ar e distributed relatively evenly throughout approximately 75% of the 1406-cM linkage map, but segments of five linkage groups comprising about 25% of t he map either lack or contain few SSR loci. Mapping of SSR loci isolated fr om BAC clones located to these segments is likely to be the most efficient method for placing SSR loci in the segments.