Genetic diversity of public inbreds of sorghum determined by mapped AFLP and SSR markers

The objectives of this study were (i) to assess the level of genetic diversity in elite sterility-maintaining (B) and fertility-restoring (R) sorghum [Sorghum bicolor (L.) Moench] lines as compared with a group of exotic and converted germplasm (IS) from the World Collection, (ii) to compare the classification of germplasm on the basis of estimates of genetic similarities obtained by means of AFLP and microsatellite (SSR) markers, and (iii) to compare the classification of germplasm obtained by different classes of molecular markers. A set of 100 SSRs, 1318 EcoRI/MseI AFLP, and 496 PstI/MseI AFLP markers with known map positions were utilized to determine the genetic similarity in a group of B, R, and IS public inbreds. Cluster analysis of genetic similarity estimates (GS_ij) revealed that the classification of sorghum inbreds is based on the sorghum working groups, Zera-zera, Kafir, Kafir-Milo, Durra, and Feterita. Cluster analyses failed to give a clear differentiation between B- and R-lines, suggesting that R- and B-lines do not represent well-defined heterotic groups in this set of public lines. By comparing the different classes of molecular markers (SSRs, AFLPs, combinations of SSRs and AFLPs), we determined that the distribution of the markers and the coverage of the genome by the markers did affect the classification of genotypes. Dendrograms of genetic similarity (GS) based on PstI/MseI AFLP markers, or a set of markers spaced at 1- to 2-cM intervals across the genome, produced clusters that were in better agreement with pedigree information than the analysis based solely on the EcoRI/MseI AFLP or SSR markers used in this study.