Development of tomato SSR markers from anchored BAC clones of chromosome 12 and their application for genetic diversity analysis and linkage mapping

In this study, we developed a total of 37 simple sequence repeat (SSR) markers from 11 bacterial artificial chromosome (BAC) clone sequences anchored on chromosome 12 of tomato available at Solanaceae Genomics Network. These SSR markers could group a set of 16 tomato genotypes comprising of Solanum lycopersicum, S. pimpinellifolium, S. habrochaites, and S. pennellii unambiguously according to their known species status. Clear subgroups of genotypes within S. lycopersicum were also observed. A subset of 16 SSR markers representing the 11 BAC clones was used for developing genetic linkage maps of three interspecific F-2 populations produced from the crosses involving a common S. lycopersicum parent (CLN2498E) with S. pennellii (LA1940), S. habrochaites (LA407) and S. pimpinellifolium (LA1579). The length of the genetic linkage maps were 112.5 cM, 109.3 cM and 114.1 cM, respectively. Finally, an integrated genetic linkage map spanning a total length of 118.7 cM was developed. The reported SSR markers are uniformly distributed on chromosome 12 and would be useful for genetic diversity and mapping studies in tomato.