Assessment of in silico BAC-based simple sequence repeat (SSR) marker development for tomato (Solanum lycopersicum L.)

Tomato landraces are less sensitive to environmental stresses and grown mainly under rain fed conditions. They are still grown in small farms due to quality and special demand of consumers. These landraces are valuable sources of genetic traits, and plant breeders can use breeding programs for crop improvement. One of the primary needs of the crop improvement is the estimation of genetic diversity. Development of microsatellite simple sequence repeat (SSR) markers from map-referenced bacterial artificial chromosomes (BAC) clones is a very effective means of targeting markers to marker scarce positions in the genome. This study was aimed at developing a set of functional SSR markers via in silico analysis of publicly available tomato DNA sequences. As a result, 17 SSR markers were developed and tested on one tomato commercial cultivar and eight local landraces. 12 loci (27 alleles) were scored and showed 100% polymorphic patterns. The calculated polymorphism information content (PIC) values for the SSR markers developed ranged from 0.62 to 0.97 (mean 0.89). The SSR motifs CT(26) AT(27) and TTC(6) TTA(4) had the highest PIC value (0.97), while CAA(5)A(8) had the lowest PIC value (0.62). According to tomato expressed sequence tag (EST) analysis, some of these developed SSR markers, such as mono and di-nucleotide are related to some genes. The T(16) motif is related to hydroxyproline-rich glycoprotein, which is a family protein from Arabidopsis thaliana. On the other hand, the SSR with tri-nucleotide repeat motif AAC(4)A(11) was related to a putative homologous protein to A7Q2S4 from Vitis vinifera.