Development of a set of PCR-based anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments

Abstract

Tomato and potato expressed sequence tag (EST) sequences contained in the solanaceae genomics network (SGN) database were screened for simple sequence repeat (SSR) motifs. A total of 609 SSRs were identified and assayed on Solanum lycopersicum LA925 (formerly Lycopersicon esculentum) and S. pennellii LA716 (formerly L. pennellii). The SSRs that did not amplify, gave multiple band products, or did not exhibit a polymorphism that could be readily detected on standard agarose gels in either of these species were eliminated. A set of 76 SSRs meeting these criteria was then placed on the S. lycopersicum (LA925) · S. pennellii (LA716) high-density map. A set of 76 selected cleaved amplified polymorphism (CAP) markers was also developed and mapped onto the same population. These 152 PCR-based anchor markers are uniformly distributed and encompass 95% of the genome with an average spacing of 10.0 cM. These PCRbased markers were further used to characterize S. pennellii introgression lines (Eshed and Zamir, Genetics 141:1147-1162 and should prove helpful in utilizing these stocks for high-resolution mapping experiments. The majority of these anchor markers also exhibit polymorphism between S. lycopersicum and two wild species commonly used as parents for mapping experiments, S. pimpinellifolium (formerly L. pimpinellifolium) and S. habrochaites (formerly L. hirsutum), indicating that they will be useful for mapping in other interspecific populations. Sixty of the mapped SSRs plus another 49 microsatellites were tested for polymorphism in seven tomato cultivars, four S. lycopersicum var. cerasiforme accessions and eight accessions of five different wild tomato species. Polymorphism information content values were highest among the wild accessions, with as many as 13 alleles detected per locus over all accessions. Most of the SSRs (90%) had accession-specific alleles, with the most unique alleles and heterozygotes usually found in accessions of selfincompatible species. The markers should be a useful resource for qualitative and quantitative trait mapping, marker-assisted selection, germplasm identification, and genetic diversity studies in tomato. The genetic map and marker information can be found on SGN (http:// www.sgn.cornell.edu).

Evaluation of Genetic Variability in Tomato (Solanum lycopersicum L. Mill) Genotypes using Microsatellite Markers

“…Several molecular marker viz. RFLP, RAPD, SSRs, ISSRs, AFLP and SNPsare presently available to assess the variability and diversity at molecular level, among which SSR markers are the most widely used (Frary et al, 2005). Earlier studies have reported the use of morphological and molecular markers viz.…”

Structural analyses of the tomato genome

“…Subsequently, several types of DNA markers have been developed, e.g., random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) or microsatellite, amplified fragment length polymorphism (AFLP), cleaved amplified polymorphic sequence (CAPS), and single nucleotide polymorphism (SNP) markers. A total of 1,088 CAPS, 1,342 RFLP, 155 SSR, and 19 SNP markers have been mapped onto an interspecific genetic linkage map based on a cross between S. lycopersicum 'LA925' and S. pennellii 'LA716'; the Tomato-EXPEN 2000 map (Frary et al 2005;Fulton et al 2002;Shirasawa et al 2010a).…”

“…Later, a whole genome sequencing strategy was also adopted, to cover the entire genome. In parallel with genome sequencing, the development of DNA markers and construction of highdensity genetic linkage maps were conducted to assist in the reconstruction of the whole genome structure by mapping (Frary et al 2005;Fulton et al 2002). The chloroplast and mitochondrial genomes were sequenced independently from the nuclear genome (Kahlau et al 2006).…”

Genetic Transformation in Tomato: Novel Tools to Improve Fruit Quality and Pharmaceutical Production

“…Most of these resources are also publicly available for the scientific community and are accessible via web (Table 2). Since the beginning of 1990s, the contribution of molecular markers and maps to tomato breeding and gene identification has been widely documented (Foolad, 2007;Frary et al, 2005;Gupta et al, 2009), and more than 15.000 different markers are collected in the SGN database, where markers can be searched by name, chromosome position and mapping population. Moreover, cytological and cytogenetic maps are also available, as well as a detailed physical map, which was the foundation for the tomato genome sequencing project (Mueller et al, 2005).…”