Marker-Assisted Selection in Tomato Breeding
ABSTRACT The cultivated tomato, Solanum lycopersicum L., is the second most consumed vegetable crop after potato and unquestionably the most popular garden crop in the world. There are more varieties of tomato sold worldwide than any other vegetable crop. Most of the commercial cultivars of tomato have been developed through phenotypic selection and traditional breeding. However, with the advent of molecular markers and marker-assisted selection (MAS) technology, tomato genetics and breeding research has entered into a new and exciting era. Molecular markers have been used extensively for genetic mapping as well as identification and characterization of genes and QTLs for many agriculturally important traits in tomato, including disease and insect resistance, abiotic stress tolerance, and flower- and fruit-related characteristics. The technology also has been utilized for marker-assisted breeding for several economically important traits, in particular disease resistance. However, the extent to which MAS has been employed in public and private tomato breeding programs has not been clearly determined. The objectives of this study were to review the publically-available molecular markers for major disease resistance traits in tomato and assess their current and potential use in public and private tomato breeding programs. A review of the literature indicated that although markers have been identified for most disease resistance traits in tomato, not all of them have been verified or are readily applicable in breeding programs. For example, many markers are not validated across tomato genotypes or are not polymorphic within tomato breeding populations, thus greatly reducing their utility in crop improvement programs. However, there seems to be a considerable use of markers, particularly in the private sector, for various purposes, including testing hybrid purity, screening breeding populations for disease resistance, and marker assisted backcross breeding. Here we provide a summary of molecular markers available for major disease resistance traits in tomato and discuss their actual use in tomato breeding programs. It appears that many of the available markers may need to be further refined or examined for trait association and presence of polymorphism in breeding populations. However, with the recent advances in tomato genome and transcriptome sequencing, it is becoming increasingly possible to develop new and more informative PCR-based markers, including single nucleotide polymorphisms (SNPs), to further facilitate the use of markers in tomato breeding. It is also expected that more markers will become available via the emerging technology of genotyping by sequencing (GBS).
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ABSTRACT: Tomato (Solanum lycopersicum L.) is one of the most important vegetable crops in the world. However, the tomato production is severely affected by many diseases. The use of host resistance is believed to be the most effective approach to control the pathogens. In this study, a total of 1003 resistance-like genes were identified from the tomato genome using individual full-length search and conserved domain verification approach. Of the predicted resistance genes, serine/threonine protein kinase was the largest class with 384 genes followed by 212 genes encoding receptor-like kinase, 107 genes encoding receptor-like proteins, 68 genes encoding coiled-coil–nucleotide-binding site (NBS)–leucine-rich repeat (LRR) and 19 genes encoding Toll interleukin-1 receptor domain-NBS-LRR. Physical map positions established for all predicted genes using the tomato WGS chromosomes SL2.40 information indicated that most resistance-like genes clustered on certain chromosomal regions. Comparisons of the sequences from the same resistance-like genes in S. pimpinellifolium and S. lycopersicum showed that 93.5% genes contained single nucleotide polymorphisms and 19.7% genes contained insertion/deletion. The data obtained here will facilitate isolation and characterization of new resistance genes as well as marker-assisted selection for disease resistance breeding in tomato.Journal of Phytopathology 08/2013; 162(3). DOI:10.1111/jph.12163 · 0.92 Impact Factor
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ABSTRACT: Fusarium oxysporum f. sp. lycopersici Snyder & Hans. (FOL) is a major soil-borne pathogen and the causal agent of Fusarium wilt of tomato, resulting in significant production yield losses. Resistant cultivars have become the most effective method for controlling this fungal disease, and the most important resistance locus to F. oxysporum f. sp. lycopersici in tomato is I2, conferring resistance to race 2 of the pathogen, and widely used in breeding programs. Although this locus was cloned, a robust codominant DNA marker for the I2 locus is not available to date. The development of such a marker has been hindered by the presence of seven homologous sequences at this locus that tend to amplify, and by the absence of information about the structure of the recessive I2 locus. We performed a comparative analysis of the I2 locus nucleotide sequences of tomato genotypes resistant and susceptible to Fusarium wilt. We developed a breeder-friendly functional codominant cleaved amplified polymorphic sequence marker of I2 based on this analysis that can be used in tomato breeding programs for resistance to FOL race 2.Molecular Breeding 02/2012; 31(2). DOI:10.1007/s11032-012-9787-7 · 2.28 Impact Factor
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ABSTRACT: Jindou 1 is a soybean cultivar from China, which is resistant to all seven Soybean mosaic virus (SMV) strains identified in the U.S. An F2 population consisted of 91 plants derived from the cross Jindou 1× Essex were used for genetic analysis of SMV resistance. The segregation analysis of the F2 population indicated that Jindou 1 contained a dominant gene for SMV G1 resistance. Co-segregating analyses showed that the gene was tightly linked to a SNP marker, 3gG2-snp2, which was derived from the SMV Rsv1 candidate gene 3gG2, with a genetic distance 1.1 cM and the gene was independent to the single nucleotide polymorphism (SNP) marker, Barc-040713-07825, which is linked to Rsv4 on chromosome 2 (linkage group D1b). The gene in Jindou 1 was assumed to be Rsv1-y based on an Rsv1-specific PCR-based marker 3gG2-f1/r1 and the SNP maker 3gG2-snp1. Beside Rsv1-y, Jindou 1 was postulated to have Rsv3 based on the reaction pattern to 7 SMV strains G1–G7 in comparisons with the patterns in SMV differential lines.Euphytica 07/2012; 192(2). DOI:10.1007/s10681-012-0816-8 · 1.69 Impact Factor