Marker-Assisted Selection in Tomato Breeding

Critical Reviews in Plant Sciences (Impact Factor: 4.36). 01/2012; 31(2):93-123. DOI: 10.1080/07352689.2011.616057

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: The most sustainable strategy to manage tomato late blight (LB) would be to deploy an integrated system including cultural practices, fungicide application, and the use of cultivars with broad-spectrum genetic resistance against LB. This chapter summarizes the current understanding of Phytophthora infestans. It discusses its effects on tomato production, and the genetics and breeding of LB resistance in tomato. LB has been identified as a major disease of tomato and potato and is one of the most devastating plant diseases of all time. P. infestans can quickly devastate tomato and potato crops at any time during plant ontogeny. The most sustainable strategy for managing tomato LB is to deploy an integrated system including cultural practices, fungicide application, and the use of cultivars with broad-spectrum genetic resistance against LB. Late blight (LB), caused by the oomycete Phytophthora infestans (Mont.) de Bary, is one of the most destructive diseases of tomato (Solanum lycopersicum L.) and potato (S. tuberosum L.) worldwide, causing significant economic losses annually. The success of P. infestans as a pathogen originates from its effective asexual and sexual life cycles, as well as its remarkable capacity to rapidly overcome plant resistance genes, a result of its high evolutionary potential. The most sustainable strategy to manage tomato LB would be to deploy an integrated system including cultural practices, fungicide application, and the use of cultivars with broad-spectrum genetic resistance against LB. Prior to the reemergence of LB in the late 1980s, cultural practices in combination with fungicide applications were highly effective measures to control the tomato LB. However, with the appearance of new and more aggressive isolates of P. infestans, many of which are resistant to LB-specific systemic fungicides, the greatest contribution to tomato LB control in the future will have to be through the development of cultivars with improved genetic resistance. Thus far, a number of major LB-resistance genes and quantitative trait loci (QTLs) have been identified in tomato and several breeding lines and cultivars, with improved resistance developed. Research is also underway to identify additional resistance genes or QTLs and to pyramid multiple resistance factors in order to develop stronger and more durable resistance. Further, as exemplified by the fast progress in potato LB research and conservation of LB signaling pathways between potato and tomato, detailed knowledge of the pathogen effectors in combination with high-throughput genomics technology will facilitate a better understanding of the LB disease and host-pathogen interactions, which in turn may lead to development of tomatoes with more durable resistance.
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    ABSTRACT: When a wild species' allele at a quantitative trait locus (QTL) conferring a desirable trait is introduced into cultivated species, undesirable effects on other traits may occur. These negative phenotypic effects may result from the presence of wild alleles at other closely-linked loci that are transferred along with the desired QTL allele (i.e., linkage drag), and/or from pleiotropic effects of the desired allele. Previously, a QTL for resistance to Phytophthora infestans on chromosome 5 of Solanum habrochaites was mapped and introgressed into cultivated tomato (S. lycopersicum). Near-isogenic lines (NILs) were generated and used for fine-mapping of this resistance QTL, which revealed coincident or linked QTL with undesirable effects on yield, maturity, fruit size, and plant architecture traits. Subsequent higher-resolution mapping with chromosome 5 sub-NILs revealed the presence of multiple P. infestans resistance QTL within this 12.3 cM region. In our present study, these sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over two years. Each previously detected single horticultural trait QTL fractionated into two or more QTL. A total of 41 QTL were detected across all traits, with ~30% exhibiting significant QTL × environment interactions. Co-location of QTL for multiple traits suggests either pleiotropy or tightly-linked genes control these traits. The complex genetic architecture of horticultural and P. infestans resistance trait QTL within this S. habrochaites region of chromosome 5 presents challenges and opportunities for breeding efforts in cultivated tomato.
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