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      Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing

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          Abstract

          Molecular markers linked to phenotypically important traits are of great interest especially when traits are difficult and/or costly to be observed. In tomato where a strong focus on resistance breeding has led to the introgression of several resistance genes, resistance traits have become important characteristics in distinctness, uniformity and stability (DUS) testing for Plant Breeders Rights (PBR) applications. Evaluation of disease traits in biological assays is not always straightforward because assays are often influenced by environmental factors, and difficulties in scoring exist. In this study, we describe the development and/or evaluation of molecular marker assays for the Verticillium genes Ve1 and Ve2, the tomato mosaic virus Tm1 (linked marker), the tomato mosaic virus Tm2 and Tm2 2 genes, the Meloidogyne incognita Mi1-2 gene, the Fusarium I (linked marker) and I2 loci, which are obligatory traits in PBR testing. The marker assays were evaluated for their robustness in a ring test and then evaluated in a set of varieties. Although in general, results between biological assays and marker assays gave highly correlated results, marker assays showed an advantage over biological tests in that the results were clearer, i.e., homozygote/heterozygote presence of the resistance gene can be detected and heterogeneity in seed lots can be identified readily. Within the UPOV framework for granting of PBR, the markers have the potential to fulfil the requirements needed for implementation in DUS testing of candidate varieties and could complement or may be an alternative to the pathogenesis tests that are carried out at present.

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          The online version of this article (doi:10.1007/s00122-009-1183-2) contains supplementary material, which is available to authorized users.

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          An efficient procedure for genotyping single nucleotide polymorphisms.

          S. Ye (2001)
          Analysis of single nucleotide polymorphisms (SNPs) has been and will be increasingly utilized in various genetic disciplines, particularly in studying genetic determinants of complex diseases. Such studies will be facilitated by rapid, simple, low cost and high throughput methodologies for SNP genotyping. One such method is reported here, named tetra-primer ARMS-PCR, which employs two primer pairs to amplify, respectively, the two different alleles of a SNP in a single PCR reaction. A computer program for designing primers was developed. Tetra-primer ARMS-PCR was combined with microplate array diagonal gel electrophoresis, gaining the advantage of high throughput for gel-based resolution of tetra-primer ARMS-PCR products. The technique was applied to analyse a number of SNPs and the results were completely consistent with those from an independent method, restriction fragment length polymorphism analysis.
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            The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond.

            Emily Mueller, Helen J. Binns, Naama Menda … (2005)
            The SOL Genomics Network (SGN; http://sgn.cornell.edu) is a rapidly evolving comparative resource for the plants of the Solanaceae family, which includes important crop and model plants such as potato (Solanum tuberosum), eggplant (Solanum melongena), pepper (Capsicum annuum), and tomato (Solanum lycopersicum). The aim of SGN is to relate these species to one another using a comparative genomics approach and to tie them to the other dicots through the fully sequenced genome of Arabidopsis (Arabidopsis thaliana). SGN currently houses map and marker data for Solanaceae species, a large expressed sequence tag collection with computationally derived unigene sets, an extensive database of phenotypic information for a mutagenized tomato population, and associated tools such as real-time quantitative trait loci. Recently, the International Solanaceae Project (SOL) was formed as an umbrella organization for Solanaceae research in over 30 countries to address important questions in plant biology. The first cornerstone of the SOL project is the sequencing of the entire euchromatic portion of the tomato genome. SGN is collaborating with other bioinformatics centers in building the bioinformatics infrastructure for the tomato sequencing project and implementing the bioinformatics strategy of the larger SOL project. The overarching goal of SGN is to make information available in an intuitive comparative format, thereby facilitating a systems approach to investigations into the basis of adaptation and phenotypic diversity in the Solanaceae family, other species in the Asterid clade such as coffee (Coffea arabica), Rubiaciae, and beyond.
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              The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes.

              P. Zabel, Andrew S Milligan, Elizabeth Williamson … (1998)
              The Mi locus of tomato confers resistance to root knot nematodes. Tomato DNA spanning the locus was isolated as bacterial artificial chromosome clones, and 52 kb of contiguous DNA was sequenced. Three open reading frames were identified with similarity to cloned plant disease resistance genes. Two of them, Mi-1.1 and Mi-1.2, appear to be intact genes; the third is a pseudogene. A 4-kb mRNA hybridizing with these genes is present in tomato roots. Complementation studies using cloned copies of Mi-1.1 and Mi-1.2 indicated that Mi-1.2, but not Mi-1.1, is sufficient to confer resistance to a susceptible tomato line with the progeny of transformants segregating for resistance. The cloned gene most similar to Mi-1.2 is Prf, a tomato gene required for resistance to Pseudomonas syringae. Prf and Mi-1.2 share several structural motifs, including a nucleotide binding site and a leucine-rich repeat region, that are characteristic of a family of plant proteins, including several that are required for resistance against viruses, bacteria, fungi, and now, nematodes.
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                Author and article information

                Contributors
                : +31-317-481589 , +31-317-483457 , paul.arens@wur.nl
                Journal
                Journal ID (nlm-ta): Theor Appl Genet
                Title: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik
                Publisher: Springer-Verlag (Berlin/Heidelberg )
                ISSN (Print): 0040-5752
                ISSN (Electronic): 1432-2242
                Publication date (Electronic): 24 October 2009
                Publication date PMC-release: 24 October 2009
                Publication date (Print): February 2010
                Volume: 120
                Issue: 3
                Pages: 655-664
                Affiliations
                [1 ]Wageningen UR Plant Breeding, P.O. Box 16, 6700 AA Wageningen, The Netherlands
                [2 ]GEVES (Groupe d’Etude et de contrôle des Varietes Et des Semences), La Miniere, 78285 Guyancourt Cedex, France
                [3 ]INRA UR1052, Génétique et amélioration des fruits et légumes, INRA, Domaine Saint-Maurice, BP 94, 84143 Montfavet Cedex, France
                [4 ]Naktuinbouw, Postbus 40, Sotaweg 22, 2370 AA Roelofarendsveen, The Netherlands
                [5 ]Centro de ensayos de Valencia, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Calle Joaquin Ballester 39, 46009 Valencia, Spain
                [6 ]Center for Biotechnology and Genomics of Plants (UPM-INIA), INIA, Autopista A6 km 7, 28040 Madrid, Spain
                Author notes

                Communicated by A. Schulman.

                Article
                Publisher ID: 1183
                DOI: 10.1007/s00122-009-1183-2
                PMC ID: 2807934
                PubMed ID: 19855951
                SO-VID: 66ab7007-415f-44ed-9aee-8907ccfc0176
                Copyright © © The Author(s) 2009
                History
                Date received : 24 April 2009
                Date accepted : 6 October 2009
                Categories
                Subject: Original Paper
                Custom metadata
                issue-copyright-statement © Springer-Verlag 2010

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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