Twenty Years of Tomato Breeding at EPSO-UMH: Transfer Resistance from Wild Types to Local Landraces—From the First Molecular Markers to Genotyping by Sequencing (GBS)
Abstract
:1. Introduction
2. Genetic Variability Studies in Tomato
3. Molecular Markers in Variability Studies
3.1. Sequence Related Amplified Polymorphism (SRAP)
3.2. Simple Sequence Repeat (SSR)
3.3. Amplified Fragment Length Polymorphisms (AFLPs)
3.4. (GATA)4 Probes
3.5. Single Nucleotide Polymorphism (SNP)
4. Traditional Tomato Variety Breeding Program
5. Molecular Markers in Resistance Gene Introgression
5.1. CAPS Linked to the Sw-5 Gene
5.2. CAPS Linked to the Ty-1 Gene
5.3. CAPS Linked to the Tm-2a Gene
5.4. Other Examples of Tomato Breeding Programs with MAS (Marker-Assisted Selection)
6. Lines Obtained in the EPSO-UMH Breeding Program
7. Massive Genotyping
7.1. Genetic Association
7.2. Obtaining Plants with the Ty-1 Gene with Less Linkage Drag
8. Future Work
Acknowledgments
Author Contributions
Conflicts of Interest
References
- Ruíz, J.J.; García-Martínez, S. Tomato varieties ‘Muchamiel’ and ‘De la Pera’ form the southeast of Spain: Genetic improvement to promote on-farm conservation. In European Landrace: On-Farm Conservation, Management and Use. Biodiversity Technical Bulletin No 15; Vetelainen, M., Negri, V., Maxted, N., Eds.; Bioversity International: Rome, Italy, 2009; pp. 171–176. [Google Scholar]
- Picó, B.; Herraiz, J.; Ruiz, J.J.; Nuez, F. Widening the genetic basis of virus resistance in tomato. Sci. Hortic. 2002, 94, 73–89. [Google Scholar] [CrossRef]
- Nuez, F.; Roselló, S.; Picó, B. La conservación y recuperación de nuestro patrimonio hortícola. Mejorar para conservar. Agrícola Vergel 1998, 194, 74–80. [Google Scholar]
- Nuez, F.; Ruiz, J.J. La Biodiversidad Agrícola Valenciana: Estrategias Para su Conservación y Utilización; Universitat Politècnica de València: Valencia, Spain, 1999. [Google Scholar]
- Miller, J.C.; Tanksley, S.D. RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor. Appl. Genet. 1990, 80, 437–448. [Google Scholar] [CrossRef] [PubMed]
- Tanksley, S.D. The Genetic, Developmental, and Molecular Bases of Fruit Size and Shape Variation in Tomato. Plant Cell 2004, 16, S181–S189. [Google Scholar] [CrossRef] [PubMed]
- Ruiz, J.J.; Martínez, N.; Valero, M.; García-Martínez, S.; Moral, R.; Serrano, M. Micronutrient composition and quality characteristics of traditional tomato cultivars in the south-east of Spain. Commun. Soil Sci. Plant Anal. 2005, 36, 649–660. [Google Scholar] [CrossRef]
- Ruiz, J.J.; Alonso, A.; García-Martínez, S.; Valero, M.; Blasco, P.; Ruiz-Bevia, F. Quantitative analisys of flavour volatiles detects differences among closely related traditional cultivars of tomato. J. Sci. Food Agric. 2005, 85, 54–60. [Google Scholar] [CrossRef]
- Alonso, A.; García-Aliaga, R.; García-Martínez, S.; Ruiz, J.J.; Carbonell-Barrachina, A.A. Characterization of Spanish tomatoes using aroma composition anddiscriminant analisys. Food Sci. Technol. Int. 2009, 15, 47–55. [Google Scholar] [CrossRef]
- Smulders, M.J.M.; Bredemeijer, G.; Rus-Kortekaas, W.; Arens, P.; Vosman, B. Use of short microsatellites from database sequences to generate polymorphisms among Lycopersiconesculentum cultivars and accessions of other Lycopersicon species. Theor. Appl. Genet. 1997, 97, 264–272. [Google Scholar] [CrossRef]
- Alvarez, A.E.; Van de Wiwl, C.C.M.; Smulders, M.J.M.; Vosman, B. Use of microsatellites to evaluate genetic diversity and species relationships in the genus Lycopersicon. Theor. Appl. Genet. 2001, 103, 1283–1292. [Google Scholar] [CrossRef]
- Park, Y.H.; West, M.A.L.; St. Clair, D.A. Evaluation of AFLPs for germplasm fingerprinting and assessment of genetic diversity in cultivars of tomato (Lycopersicon esculentum L.). Genome 2004, 47, 510–518. [Google Scholar] [CrossRef] [PubMed]
- Bredemeijer, G.M.M.; Cooke, R.J.; Ganal, M.W.; Peeters, R.; Isaac, P.; Noordijk, Y.; Rendell, S.; Jackson, J.; Röder, M.S.; Wndehake, K.; et al. Construction and testing of a microsatellite database containing more than 500 tomato varieties. Theor. Appl. Genet. 2002, 105, 1019–1026. [Google Scholar] [PubMed]
- He, C.; Poysa, V.; Yu, K. Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theor. Appl. Genet. 2003, 106, 363–373. [Google Scholar] [CrossRef] [PubMed]
- Andreakis, N.; Giordano, I.; Pentangelo, A.; Fogliano, V.; Graziani, G.; Monti, L.M.; Rao, R. DNA fingerprinting and quality traits of Corbarino Cherry-like tomato landraces. J. Agric. Food Chem. 2004, 52, 3366–3371. [Google Scholar] [CrossRef] [PubMed]
- Rao, R.; Corrado, G.; Bianchi, M.; Di Mauro, A. (GATA)4 DNA fingerprinting identifies morphologically characterized San Marzano tomato plants. Plant Breed. 2006, 125, 173–176. [Google Scholar] [CrossRef]
- Li, G.; Quiros, C.F. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: Its application to mapping and gene tagging in Brassica. Theor. Appl. Genet. 2001, 103, 455–461. [Google Scholar] [CrossRef]
- Ruiz, J.J.; García-Martínez, S.; Picó, B.; Gao, M.; Quiros, C.F. Genetic variability and relationship of closely related Spanish traditional cultivars of tomato as detected by SRAP and SSR markers. J. Am. Soc. Hortic. Sci. 2005, 130, 88–94. [Google Scholar]
- Tautz, D. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 1989, 17, 6463–6471. [Google Scholar] [CrossRef] [PubMed]
- García-Martínez, S.; Andreani, L.; García-Gusano, M.; Geuna, F.; Ruiz, J.J. Evaluation of amplified fragment length polymorfism and simple sequence repeats for tomato germplasm fingerprinting: Utility for grouping closely related traditional cultivars. Genome 2006, 49, 648–656. [Google Scholar] [CrossRef] [PubMed]
- Vos, P.; Hogers, R.; Bleecker, M.; Reijans, M.; van de Lee, T.; Hornes, M. AFLP: A new technique for DNA fingerprinting. Nucleic Acid Res. 1995, 23, 4407–4414. [Google Scholar] [CrossRef] [PubMed]
- Kaemmer, D.; Weising, K.; Bayermann, B.; Borner, T.; Epplen, J.T.; Kahl, G. Oligonucleotide fingerprinting of tomatoDNA. Plant Breed. 1995, 114, 12–17. [Google Scholar] [CrossRef]
- Caramante, M.; Rao, R.; Monti, L.M.; Corrado, G. Discrimination of San Marzano accessions: A comparison of minisatellite, CAPS and SSR markers in relation to morphological traits. Sci. Hortic. 2009, 120, 560–564. [Google Scholar] [CrossRef]
- García-Martínez, S.; Corrado, G.; Ruiz, J.J.; Rao, R. Diversity and structure of a sample of traditional Italian and Spanish tomato accesions. Genet. Resour. Crop Evol. 2013, 60, 789–798. [Google Scholar] [CrossRef]
- Wang, D.G.; Fan, J.B.; Siao, C.J.; Berno, A.; Young, P.; Sapolsky, R.; Ghandour, G.; Perkins, N.; Winchester, E.; Spencer, J.; et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 1998, 280, 1077–1082. [Google Scholar] [CrossRef] [PubMed]
- García-Gusano, M. Empleo de Marcadores Moleculares Para el Estudio de la Variabilidad Intraespecífica en Tomate (Solanum lycopersicum L.). Ph.D. Thesis, Miguel Hernandez University, Elche, Spain, 2007. [Google Scholar]
- Le Corre, V.; Kremer, A. Genetic variability al neutral markers, quantitative trait loci and trait in a subdivided population under selection. Genetics 2003, 164, 1205–1219. [Google Scholar] [PubMed]
- Alexander, L.J. Transfer of a dominant type of resistanceto the four known Ohio pathogenic strains of tobacco mosaicvirus (TMV), from Lycopersicon peruvianum to L. esculentum. Phytopathology 1963, 53, 869. [Google Scholar]
- Stevens, M.R.; Scott, S.J.; Gergerich, R.C. Inheritance of a gene for resistance totomato spotted wilt virus (TSWV) from Lycopersicon peruvianum Mill. Euphytica 1992, 59, 9–17. [Google Scholar]
- Zamir, D.; Ekstein-Michelson, I.; Zakay, Y.; Navot, N.; Zeidan, M.; Safatti, M.; Eshed, Y.; Harel, E.; Pleban, T.; van-Oss, H.; et al. Mapping and introgression of a Tomato yellow leaf curl virus tolerante gene, TY-1. Theor. Appl. Genet. 1994, 88, 141–146. [Google Scholar] [CrossRef] [PubMed]
- Folkertsma, R.T.; Spassova, M.I.; Prins, M.; Stevens, M.R.; Hille, J.; Goldbach, R.W. Construction of a bacterial artificial chromosome (BAC) library of Lycopersicon esculentum cv. Stevens and its application to physically map the Sw-5 locus. Mol. Breed. 1999, 5, 197–207. [Google Scholar] [CrossRef]
- Rick, C.M.; Fobes, J.A. Association of an allozyme with nematodes resistance. Tomato Genet. Coop. Rep. 1974, 24, 25. [Google Scholar]
- Dax, E.; Livneh, O.; Aliskevicius, E.; Edelbaum, O.; Kedar, N.; Gavish, N.; Milo, J.; Geffen, F.; Blumenthal, A.; Rabinowich, H.D.; et al. A SCAR marker linked to the ToMV resistance gene, Tm-22, in tomato. Euphytica 1998, 101, 73–77. [Google Scholar] [CrossRef]
- Omori, T.; Murata, M.; Motoyoshi, F. Molecular characterization of the SCAR markers tightly linked to the Tm-2 locus of the genus Lycopersicon. Theor. Appl. Genet. 2000, 101, 64–69. [Google Scholar]
- Lanfermeijer, F.C.; Dijkhuis, J.; Sturre, M.J.G.; de Haan, P.; Hille, J. Cloning and characterization of the durable tomato mosaic virus resistance gene Tm-22 from Lycopersicon esculentum. Plant Mol. Biol. 2003, 52, 1037–1049. [Google Scholar] [CrossRef] [PubMed]
- Tanksley, S.D. Molecular markers in plant breeding. Plant Mol. Biol. Rep. 1983, 1, 3–8. [Google Scholar] [CrossRef]
- Foolad, M. Genome mapping and molecular breeding of tomato. Int. J. Plant Genom. 2007, 52, 64358. [Google Scholar] [CrossRef] [PubMed]
- Foolad, M.R.; Panthee, D.R. Marker-Assisted Selection in Tomato Breeding. Crit. Rev. Plant Sci. 2012, 31, 93–123. [Google Scholar] [CrossRef]
- García-Martínez, S.; Grau, A.; Alonso, A.; Rubio, F.; Valero, M.; Ruiz, J.J. UMH 1200, a breeding line within the Muchamiel tomato type resistant to three viruses. HortScience 2011, 46, 1054–1055. [Google Scholar]
- García-Martínez, S.; Grau, A.; Alonso, A.; Rubio, F.; Valero, M.; Ruiz, J.J. UMH 1203, a multiple virus-resistant fresh-market toamto breeding line for open-field conditions. HortScience 2012, 47, 124–125. [Google Scholar]
- Tanksley, S.D.; Bernachi, D.; BeckBunn, T.; Emmatty, D.; Eshed, Y.; Inai, S. Yield and quality evaluations on a pair of processing tomato lines nearly isogenic for the Tm2a gene for resistance to the Tobacco mosaic virus. Euphytica 1998, 99, 77–83. [Google Scholar] [CrossRef]
- Lewis, R.S.; Linger, L.R.; Wolff, M.F.; Wernsman, E.A. The negative influence of N-mediated TMV resistance on yield in tobacco: Linkage drag versus pleitropy. Theor. Appl. Genet. 2007, 115, 169–178. [Google Scholar] [CrossRef] [PubMed]
- Rubio, F.; Alonso, A.; García-Martínez, S.; Ruiz, J.J. Introgression of virus-resistance genes into traditional Spanish tomato cultivars (Solanum lycopersicum L.): Effects on yield and quality. Sci. Hortic. 2016, 198, 183–190. [Google Scholar] [CrossRef]
- García-Martínez, S.; Grau, A.; Alonso, A.; Rubio, F.; Valero, M.; Ruiz, J.J. UMH 1422 and UMH 1415: Two fresh-market tomato breeding lines resistant to Tomato Mosaic Virus and Tomato Spotted Wilt Virus. HortScience 2014, 49, 1465–1466. [Google Scholar]
- García-Martínez, S.; Grau, A.; Alonso, A.; Rubio, F.; Carbonell, P.; Ruiz, J.J. UMH 916, UMH 972, UMH 1093, UMH 1127 and UMH 1139: Four fresh-market breeding lines resistant to viruses within the Muchamiel tomato type. HortScience 2015, 50, 927–929. [Google Scholar]
- García-Martínez, S.; Grau, A.; Alonso, A.; Rubio, F.; Carbonell, P.; Ruiz, J.J. New breeding lines resistant to Tomato Mosaic Virus and Tomato Spotted Wilt Virus within the ‘De la Pera’ tomato type: UMH 1353 and UMH 1354. HortScience 2016, 51, 456–458. [Google Scholar]
- Alonso, A.; García-Martínez, S.; Arroyo, A.; García-Gusano, M.; Grau, A.; Giménez-Ros, M.; Romano, M.E.; Valero, M.; Ruiz, J.J. Efecto de la introducción de resistencia genética a TYLCV (gen Ty-1) en caracteresproductivos y de calidad en tomate. Actas Hortic. 2008, 51, 175–176. [Google Scholar]
- Sim, S.C.; Durstewitz, G.; Plieske, J.; Wieseke, R.; Ganal, M.W.; Van Deynze, A.; Hamilton, J.P.; Buell, C.R.; Causse, M.; Wijeratne, S.; et al. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS ONE 2012, 7, e40563. [Google Scholar] [CrossRef] [PubMed]
- Young, N.D.; Tanksley, S.D. RFLP analisys of the size of chromosomal segments retained around the TM-2 locus of tomato during backcross breeding. Theor. Appl. Genet. 1989, 77, 353–359. [Google Scholar] [CrossRef] [PubMed]
- Verlaan, M.G.; Szinay, D.; Hutton, S.F.; de Jong, H.; Kormelink, R.; Visser, G.F. Chromosomal rearrangements between tomato and Solanum chilense hamper mapping and breeding of the TYLCV resistance gene Ty-1. Plant J. 2011, 68, 1093–1103. [Google Scholar] [CrossRef] [PubMed]
- Hutton, S.F.; Scott, J.W.; Schuster, D.J. Recessive Resistance to Tomato yellow leaf curl virus from the Tomato Cultivar Tyking is located in the Same Region as Ty-5 on Chromosome 4. HortScience 2012, 47, 324–327. [Google Scholar]
- Pereira-Carvalho, R.C.; Díaz-Pendón, J.A.; Fonseca, M.E.N.; Boiteux, L.S.; Fernández-Muñoz, R.; Moriones, E.; Resende, R.O. Recessive Resistance Derived from Tomato cv. Tyking-Limits Drastically the Spread of Tomato Yellow Leaf Curl Virus. Viruses 2015, 7, 2518–2533. [Google Scholar] [CrossRef] [PubMed]
Marker | Number | Number of Bands | % of Polymorphic Bands | Usability |
---|---|---|---|---|
SRAP | 26 | 384 | 60 | Distinguish between cultivar types, wild relatives and 14 of 16 traditional cultivars studied |
SSR | 10 + 9 | 77 | 98 | Distinguish between cultivar types, wild relatives and 23 of 34 traditional cultivars studied |
AFLP | 7 | 470 | 40 | Distinguish between cultivar types, wild relatives and 24 of 31 traditional cultivars studied |
(GATA)4 | N.A. | 30 | 100 | Distinguish between cultivar types, Spanish traditional cultivars and 4 of 10 Italian traditional cultivars studied |
SNP | 41 | N.A. | 76 | Distinguish traditional cultivars from modern cultivars, hybrids and wild relatives |
Breeding Program | Coordinators | Traits |
---|---|---|
University of Florida (USA) | J.W. Scott and S.F. Hutton | Fusarium oxysporum f. sp. lycopersici, Verticillium dahliae, Stemphyllium solani, TSWV, TYLCV |
University of North Carolina (USA) | R.G. Gardner | Fusarium oxysporum f. sp. lycopersici, Verticillium dahliae, Alternaria solani, TSWV |
United States Department of Agriculture (ARS) | J.R. Stommel | Beta carotene content |
Ohio State University (USA) | M. Francis | Xanthomonas euvesicatoria |
Varietal Type | Line | Resistance | Sent to Registry | Title Obtained |
---|---|---|---|---|
ToMV-TYLCV-TSWV | ||||
Muchamiel | UMH 1200 | RR-RR-RR | 2011 | 2013 |
Muchamiel | UMH 1139 | RR-ss-RR | 2013 | 2017 |
Muchamiel | UMH 1101xIF | Rs-Rs-Rs | 2014 | 2017 |
De la pera | UMH 1203 | RR-RR-RR | 2011 | 2013 |
De la pera | UMH 1422 | RR-ss-ss | 2013 | 2017 |
De la pera | UMH 1415 | RR-ss-RR | 2013 | 2017 |
De la pera | UMH 1353 | RR-ss-RR | 2013 | 2017 |
De la pera | UMH 1354 | RR-ss-RR | 2013 | 2017 |
© 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Carbonell, P.; Alonso, A.; Grau, A.; Salinas, J.F.; García-Martínez, S.; Ruiz, J.J. Twenty Years of Tomato Breeding at EPSO-UMH: Transfer Resistance from Wild Types to Local Landraces—From the First Molecular Markers to Genotyping by Sequencing (GBS). Diversity 2018, 10, 12. https://doi.org/10.3390/d10010012
Carbonell P, Alonso A, Grau A, Salinas JF, García-Martínez S, Ruiz JJ. Twenty Years of Tomato Breeding at EPSO-UMH: Transfer Resistance from Wild Types to Local Landraces—From the First Molecular Markers to Genotyping by Sequencing (GBS). Diversity. 2018; 10(1):12. https://doi.org/10.3390/d10010012
Chicago/Turabian StyleCarbonell, Pedro, Aranzazu Alonso, Adrián Grau, Juan Francisco Salinas, Santiago García-Martínez, and Juan José Ruiz. 2018. "Twenty Years of Tomato Breeding at EPSO-UMH: Transfer Resistance from Wild Types to Local Landraces—From the First Molecular Markers to Genotyping by Sequencing (GBS)" Diversity 10, no. 1: 12. https://doi.org/10.3390/d10010012
APA StyleCarbonell, P., Alonso, A., Grau, A., Salinas, J. F., García-Martínez, S., & Ruiz, J. J. (2018). Twenty Years of Tomato Breeding at EPSO-UMH: Transfer Resistance from Wild Types to Local Landraces—From the First Molecular Markers to Genotyping by Sequencing (GBS). Diversity, 10(1), 12. https://doi.org/10.3390/d10010012