High Density Molecular Linkage Maps of the Tomato and Potato Genomes

INVESTIGATIONS

High Density Molecular Linkage Maps of the Tomato and Potato Genomes

S. D. Tanksley, M. W. Ganal, J. P. Prince, M. C. de-Vicente, M. W. Bonierbale, P. Broun, T. M. Fulton, J. J. Giovannoni, S. Grandillo, G. B. Martin, R. Messeguer, J. C. Miller, L. Miller, A. H. Paterson, O. Pineda, M. S. Roder, R. A. Wing, W. Wu and N. D. Young
Department of Plant Breeding and Biometry, Cornell University, Ithaca, New York 14853

High density molecular linkage maps, comprised of more than 1000 markers with an average spacing between markers of approximately 1.2 cM (ca. 900 kb), have been constructed for the tomato and potato genomes. As the two maps are based on a common set of probes, it was possible to determine, with a high degree of precision, the breakpoints corresponding to 5 chromosomal inversions that differentiate the tomato and potato genomes. All of the inversions appear to have resulted from single breakpoints at or near the centromeres of the affected chromosomes, the result being the inversion of entire chromosome arms. While the crossing over rate among chromosomes appears to be uniformly distributed with respect to chromosome size, there is tremendous heterogeneity of crossing over within chromosomes. Regions of the map corresponding to centromeres and centromeric heterochromatin, and in some instances telomeres, experience up to 10-fold less recombination than other areas of the genome. Overall, 28% of the mapped loci reside in areas of putatively suppressed recombination. This includes loci corresponding to both random, single copy genomic clones and transcribed genes (detected with cDNA probes). The extreme heterogeneity of crossing over within chromosomes has both practical and evolutionary implications. Currently tomato and potato are among the most thoroughly mapped eukaryotic species and the availability of high density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies in these two important and well studied crop species.

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				D.-H. Koo, S.-H. Jo, J.-W. Bang, H.-M. Park, S. Lee, and D. Choi Integration of Cytogenetic and Genetic Linkage Maps Unveils the Physical Architecture of Tomato Chromosome 2 Genetics, July 1, 2008; 179(3): 1211 - 1220. [Abstract] [Full Text] [PDF]

				M. Troggio, S. Vezzulli, M. Pindo, G. Malacarne, P. Fontana, F. M. Moreira, L. Costantini, M. S. Grando, R. Viola, and R. Velasco ASEV Honorary Research Lecture 2007: Beyond the Genome, Opportunities for a Modern Viticulture: A Research Overview Am. J. Enol. Vitic., June 1, 2008; 59(2): 117 - 127. [Abstract] [Full Text] [PDF]

				C. S. Barry, R. P. McQuinn, M.-Y. Chung, A. Besuden, and J. J. Giovannoni Amino Acid Substitutions in Homologs of the STAY-GREEN Protein Are Responsible for the green-flesh and chlorophyll retainer Mutations of Tomato and Pepper Plant Physiology, May 1, 2008; 147(1): 179 - 187. [Abstract] [Full Text] [PDF]

				L. A. Mueller, A. A. Mills, B. Skwarecki, R. M. Buels, N. Menda, and S. D. Tanksley The SGN comparative map viewer Bioinformatics, February 1, 2008; 24(3): 422 - 423. [Abstract] [Full Text] [PDF]

				T. Stadler, U. Arunyawat, and W. Stephan Population Genetics of Speciation in Two Closely Related Wild Tomatoes (Solanum Section Lycopersicon) Genetics, January 1, 2008; 178(1): 339 - 350. [Abstract] [Full Text] [PDF]

				C. Chen, Q. Yu, S. Hou, Y. Li, M. Eustice, R. L. Skelton, O. Veatch, R. E. Herdes, L. Diebold, J. Saw, et al. Construction of a Sequence-Tagged High-Density Genetic Map of Papaya for Comparative Structural and Evolutionary Genomics in Brassicales Genetics, December 1, 2007; 177(4): 2481 - 2491. [Abstract] [Full Text] [PDF]

				Y. Bai and P. Lindhout Domestication and Breeding of Tomatoes: What have We Gained and What Can We Gain in the Future? Ann. Bot., October 1, 2007; 100(5): 1085 - 1094. [Abstract] [Full Text] [PDF]

				U. Arunyawat, W. Stephan, and T. Stadler Using Multilocus Sequence Data to Assess Population Structure, Natural Selection, and Linkage Disequilibrium in Wild Tomatoes Mol. Biol. Evol., October 1, 2007; 24(10): 2310 - 2322. [Abstract] [Full Text] [PDF]

				K. Ishibashi, K. Masuda, S. Naito, T. Meshi, and M. Ishikawa An inhibitor of viral RNA replication is encoded by a plant resistance gene PNAS, August 21, 2007; 104(34): 13833 - 13838. [Abstract] [Full Text] [PDF]

				S.-B. Chang, L. K. Anderson, J. D. Sherman, S. M. Royer, and S. M. Stack Predicting and Testing Physical Locations of Genetically Mapped Loci on Tomato Pachytene Chromosome 1 Genetics, August 1, 2007; 176(4): 2131 - 2138. [Abstract] [Full Text] [PDF]

				M. Troggio, G. Malacarne, G. Coppola, C. Segala, D. A. Cartwright, M. Pindo, M. Stefanini, R. Mank, M. Moroldo, M. Morgante, et al. A Dense Single-Nucleotide Polymorphism-Based Genetic Linkage Map of Grapevine (Vitis vinifera L.) Anchoring Pinot Noir Bacterial Artificial Chromosome Contigs Genetics, August 1, 2007; 176(4): 2637 - 2650. [Abstract] [Full Text] [PDF]

				J. M. Blanca, J. Prohens, G. J. Anderson, E. Zuriaga, J. Canizares, and F. Nuez AFLP and DNA sequence variation in an Andean domesticate, pepino (Solanum muricatum, Solanaceae): implications for evolution and domestication Am. J. Botany, July 1, 2007; 94(7): 1219 - 1229. [Abstract] [Full Text] [PDF]

				C. M. Jones, C. M. Rick, D. Adams, J. Jernstedt, and R. T. Chetelat Genealogy and fine mapping of obscuravenosa, a gene affecting the distribution of chloroplasts in leaf veins, and evidence of selection during breeding of tomatoes (Lycopersicon esculentum; Solanaceae) Am. J. Botany, June 1, 2007; 94(6): 935 - 947. [Abstract] [Full Text] [PDF]

				T.-H. Park, J.-B. Kim, R. C. B. Hutten, H. J. van Eck, E. Jacobsen, and R. G. F. Visser Genetic Positioning of Centromeres Using Half-Tetrad Analysis in a 4x-2x Cross Population of Potato Genetics, May 1, 2007; 176(1): 85 - 94. [Abstract] [Full Text] [PDF]

				R. Stevens, M. Buret, P. Duffe, C. Garchery, P. Baldet, C. Rothan, and M. Causse Candidate Genes and Quantitative Trait Loci Affecting Fruit Ascorbic Acid Content in Three Tomato Populations Plant Physiology, April 1, 2007; 143(4): 1943 - 1953. [Abstract] [Full Text] [PDF]

				L. C. Moyle Comparative Genetics of Potential Prezygotic and Postzygotic Isolating Barriers in a Lycopersicon Species Cross J. Hered., March 1, 2007; 98(2): 123 - 135. [Abstract] [Full Text] [PDF]

				F. G.P. Lhuissier, H. H. Offenberg, P. E. Wittich, N. O.E. Vischer, and C. Heyting The Mismatch Repair Protein MLH1 Marks a Subset of Strongly Interfering Crossovers in Tomato PLANT CELL, March 1, 2007; 19(3): 862 - 876. [Abstract] [Full Text] [PDF]

				L. E. Rose, R. W. Michelmore, and C. H. Langley Natural Variation in the Pto Disease Resistance Gene Within Species of Wild Tomato (Lycopersicon). II. Population Genetics of Pto Genetics, March 1, 2007; 175(3): 1307 - 1319. [Abstract] [Full Text] [PDF]

				M. A. Canady, Y. Ji, and R. T. Chetelat Homeologous Recombination in Solanum lycopersicoides Introgression Lines of Cultivated Tomato Genetics, December 1, 2006; 174(4): 1775 - 1788. [Abstract] [Full Text] [PDF]

				L. Timms, R. Jimenez, M. Chase, D. Lavelle, L. McHale, A. Kozik, Z. Lai, A. Heesacker, S. Knapp, L. Rieseberg, et al. Analyses of Synteny Between Arabidopsis thaliana and Species in the Asteraceae Reveal a Complex Network of Small Syntenic Segments and Major Chromosomal Rearrangements Genetics, August 1, 2006; 173(4): 2227 - 2235. [Abstract] [Full Text] [PDF]

				N. Galpaz, G. Ronen, Z. Khalfa, D. Zamir, and J. Hirschberg A Chromoplast-Specific Carotenoid Biosynthesis Pathway Is Revealed by Cloning of the Tomato white-flower Locus PLANT CELL, August 1, 2006; 18(8): 1947 - 1960. [Abstract] [Full Text] [PDF]

				S. Ruffel, J.-L. Gallois, B. Moury, C. Robaglia, A. Palloix, and C. Caranta Simultaneous mutations in translation initiation factors eIF4E and eIF(iso)4E are required to prevent pepper veinal mottle virus infection of pepper J. Gen. Virol., July 1, 2006; 87(7): 2089 - 2098. [Abstract] [Full Text] [PDF]

				T. Nakazato, M.-K. Jung, E. A. Housworth, L. H. Rieseberg, and G. J. Gastony Genetic Map-Based Analysis of Genome Structure in the Homosporous Fern Ceratopteris richardii Genetics, July 1, 2006; 173(3): 1585 - 1597. [Abstract] [Full Text] [PDF]

				H. van Os, S. Andrzejewski, E. Bakker, I. Barrena, G. J. Bryan, B. Caromel, B. Ghareeb, E. Isidore, W. de Jong, P. van Koert, et al. Construction of a 10,000-Marker Ultradense Genetic Recombination Map of Potato: Providing a Framework for Accelerated Gene Isolation and a Genomewide Physical Map Genetics, June 1, 2006; 173(2): 1075 - 1087. [Abstract] [Full Text] [PDF]

				C. Li, J. Zhao, H. Jiang, X. Wu, J. Sun, C. Zhang, X. Wang, Y. Lou, and C. Li The Wound Response Mutant suppressor of prosystemin-mediated responses6 (spr6) is a Weak Allele of the Tomato Homolog of CORONATINE-INSENSITIVE1 (COI1) Plant Cell Physiol., May 1, 2006; 47(5): 653 - 663. [Abstract] [Full Text] [PDF]

				Y. Wang, X. Tang, Z. Cheng, L. Mueller, J. Giovannoni, and S. D. Tanksley Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome Genetics, April 1, 2006; 172(4): 2529 - 2540. [Abstract] [Full Text] [PDF]

				K. M. Devos, J. Ma, A. C. Pontaroli, L. H. Pratt, and J. L. Bennetzen Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat PNAS, December 27, 2005; 102(52): 19243 - 19248. [Abstract] [Full Text] [PDF]

				H. Yan, W. Jin, K. Nagaki, S. Tian, S. Ouyang, C. R. Buell, P. B. Talbert, S. Henikoff, and J. Jiang Transcription and Histone Modifications in the Recombination-Free Region Spanning a Rice Centromere PLANT CELL, December 1, 2005; 17(12): 3227 - 3238. [Abstract] [Full Text] [PDF]

				J. F. HANCOCK Contributions of Domesticated Plant Studies to our Understanding of Plant Evolution Ann. Bot., November 1, 2005; 96(6): 953 - 963. [Abstract] [Full Text] [PDF]