Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex

Genome

Volumn 57, Issue 3, 2014, Pages 169-180

  Labate, Joanne A ^a   Robertson, Larry D ^a   Strickler, Susan R ^b   Mueller, Lukas A ^b  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b Boyce Thompson Institute for Plant Research   (United States)

Author keywords

Genotyping by sequencing; Geographic information systems; Population genetics; Selection; Single nucleotide polymorphism

Indexed keywords

CLASSIFICATION; GENETIC SELECTION; GENETICS; PHYLOGENY; PHYLOGEOGRAPHY; PLANT GENOME; REPRODUCTIVE ISOLATION; SINGLE NUCLEOTIDE POLYMORPHISM; SOLANUM; SPECIES DIFFERENTIATION;

GENETIC SPECIATION; GENOME, PLANT; PHYLOGENY; PHYLOGEOGRAPHY; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCTIVE ISOLATION; SELECTION, GENETIC; SOLANUM;

EID: 84901757045     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/gen-2014-0003     Document Type: Article

References (70)

1. Anderson L.K. Covey P.A. Larsen L.R. Bedinger P. Stack S.M. 2010. Structural differences in chromosomes distinguish species in the tomato clade. Cytogenet. Genome Res. 129: 24-34. 10.1159/000313850.
2. ST-outlier method. BMC Bioinform. 9 (1): 323. 10.1186/1471-2105-9-323.
3. Arumuganathan K. Earle E.D. 1991. Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9: 208-218. 10.1007/BF02672069.
4. Arunyawat U. Stephan W. Städler T. 2007. Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes. Mol. Biol. Evol. 24: 2310-2322. 10.1093/molbev/msm162. 17675653.
5. Baird N.A. Etter P.D. Atwood T.S. Currey M.C. Shiver A.L. Lewis Z.A. et al 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PloS ONE, 3: e3376. 10.1371/journal.pone.0003376. 18852878.
6. Baldo A.M. Francis D.M. Caramante M. Robertson L.D. Labate J.A. 2011. AlleleCoder: a PERL script for coding co-dominant polymorphism data for PCA analysis. Plant Genet. Resour. 9: 528-530. 10.1017/S1479262111000839.
7. Barrett T. Clark K. Gevorgyan R. Gorelenkov V. Gribov E. Karsch-Mizrachi I. et al 2012. BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res. 40 (D1): D57-D63. 10.1093/nar/gkr1163. PMID: 22139929.
8. Beaumont M.A. Balding D.J. 2004. Identifying adaptive genetic divergence among populations from genome scans. Mol. Ecol. 13: 969-980. 10.1111/j.1365-294X.2004.02125.x. 15012769.
9. Beaumont M.A. Nichols R.A. 1996. Evaluating loci for use in the genetic analysis of population structure. Proc. R. Soc. B Biol. Sci. 263: 1619-1626. 10.1098/rspb.1996.0237.
10. Bombarely A. Menda N. Tecle I.Y. Buels R.M. Strickler S. Fischer-York T. et al 2011. The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res. 39 (s1): D1149-1155. 10.1093/nar/gkq866.
11. Bradbury P.J. Zhang Z. Kroon D.E. Casstevens T.M. Ramdoss Y. Buckler E.S. 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 23: 2633-2635. 10.1093/bioinformatics/btm308. 17586829.
12. Bukowski, R., Sun, Q., Howard, M., and Pillardy, J. 2010. BioHPC: computational biology application suite for high performance computing. J. Biomol. Tech. 21 (3 Suppl.): S23.
13. Earl D.A. von Holdt B.M. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Res. 4: 359-361. 10.1007/s12686-011-9548-7.
14. Efron, B., and Tibshirani, R. 1993. An introduction to the bootstrap. Chapman and Hall, New York.
15. Elshire R.J. Glaubitz J.C. Sun Q. Poland J.A. Kawamoto K. Buckler E.S. Mitchell S.E. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6: e19379. 10.1371/journal.pone.0019379. 21573248.
16. Evanno G. Regnaut S. Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611-2620. 10.1111/j.1365-294X.2005.02553.x. 15969739.
17. Foolad M. Panthee D. 2012. Marker-assisted selection in tomato breeding. Crit. Rev. Plant Sci. 31: 93-123. 10.1080/07352689.2011.616057.
18. Glaubitz J.C. Casstevens T.M. Lu F. Harriman J. Elshire R.J. Sun Q. Buckler E.S. 2014. TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS ONE, 9: e90346. 10.1371/journal.pone.0090346. 24587335.
19. Grills, G., Schweitzer, P., Sun, Q., Pillardy, J., Wang, W., Stelick, T., et al. 2011. Integrated core facility support and optimization of next generation sequencing technologies. J. Biomol. Tech. 22 (Suppl.): S32.
20. Hardy O.J. Vekemans X. 2002. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes, 2: 618-620. 10.1046/j.1471-8286.2002.00305.x.
21. Hill, R. 2012. Tomato genome sequence bears fruit. Nature News, 10.1038/nature.2012.10751.
22. Howell, D. 2001. Resampling procedures, ver. 1.3 [online]. Available from http://www.uvm.edu/~dhowell/StatPages/Resampling/Resampling.html [accessed 29 October 2013].
23. Kharkongar, H.P., Khanna, V.K., Tyagi, W., Rai, M., and Meetei, N.T. 2013. Wide hybridization and embryo-rescue for crop improvement in Solanum. Agrotechnology, S11: 004.
24. Labate J.A. Robertson L.D. 2012. Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles. BMC Plant Biol. 12: 133. 10.1186/1471-2229-12-133. 22871151.
25. Li H. Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25: 1754-1760. 10.1093/ bioinformatics/btp324. 19451168.
26. Maloney P.E. Vogler D.R. Eckert A.J. Jensen C.E. Neale D.B. 2011. Population biology of sugar pine (Pinus lambertiana Dougl.) with reference to historical disturbances in the Lake Tahoe basin: implications for restoration. For. Ecol. Manage. 262: 770-779. 10.1016/j.foreco.2011.05.011.
27. McClean P.E. Hanson M.R. 1986. Mitochondrial DNA sequence divergence among Lycopersicon and related Solanum species. Genetics, 112: 649-667. 17246320.
28. Merino Méndez, C.G. 2009. Population genetic approaches to speciation of wild tomatoes with special reference to Solanum habrochaites and S. arcanum. Ph.D. dissertation, Ludwig-Maximilians-Universität, München. pp. 119.
29. Miller J.C. Tanksley S.D. 1990. RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor. Appl. Genet. 80: 437-448. 10.1007/BF00226743. 24221000.
30. Miller M.R. Dunham J.P. Amores A. Cresko W.A. Johnson E.A. 2007. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 17: 240-248. 10.1101/gr.5681207. 17189378.
31. Nakazato T. Warren D.L. Moyle L.C. 2010. Ecological and geographic modes of species divergence in wild tomatoes. Am. J. Bot. 97: 680-693. 10.3732/ajb.0900216. 21622430.
32. Nakazato T. Franklin R.A. Kirk B.C. Housworth E.A. 2012. Population structure, demographic history, and evolutionary patterns of a green-fruited tomato, Solanum peruvianum (Solanaceae), revealed by spatial genetics analyses. Am. J. Bot. 99: 1207-1216. 10.3732/ajb.1100210. 22711557.
33. Nesbitt T.C. Tanksley S.D. 2002. Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics, 162: 365-379. 12242247.
34. Palmer J.D. Zamir D. 1982. Chloroplast DNA evolution and phylogenetic relationships in Lycopersicon. Proc. Natl. Acad. Sci. U.S.A. 79: 5006-5010. 10.1073/pnas.79.16.5006. 16593219.
35. Peralta I.E. Spooner D.M. 2001. Granule-bound starch synthase (GBSSI) gene phylogeny of wild tomatoes (Solanum L. section Lycopersicon [Mill] Wettst. subsection Lycopersicon). Am. J. Bot. 88: 1888-1902. 10.2307/3558365. 21669622.
36. Peralta I.E. Spooner D.M. 2005. Morphological characterization and relationships of wild tomatoes (Solanum L. section Lycopersicon). Monogr. Syst. Bot. Mo. Bot. Gard. 104: 227-257.
37. Peralta I.E. Knapp S. Spooner D.M. 2005. New species of wild tomatoes (Solanum section Lycopersicon: Solanaceae) from northern Peru. Syst. Bot. 30: 424-434. 10.1600/0363644054223657.
38. Peralta I.E. Knapp S. Spooner D. 2008. The taxonomy of tomatoes: a revision of wild tomatoes (Solanum section Lycopersicon) and their outgroup relatives (Solanum sections Juglandifolium and Lycopersicoides). Syst. Bot. Monogr. 84: 1-186.
39. Pickrell J.K. Pritchard J.K. 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8: e1002967. 10.1371/journal.pgen.1002967. 23166502.
40. Poysa V. 1990. The development of bridge lines for interspecific gene transfer between Lycopersicon esculentum and L. peruvianum. Theor. Appl. Genet. 79: 187-192. 10.1007/BF00225950. 24226217.
41. Pritchard J.K. Stephens M. Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155: 945-959. 10835412.
42. Purcell S. Neale B. Todd-Brown K. Thomas L. Ferreira M.A.R. Bender D. et al 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am. J. Hum. Genet. 81: 559-575. 10.1086/519795. 17701901.
43. Raymond M. Rousset F. 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered. 86: 248-249.
44. Reich D. Thangaraj K. Patterson N. Price A.L. Singh L. 2009. Reconstructing Indian population history. Nature, 461: 489-494. 10.1038/nature08365. 19779445.
45. Rick C.M. 1963. Barriers to interbreeding in Lycopersicon peruvianum. Evolution, 17: 216-232. 10.2307/2406467.
46. Rick, C.M. 1979 a. Biosystematic studies in Lycopersicon and closely related species of Solanum. In The biology and taxonomy of the Solanaceae. Edited by J.G. Hawkes, R.N. Lester, and A.D. Skelding. Linnean Soc. Symp. Ser. No. 7, Academic Press, NY. pp. 667-678.
47. Rick, C.M.P. 1979 b. Evolution of interspecific barriers in Lycopersicon. In Proceedings of the conference broadening the genetic base of crops. Wageningen, the Netherlands. pp. 283-286.
48. Rick, C.M. 1982. The potential of exotic germplasm for tomato improvement. In Plant improvement and somatic cell genetics. Edited by I.K. Vasil, W.R. Scowcroft, and K.J. Frey. Academic Press, NY. pp. 1-28.
49. Rick, C.M. 1983. Tomato (Lycopersicon). In Isozymes in plant genetics and breeding, Part B. Edited by S.D. Tanksley and T.J. Orton. Elsevier Science, Amsterdam. pp. 147-165.
50. Rick, C.M. 1986. Reproductive isolation in the Lycopersicon peruvianum complex. In Solanaceae, biology and systematics. Edited by W.G. D'Arcy. Columbia University Press, NY. pp. 477-495.
51. Rick C.M. 1991. Tomato resources of South America reveal many genetic treasures. Diversity, 7: 54-56.
52. Rick C.M. Fobes J.F. 1974. Association of an allozyme with nematode resistance. Tomato Genet. Coop. Rep. 24: 25.
53. Rick C.M. Kesicki E. Fobes J.F. Holle M. 1976. Genetic and biosystematic studies on two new sibling species of Lycopersicon from interandean Peru. Theor. Appl. Genet. 47: 55-68. 24414383.
54. Rodriguez F. Wu F. Ané C. Tanksley S. Spooner D.M. 2009. Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? BMC Evol. Biol. 9: 191. 10.1186/1471-2148-9- 191. 19664206.
55. Rosenberg N.A. 2004. DISTRUCT: a program for the graphical display of population structure. Mol. Ecol. Notes, 4: 137-138. 10.1046/j.1471-8286.2003. 00566.x.
56. Rousset F. 2000. Genetic differentiation between individuals. J. Evol. Biol. 13: 58-62. 10.1046/j.1420-9101.2000.00137.x.
57. Rousset F. 2008. genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Mol. Ecol. Resour. 8: 103-106. 10.1111/j.1471-8286.2007.01931.x. 21585727.
58. Sacks E.J. Gerhardt L.M. Graham E.B. Jacobs J. Thorrup T.A. St. Clair D.A. 1997. Variation among 41 genotypes of tomato (Lycopersicon esculentum Mill.) for crossability to L. peruvianum (L.) Mill. Ann. Bot. 80: 469-477.
59. Sayers E.W. Barrett T. Benson D.A. Bolton E. Bryant S.H. Canese K. et al 2011. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 39 (Suppl. 1): D38-D51. 10.1093/nar/gkn741.
60. Shirasawa K. Hirakawa H. 2013. DNA marker applications to molecular genetics and genomics in tomato. Breed. Sci. 63: 21-30. 10.1270/jsbbs.63.21. 23641178.
61. Spooner D.M. Peralta I.E. Knapp S. 2005. Comparison of AFLPs with other markers for phylogenetic inference in wild tomatoes [ Solanum L section Lycopersicon (Mill.) Wettst. subsection Lycopersicon ]. Taxon, 54: 43-61.
62. Storz J.F. 2005. Using genome scans of DNA polymorphism to infer adaptive population divergence. Mol. Ecol. 14: 671-688. 10.1111/j.1365-294X.2005.02437. x. 15723660.
63. Sumner J. Rousset F. Estoup A. Moritz C. 2001. 'Neighbourhood' size, dispersal and density estimates in the prickly forest skink (Gnypetoscincus queenslandiae) using individual genetic and demographic methods. Mol. Ecol. 10: 1917-1927. 10.1046/j.0962-1083.2001.01337.x. 11555236.
64. Tanksley S.D. Rick C.M. 1980. Isozymic gene linkage map of the tomato: applications in genetics and breeding. Theor. Appl. Genet. 58: 161-170. 10.1007/BF00279708. 24301284.
65. Taylor I.B. Al-Kummer M.K. 1982. The formation of complex hybrids between Lycopersicon esculentum and L. peruvianum, and their potential use in promoting interspecific gene transfer. Theor. Appl. Genet. 61: 59-63. 10.1007/BF00261511.
66. Tellier A. Fischer I. Merino C. Xia H. Camus-Kulandaivelu L. Städler T. Stephan W. 2011. Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure. Heredity, 107: 189-199. 10.1038/hdy.2010.175. 21245893.
67. The Tomato Genome Consortium 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485: 635-641. 10.1038/nature11119. 22660326.
68. Vincent H. Wiersema J. Kell S. Fielder H. Dobbie S. Castañeda- Álvarez N.P. et al 2013. A prioritized crop wild relative inventory to help underpin global food security. Biol. Conserv. 167: 265-275. 10.1016/j.biocon.2013.08.011.
69. Xia H. Camus-Kulandaivelu L. Stephan W. Tellier A. Zhang Z. 2010. Nucleotide diversity patterns of local adaptation at drought-related candidate genes in wild tomatoes. Mol. Ecol. 19: 4144-4154. 10.1111/j.1365-294X.2010. 04762.x.
70. Zuriaga E. Blanca J. Nuez F. 2009. Classification and phylogenetic relationships in Solanum section Lycopersicon based on AFLP and two nuclear gene sequences. Genet. Resour. Crop Evol. 56: 663-678. 10.1007/s10722-008-9392-0.