Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens

Annals of Botany

Volumn 105, Issue 4, 2010, Pages 535-554

  Albrecht, Elena ^a,c   Escobar, Miguel ^b   Chetelat, Roger T ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CHILE   (Chile)

^c KEYGENE N V   (Netherlands)

Author keywords

Allozymes; Biogeography; Genetic diversity; Microsatellites; Solanum chilense; Solanum lycopersicoides; Solanum section Lycopersicoides; Solanum sitiens; Tomato

Indexed keywords

LYCOPERSICON CHILENSE; LYCOPERSICON ESCULENTUM; SOLANUM; SOLANUM LYCOPERSICOIDES; SOLANUM SITIENS;

MICROSATELLITE DNA;

ALLELE; ARGENTINA; ARTICLE; GENE FLOW; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; PHYLOGENY; POPULATION DYNAMICS; POPULATION GENETICS; SOLANUM; TOMATO;

ALLELES; ARGENTINA; GENE FLOW; GENE FREQUENCY; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; LINKAGE DISEQUILIBRIUM; LYCOPERSICON ESCULENTUM; MICROSATELLITE REPEATS; PHYLOGENY; POPULATION DYNAMICS; SOLANUM;

EID: 77953925302     PISSN: 03057364     EISSN: 10958290     Source Type: Journal    
DOI: 10.1093/aob/mcq009     Document Type: Article

References (81)

1. Allendorf FW. 1983. Isolation, gene flow and genetic differentiation among populations. In: Schonewalk-Cox CM, Chambers SM, MacBryde B, Thomas L. eds. Genetics and conservation. London: Benjamin/ Cummings, 51-65.
2. Alvarez AE, van de Wiel CCM, Smulders MJM, Vosman B. 2001. Use of microsatellites to evaluate genetic diversity and species relationships in the genus Lycopersicon. Theoretical and Applied Genetics 103: 1283-1292.
3. Avise JC. 2004. Molecular markers, natural history, and evolution. Sunderland, MA: Sinauer Associates, Inc. Publishers.
4. Barton NH, Slatkin M. 1986. A quasi-equilibrium theory of the distribution of rare alleles in a subdivided population. Heredity 56: 409-416.
5. Baudry E, Kerdelhue C, Innan H, Stephan W. 2001. Species and recombination effects on DNA variability in the tomato genus. Genetics 158: 1725-1735.
6. Bindler G, van der Hoeven R, Gunduz I, et al. 2007. A microsatellite marker based linkage map of tobacco. Theoretical and Applied Genetics 114: 341-349.
7. Breto MP, Asins MJ, Carbonell EA. 1993. Genetic variability in Lycopersicon species and their genetic relationships. Theoretical and Applied Genetics 86: 113-120.
8. Caicedo AL, Schaal BA. 2004. Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Molecular Ecology 13: 1871-1882.
9. Canady MA, Meglic V, Chetelat RT. 2005. A library of Solanum lycopersicoides introgression lines in cultivated tomato. Genome 48: 685-697.
10. Cavalli-Sforza LL, Edwards AWF. 1967. Phylogenetic analysis: models and estimation procedures. Evolution 32: 550-570.
11. Chetelat RT, Cisneros P, Stamova L, Rick CM. 1997. A male-fertile Lycopersicon esculentum - Solanum lycopersicoides hybrid enables direct backcrossing to tomato at the diploid level. Euphytica 95: 99-108.
12. Chetelat RT, Pertuzé RA, Faúndez L, Graham EB, Jones CM. 2009. Distribution, ecology and reproductive biology of wild tomatoes and related nightshades from the Atacama Desert region of northern Chile. Euphytica 167: 77-93.
13. Cornuet JM, Luikart G. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014.
14. Davis J, Yu D, Evans W, Gokirmak T, Chetelat RT, Stotz H. 2009. Mapping of loci from Solanum lycopersicoides conferring resistance or susceptibility to Botrytis cinerea in tomato. Theoretical and Applied Genetics 119: 305-314.
15. Dhuyvetter H, Gaublomme E, Desender K. 2004. Genetic differentiation and local adaptation in the salt-marsh beetle Pogonus chalceus: a comparison between allozyme and microsatellite loci. Molecular Ecology 13: 1065-1074.
16. Egashira H, Ishihara H, Takashina T, Imanishi S. 2000. Genetic diversity of the 'peruvianum-complex' (Lycopersicon peruvianum (L.) Mill. and L. Chilense Dun.) revealed by RAPD analysis. Euphytica 116: 23-31.
17. El Mousadik A, Petit RJ. 1996. High level of genetic differentiation for allelic richness among populations of the argan tree (Argania spinosa L. Skeels) endemic to Morocco. Theoretical and Applied Genetics 92: 832-839.
18. Ellstrand NC, Elam DR. 1993. Population genetic consequences of small population size: implications for plant conservation. Annual Review of Ecology and Systematics 24: 217-242.
19. Ercolano MR, Sebastiano A, Monti L, Frusciante L, Barone A. 2005. Molecular characterization of Solanum habrochaites accessions. Journal of Genetics and Breeding 59: 15-20.
20. Estoup A, Rousset F, Michalakis Y, Cornuet JM, Adriamanga M, Guyomard R. 1998. Comparative analysis of microsatellite and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta). Molecular Ecology 7: 339-353.
21. Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611-2620.
22. Excoffier L, Laval G, Schneider S. 2005. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47-50.
23. Falush D, Stephens M, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
24. Falush D, Stephens M, Pritchard JK. 2007. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes 7: 574-578.
25. Felsenstein J. 2005. PHYLIP (phylogeny inference package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
26. Frary A, Xu Y, Liu J, Mitchell S, Tedeschi E, Tanksley S. 2005. Development of a set of PCR-based anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments. Theoretical and Applied Genetics 111: 291-312.
27. Fulton TM, Chunwongse J, Tanksley SD. 1995. Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Molecular Biology Reporter 13: 207-209.
28. Gao LZ, Schaal BA, Zhang CH, Jia JZ, Dong YS. 2002. Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. using microsatellite and allozyme markers. Theoretical and Applied Genetics 106: 173-180.
29. Glaubitz JC. 2004. CONVERT: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Molecular Ecology Notes 4: 309-310.
30. Goudet J. 2001. FSTAT a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from http://www2.unil.ch/ popgen/softwares/fstat.htm.
31. Goudet J, Raymond M, Demeeus T, Rousset F. 1996. Testing differentiation in diploid populations. Genetics 144: 1933-1940.
32. Graham EB. 2005. Genetic diversity and crossing relationships of Lycopersicon chilense. PhD thesis, University of California, Davis, USA.
33. Gregory-Wodzicki KM. 2000. Uplift history of the central and northern Andes: a review. GSA Bulletin 112: 1091-1105.
34. Guo SW, Thompson EA. 1992. Performing the exact test of Hardy-Weinberg proportions for multiple alleles. Biometrics 48: 361-372.
35. Haldane JBS. 1954. An exact test for randomness of mating. Journal of Genetics 52: 631-635.
36. Houston J. 2006. Variability of precipitation in the Atacama Desert: its causes and hydrological impact. International Journal Climatology 26: 2181-2198.
37. Kahler AL, Allard RW, Miller RD. 1984. Mutation rates for enzyme and morphological loci in barley (Hordeum vulgare). Genetics 106: 729-734.
38. Karl SA, Avise JC. 1992. Balancing selection at allozyme loci in oysters. Implications from nuclear RFLPs. Science 256: 100-102.
39. Kimura M, Crow JF. 1964. The number of alleles that can be maintained in a finite population. Genetics 49: 725-738.
40. Li Y-C, Korol AB, Fahima T, Beiles A, Nevo E. 2002. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Molecular Ecology 11: 2453-2465.
41. Loridon K, McPhee K, Morin J, et al. 2005. Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.). Theoretical and Applied Genetics 111: 1022-1031.
42. Luikart G. 1997. Usefulness of molecular markers for detecting population bottlenecks and monitoring genetic change. PhD thesis, University of Montana, Missoula, USA.
43. Mantel N. 1967. The detection of disease clustering and generalized regression approach. Cancer Research 27: 209-220.
44. Maruyama T, Fuerst PA. 1985. Population bottlenecks and non equilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics 111: 675-689.
45. Miller JC, Tanksley SD. 1990. RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theoretical and Applied Genetics 80: 437-448.
46. Morgante M, Olivieri AM. 1993. PCR-amplified microsatellites as markers in plant genetics. Plant Journal 3: 175-182.
47. Nakazato T, Bogonovich M, Moyle LC. 2008. Environmental factors predict adaptive phenotypic differentiation within and between two wild Andean tomatoes. Evolution 62: 774-792.
48. Nei M. 1972. Genetic distance between populations. American Naturalist 106: 283-292.
49. Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
50. Nuez F, Prohens J, Blanca JM. 2004. Relationships, origin, and diversity of Galapagos tomatoes: implications for the conservation of natural populations. American Journal of Botany 91: 86-99.
51. Ohta T, Kimura M. 1973. A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genetic Research (Cambridge) 22: 201-204.
52. Page RDM. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358.
53. Peralta IE, Spooner DM, Knapp S. 2008. Taxonomy of wild tomatoes and their relatives (Solanum sect. Lycopersicoides, sect. Juglandifolia, sect. Lycopersicon; Solanaceae). Systematic Botany Monographs 84: 1-186.
54. Pertuze RA, Ji Y, Chetelat RT. 2003. Transmission and recombination of homeologous Solanum sitiens chromosomes in tomato. Theoretical and Applied Genetics 107: 1391-1401.
55. Piry S, Luikart G, Cornuet J. 1999. A computer program for detecting recent reductions in the effective population size using allele frequency data. Journal of Heredity 90: 502-503.
56. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
57. Raymond M, Rousset F. 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity 86: 248-249.
58. Reynolds J, Weir BS, Cockerham CC. 1983. Estimation for the coancestry coefficient: basis for a short-term genetic distance. Genetics 105: 767-779.
59. Rick CM. 1988. Tomato-like nightshades: affinities, autecology, and breeders opportunities. Economic Botany 42: 145-154.
60. Rick CM, Chetelat RT. 1995. Utilization of related wild species for tomato improvement. Acta Horticulturae 412: 21-38.
61. Rick CM, Fobes JF. 1975. Allozyme variation in the cultivated tomato and closely related species. Torrey Botanical Club Bulletin 102: 376-384.
62. Rick CM, Holle M. 1990. Andean Lycopersicon esculentum var. Cerasiforme. Genetic variation and its evolutionary significance. Economic Botany 44: 69-78.
63. Rick CM, Tanksley SD. 1981. Genetic variation in Solanum pennellii. Comparisons with two other sympatric tomato species. Plant Systematics and Evolution 139: 11-46.
64. Rick CM, Kesicki E, Fobes JF, Holle M. 1976. Genetic and biosystematic studies on two new sibling species of Lycopersicon from interandean Peru. Theoretical and Applied Genetics 47: 55-68.
65. Rick CM, Fobes JF, Holle M. 1977. Genetic variation in Lycopersicon pimpinellifolium. Evidence of evolutionary change in mating systems. Plant Systematics and Evolution 127: 139-170.
66. Rick CM, Fobes JF, Tanksley SD. 1979. Evolution of mating systems in Lycopersicon hirsutum as deduced from genetic variation in electrophoretic and morphological characters. Plant Systematics and Evolution 132: 279-298.
67. Roselius K, StephanW, Stadler T. 2005. The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species. Genetics 171: 753-763.
68. Rousset F. 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145: 1219-1228.
69. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406-425.
70. Smith SD, Peralta IE. 2002. Ecogeographic surveys as tools for analyzing potential reproductive isolating mechanisms: an example using Solanum juglandifolium Dunal, S. ochranthum Dunal, S. Lycopersicoides Dunal, and S. sitiens I.M. Johnston. Taxon 51: 341-349.
71. Smouse PE, Long JC, Sokal RR. 1986. Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Systematic Zoology 35: 627-632.
72. Sokal RR, Sneath PHA. 1963. Principles of numerical taxonomy. San Francisco: WH Freeman.
73. Tanksley SD, McCouch SR. 1997. Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277: 1063-1066.
74. Tanksley SD, Ganal MW, Prince JP, et al. 1992. High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141-1160.
75. Vigouroux Y, Jaqueth JS, Matsuoka Y, et al. 2002. Rate and pattern of mutation at microsatellite loci in maize. Molecular Biology and Evolution 19: 1251-1260.
76. Weber JL, Wong C. 1993. Mutation of human short tandem repeats. Human Molecular Genetics 2: 1123-1128.
77. Weir BS. 1990. Genetic data analysis. Sunderland, MA: Sinauer Publications.
78. Weir BS, Cockerham CC. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
79. Wikstrom N, Savolainen V, ChaseMW. 2001. Evolution of the angiosperms: Calibrating the family tree. Proceedings of the Royal Society Biological Sciences Series B 268: 2211-2220.
80. Wright S. 1951. The genetical structure of populations. Annals of Eugenics 15: 323-354.
81. Zamir D. 2001. Improving plant breeding with exotic genetic libraries. Nature Reviews Genetics 2: 983-989.