Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L.

Heredity

Volumn 110, Issue 3, 2013, Pages 267-276

  Mamidi, S ^a   Rossi, M ^b   Moghaddam, S M ^a   Annam, D ^a   Lee, R ^a   Papa, R ^b,c   McClean, P E ^a  

^a NORTH DAKOTA STATE UNIVERSITY   (United States)

^b UNIVERSITÀ POLITECNICA DELLE MARCHE   (Italy)

^c ISTITUTO NAZIONALE DELLA NUTRIZIONE   (Italy)

Author keywords

bottleneck; demography; divergence; geneflow; Phaseolus vulgaris; wildtypes

Indexed keywords

PLANT DNA;

DATA SET; DEMOGRAPHY; DIVERGENCE; GENETIC DIFFERENTIATION; GEOGRAPHICAL REGION; LATITUDINAL GRADIENT; LEGUME; NUMERICAL MODEL; POPULATION BOTTLENECK; POPULATION DISTRIBUTION; POPULATION SIZE; POPULATION STRUCTURE; SPECIES DIVERSITY; SUBPOPULATION; WILD POPULATION;

ARTICLE; BAYES THEOREM; CLASSIFICATION; GENE FLOW; GENE LOCUS; GENE POOL; GENETIC VARIABILITY; GENETICS; GENOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHASEOLUS; PHYLOGENY; PHYLOGEOGRAPHY; PLANT DISPERSAL; PLANT LEAF; SOUTH AND CENTRAL AMERICA; SPECIES DIFFERENTIATION;

BASE SEQUENCE; BAYES THEOREM; DNA, PLANT; GENE FLOW; GENE POOL; GENETIC LOCI; GENETIC SPECIATION; GENETIC VARIATION; GENOTYPE; LATIN AMERICA; MOLECULAR SEQUENCE DATA; PHASEOLUS; PHYLOGENY; PHYLOGEOGRAPHY; PLANT DISPERSAL; PLANT LEAVES;

ARGENTINA; MEXICO [NORTH AMERICA];

PHASEOLUS VULGARIS;

EID: 84873994199     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2012.82     Document Type: Article

References (81)

1. Acosta-Gallegos JA, Kelly JD, Gepts P (2007). Prebreeding in common bean and use of genetic diversity from wild germplasm. Crop Sci 47: S44-S59.
2. Arunyawat U, Stephan W, Stadler T (2007). Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes. Mol Biol Evol 24: 2310-2322.
3. Astle W, Balding DJ (2009). Population structure and cryptic relatedness in genetic association studies. Stat Sci 24: 2310-2322.
4. Becerra Velasquez VL, Gepts P (1994). RFLP diversity of common bean (Phaseolus vulgaris) in its centers of origin. Genome 37: 256-263.
5. Becquet C, Przeworski M (2007). A new approach to estimate parameters of speciation models with application to apes. Genome Res 17: 1505-1519.
6. Becquet C, Przeworski M (2009). Learning bout modes of speciation by computational approaches. Evolution 63: 2547-2562.
7. Bitocchi E, Nanni L, Rossi M, Giardini A, Zeuli PS, Logozzo G et al. (2012). The Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. Proc Natl Acad Sci USA 109: E788-E796.
8. Brachi B, Faure N, Horton M, Flahauw E, Vazquez A, Nordborg M et al. (2010). Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet 6: e1000940.
9. Brady L, Bassett MJ, McClean PE (1998). Molecular markers associated with T and Z, two genes controlling partly colored seed coat patterns in common bean. Crop Sci 38: 1073-1075.
10. Charlesworth D (2003). Effects of inbreeding on the genetic diversity of populations. Philos Trans R Soc Lond 358: 1051-1070.
11. Chen J, Källman T, Gyllenstrand N, Lascoux M (2010). New insights on the speciation history and nucleotide diversity of three boreal spruce species and a tertiary relict. Heredity 104: 3-14.
12. 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.
13. Freyre R, Ríos R, Guzmán L, Debouck DG, Gepts P (1996). Ecogeographic distribution of Phaseolus spp.(Fabaceae) in Bolivia. Econ Bot 50: 195-215.
14. Gepts P, Bliss FA (1986). Phaseolin variability among wild and cultivated common beans (Phaseolus vulgaris) from Colombia. Econ Bot 40: 469-478.
15. Gepts P, Debouck D (1991). Origin, domestication, and evolution of the common bean (Phaseolus vulgaris L.). In: Van Schoonhoven A, Voysest O (eds) Common Beans: Research for Crop Improvement. CAB Int: Wallingford, UK and CIAT: Cali, Colombia, pp 7-53.
16. Gepts P, Osborn TC, Rashka K, Bliss FA (1986). Phaseolin-protein variability in wild forms and landraces of the common bean (Phaseolus vulgaris): evidence for multiple centers of domestication. Econ Bot 40: 451-468.
17. Graham P, Vance C (2003). Legumes: importance and constraints to greater use. Plant Physiol 131: 872-877.
18. Hamblin MT, Buckler ES, Jannink JL (2011). Population genetics of genomics-based crop improvement methods. Trends Genet 27: 98-106.
19. Haudry A, Cenci A, Ravel C, Batallion T, Brunel D, Poncet C et al. (2007). Grinding up wheat: a massive loss of nucleotide diversity since domestication. Mol Biol Evol 24: 1506-1517.
20. Hey J (2006). Recent advances in assessing gene flow between diverging populations and species. Curr Opin Genet Dev 16: 592-596.
21. Hudson RR (2000). A new statistic for detecting genetic differentiation. Genetics 155: 2011-2014.
22. Hudson RR (2002). Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
23. Hudson RR, Kaplan NL (1985). Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
24. Hudson RR, Kreitman M, Aguade M (1987). A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
25. Hudson RR, Slatkin M, Maddison WP (1992). Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
26. Ibarra-Perez FJ, Ehdaie B, Waines JG (1997). Estimation of outcrossing rate in common bean. Crop Sci 37: 60-65.
27. Ingvarsson P (2008). Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. Genetics 180: 329-340.
28. Ingvarsson PK (2005). Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics 169: 945-953.
29. Kaplan L, Lynch TF (1999). Phaseolus (Fabaceae) in Archaeology: AMS. Econ Bot 53: 261-272.
30. Khairallah MM, Sears BB, Adams MW (1992). Mitochondrial restriction fragment length polymorphisms in wild Phaseolus vulgaris L.: insights on the domestication of the common bean. Theor Appl Genet 84: 915-922.
31. Kilian B, Ozkan H, Walther A, Kohl J, Dagan T, Salamini F et al. (2007). Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum (Einkorn) domestication: implications for the origin of agriculture. Mol Biol Evol 24: 2657-2668.
32. Koenig R, Gepts P (1989). Allozyme diversity in wild Phaseolus vulgaris: further evidence for two major centers of genetic diversity. Theor Appl Genet 78: 809-817.
33. Kwak M, Gepts P (2009). Structure of genetic diversity in the two major genepools of common bean (Phaseolus vulgaris L., Fabaceae). Theor Appl Genet 118: 979-992.
34. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
35. Leman SC, Chen Y, Stajich JE, Noor MAF, Uyenoyama MK (2005). Likelihoods from summary statistics: recent divergence between species. Genetics 171: 1419-1436.
36. Leuenberger C, Wegmann D (2010). Bayesian computation and model selection without likelihoods. Genetics 184: 243-252.
37. Liu A, Burke JM (2006). Patterns of nucleotide diversity in wild and cultivated sunflower. Genetics 173: 321-330.
38. Lopes JS, Boessenkool S (2010). The use of approximate Bayesian computation in conservation genetics and its application in a case study on yellow-eyed penguins. Conserv Genet 11: 421-433.
39. Lynch M, Conery J (2000). The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
40. Machado CA, Haselkorn TS, Noor MAF (2007). Evaluation of the genomic extent of effects of fixed inversion differences on intraspecific variation and interspecific gene flow in Drosophila pseudoobscura and D. persimilis. Genetics 175: 1289-1306.
41. Mamidi S, Rossi M, Annam D, Moghaddam S, Lee RK, Papa R et al. (2011). Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data. Funct Plant Biol 38: 953-967.
42. McClean P, Lee R, Miklas P (2004). Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean. Genome 47: 266-280.
43. McClean PE, Burridge J, Beebe S, Rao IM, Porch TG (2011). Crop improvement in the era of climate change: an integrated, multi-disciplinary approach for common bean (Phaseolus vulgaris). Funct Plant Biol 38: 927-933.
44. McClean PE, Lee RK (2007). Genetic architecture of chalcone isomerase non-coding regions in common bean (Phaseolus vulgaris L.). Genome 50: 203-214.
45. McClean PE, Lee RK, Otto C, Gepts P, Bassett MJ (2002). Molecular and phenotypic mapping of genes controlling seed coat pattern and color in common bean (Phaseolus vulgaris L.). J Hered 93: 148-152.
46. McConnell M, Mamidi S, Lee R, Chikara S, Rossi M, Papa R et al. (2010). Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.). Theor Appl Genet 121: 1103-1116.
47. Moeller DA, Tenaillon MI, Tiffin P (2007). Population structure and its effects on patterns of nucleotide polymorphism in teosinte (Zea mays ssp. parviglumis). Genetics 176: 1799-1809.
48. Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A et al. (2011). Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci USA 108: 8351-8356.
49. Morjan CL, Rieseberg LH (2004). How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles. Mol Ecol 13: 1341-1356.
50. Morrell PL, Lundy KE, Clegg MT (2003). Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. Spontaneum) despite migration. Proc Natl Acad Sci USA 100: 10812-10817.
51. Muraya MM, Sagnard F, Parzies HK (2010). Investigation of recent population bottlenecks in Kenyan wild sorghum populations (Sorghum bicolor (L.) Moench ssp. verticilliflorum (Steud.) De Wet) based on microsatellite diversity and genetic disequilibria. Genet Resour Crop Evol 57: 995-1005.
52. Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE et al. (2009). Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21: 2194-2202.
53. Ness RW, Wright SI, Barrett SCH (2010). Mating-system variation, demographic history and patterns of nucleotide diversity in the tristylous plant Eichhornia paniculata. Genetics 184: 381-392.
54. Nordborg M, Donnelly P (1997). The coalescent process with selfing. Genetics 146: 1185-1195.
55. Papa R, Acosta J, Delgado-Salinas A, Gepts P (2005). A genome-wide analysis of differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica. Theor Appl Genet 111: 1147-1158.
56. Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
57. Pyhajarvi T, Garcia-Gil MR, Knurr T, Mikkonen M, Wachowiak W, Savolainen O (2007). Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics 177: 1713-1724.
58. Rafalski A, Morgante M (2004). Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends Genet 20: 103-111.
59. Remington DL, Thornsberry JM, Matsuoka M, Wilson LM, Whitt SR, Doebley J et al. (2001). Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98: 11479-11484.
60. Ross-Ibarra J, Tenaillon M, Gaut BS (2009). Historical divergence and gene flow in the genus Zea. Genetics 181: 1399-1413.
61. Rossi M, Bitocchi E, Bellucci E, Nanni L, Rau D, Attene G et al. (2009). Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L. Evol Appl 2: 504-522.
62. Rozas J, Rozas R (1999). DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
63. Schmid KJ, Ramos-Onsins S, Ringys-Beckstein H, Weisshaar B, Mitchell-Olds T (2005). A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism. Genetics 169: 1601-1615.
64. Singh SP (2001). Broadening the genetic base of common bean cultivars: a review. Crop Sci 41: 1659-1675.
65. Singh SP, Nodari R, Gepts P (1991). Genetic diversity in cultivated common bean: I. Allozymes. Crop Sci 31: 19-23.
66. Staden R (1996). The Staden sequence analysis package. Mol Biotechnol 5: 233-241.
67. Stadler T, Arunyawat U, Stephan W (2008). Population genetics of speciation in two closely related wild tomatoes (Solanum section Lycopersicon). Genetics 178: 339-350.
68. Strasburg JL, Rieseberg LH (2008). Molecular demographic history of the annual sunflowers Helianthus annuus and H. petiolaris-large effective population sizes and rates of long-term gene flow. Evolution 62: 1936-1950.
69. Strasburg JL, Rieseberg LH (2010). How robust are 'Isolation with Migration' analyses to violations of the IM model? A simulation study. Mol Biol Evol 27: 397-310.
70. Städler T, Haubold B, Merino C, Stephan W, Pfaffelhuber P (2009). The impact of sampling schemes on the site frequency spectrum in non-equilibrium subdivided populations. Genetics 182: 205-216.
71. Tajima F (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
72. Tenaillon MI, U'Ren J, Tenaillon O, Gaut BS (2004). Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol 21: 1214-1225.
73. Tiffin P, Gaut BS (2001). Molecular evolution of the wound-induced serine protease inhibitor wip1 in Zea and related genera. Mol Biol Evol 18: 2092-2101.
74. Tohme J, Gonzalez D, Beebe S, Duque MC (1996). AFLP analysis of genepools of a wild bean core collection. Crop Sci 36: 1375-1384.
75. Wakeley J (2001). The coalescent in an island model of population subdivision with variation among demes. Theor Popul Biol 59: 133-144.
76. Wakeley J, Hey J (1997). Estimating ancestral population parameters. Genetics 145: 847-855.
77. Wright SI, Gaut BS (2005). Molecular population genetics and the search for adaptive evolution in plants. Mol Biol Evol 22: 506-519.
78. Wright SI, Lauga B, Charlesworth D (2003). Subdivision and haplotype structure in natural populations of Arabidopsis lyrata. Mol Ecol 12: 1247-1263.
79. Zhang LB, Ge S (2007). Multilocus analysis of nucleotide variation and speciation in Oryza officinalis and its close relatives. Mol Biol Evol 24: 769-783.
80. Zhou HF, Zheng XM, Wei RX, Second G, Vaughan DA, Ge S (2008). Contrasting population genetic structure and gene flow between Oryza rufipogon and Oryza nivara. Theor Appl Genet 117: 1181-1189.
81. Zhu Q, Zheng X, Luo J, Gaut BS, Ge S (2007). Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24: 875-888.