Integration of genome and phenotypic scanning gives evidence of genetic structure in Mesoamerican common bean (Phaseolus vulgaris L.) landraces from the southwest of Europe

Theoretical and Applied Genetics

Volumn 120, Issue 8, 2010, Pages 1635-1651

  Santalla, M ^a   de Ron, A M ^a   de La Fuente, M ^a  

^a MISIÓN BIOLÓGICA DE GALICIA CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AGRONOMIC TRAITS; ALLOZYMES; COMMON BEANS; ENVIRONMENTAL CONDITIONS; EXPERIMENTAL SYSTEM; GENE POOLS; GENETIC DISTANCES; GENETIC DIVERSITY; GENETIC RESISTANCE; GENETIC STRUCTURE; GENOMICS; INFORMATION CONTENTS; LANDRACES; LOCI ANALYSIS; MICROSATELLITE LOCI; MODEL BASED APPROACH; MULTI VARIATE ANALYSIS; NEUTRAL MARKERS; PHASEOLIN; PHASEOLUS VULGARIS; PHENOTYPIC DATA; PHENOTYPIC TRAITS; PUTATIVE HYBRIDS; QUANTITATIVE TRAIT LOCUS; SEED PROTEIN; SEED SIZE; SIMPLE SEQUENCE REPEATS; SOFTWARE STRUCTURES; SOUTHERN EUROPE; VEGETATIVE GROWTH;

BIODIVERSITY; GENES; PLANTS (BOTANY); POLYMORPHISM;

MULTIVARIANT ANALYSIS;

PHASEOLUS VULGARIS;

ISOENZYME; MICROSATELLITE DNA;

ARTICLE; BIOLOGICAL MODEL; CLUSTER ANALYSIS; COMPUTER PROGRAM; EUROPE; GENETIC POLYMORPHISM; GENETICS; GENOME; GEOGRAPHY; LEGUME; MULTIGENE FAMILY; MULTIVARIATE ANALYSIS; PHENOTYPE; PLANT GENE; QUANTITATIVE TRAIT LOCUS;

CLUSTER ANALYSIS; EUROPE; FABACEAE; GENES, PLANT; GENOME; GEOGRAPHY; ISOENZYMES; MICROSATELLITE REPEATS; MODELS, GENETIC; MULTIGENE FAMILY; MULTIVARIATE ANALYSIS; PHENOTYPE; POLYMORPHISM, GENETIC; QUANTITATIVE TRAIT LOCI; SOFTWARE;

EID: 77955300608     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-010-1282-0     Document Type: Article

References (97)

1. Afanador L, Hadley S, Kelly JD (1993) Adoption of a mini-prep DNA extraction method for RAPD marker analysis in common bean (Phaseolus vulgaris L.). Bean Improv Coop 36: 10-11.
2. Antao T, Lopes A, Lopes RJ, Beja-Pereira A (2008) LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 9: 323.
3. Balardin RS, Kelly JD (1998) Interaction between Colletotrichum lindemuthianum races and gene pool diversity in Phaseolus vulgaris. J Am Soc Hortic Sci 123: 1038-1047.
4. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proc R Soc B 263: 1619-1626.
5. Beaver JS, Kelly JD (1994) Comparison of selection methods for dry bean landraces derived from crosses between gene pools. Crop Sci 25: 923-926.
6. Becerra Velasquez L, Gepts P (1994) RFLP diversity of common bean (Phaseolus vulgaris L.) in its centers of origin. Genome 37: 256-263.
7. Beebe S, Toro O, González AV, Chacón MI, Debouck D (1997) Wildweed-crop complex of common bean (Phaseolus vulgaris L., Fabaceae) in the Andes of Peru and Colombia, and their implications for conservation and breeding. Genet Resour Crop Evol 44: 73-91.
8. Beebe SE, Skroch PW, Tohme J, Duque MC, Pedraza F, Nienhuis J (2000) Structure of genetic diversity among common bean landraces of Middle American origin based on correspondence analysis of RAPD. Crop Sci 40: 264-273.
9. Beebe SE, Rengifo J, Gaitan E, Duque MC, Tohme J (2001) Diversity and origin of Andean landraces of common bean. Crop Sci 41: 854-862.
10. Blair MW, Pedraza F, Buendia H, Gaitan E, Beebe S, Gepts P, Tohme J (2003) Development of a genome wide anchored microsatellite for common bean (Phaseolus vulgaris L). Theor Appl Genet 107: 1362-1374.
11. Blair MW, Giraldo MC, Buendia HF, Tovar E, Duque MC, Beebe S (2006a) Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 113: 100-109.
12. Blair MW, Iriarte G, Beebe S (2006b) QTL analysis of yield traits in an advanced backcross landrace derived from a cultivated Andean wild common bean (Phaseolus vulgaris L) cross. Theor Appl Genet 112: 1149-1163.
13. Blair MW, Fregene MA, Beebe SE, Ceballos H (2007) Marker-Assisted Selection in Common Beans and Cassava. Chap. 7. In: Guimaraes E (ed) Marker-assisted selection (MAS) in crops, livestock, forestry and fish: Current status and the way forward. FAO, Rome, Italy.
14. Bonin A, Taberlet P, Claude M, Pompanon F (2006) Explorative genome scans to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria). Mol Biol Evol 23(4): 773-783.
15. Brown JWS, Ma Y, Bliss FA (1981) Genetic variation in the subunits of globulin 1-storage protein of French bean. Theor Appl Genet 59: 83-88.
16. Buso GSC, Amaral ZPS, Brondani RPV, Ferreira ME (2006) Microsatellite markers for the common bean - Phaseolus vulgaris. Mol Ecol Notes 6: 252-254.
17. Caixeta ET, Borem A, Alzate-Marin AL, Fagundes S (2005) Allelic relationships for genes that confer resistance to angular leaf sport in common bean. Euphytica 145: 237-245.
18. Campbell D, Bernatchez L (2004) Generic Scan Using AFLP Markers as a Means to Assess the Role of Directional Selection in the Divergence of Sympatric Whitefish Ecotypes. Mol Biol Evol 21(5): 945-956.
19. Chacón MI, Pickersgill S, Debouck D (2005) Domestication patterns in common bean (Phaseolus vulgaris L.) and the origin of Mesoamerican and Andean cultivated races. Theor Appl Genet 110: 432-444.
20. Checa C, Blair MW (2008) Mapping QTL for climbing ability and component traits in common bean (Phaseolus vulgaris L.). Molecular Breed 22: 201-215.
21. Chen Y, Nelson RL (2005) Relationship between origin and genetic diversity in chinese soybean germplasm. Crop Sci 45: 1645-1651.
22. Crow JF, Aoki K (1984) Group selection for a polygenic behavioral trait: estimating the degree of landrace subdivision. Proc Natl Acad Sci USA 81: 6073-6077.
23. Debouck DG, Araya Villalobos R, Ocampo Sánchez RA, González UWG (1989) Collecting Phaseolus in Costa Rica. FAO/IBPGR Plant Genet Resour Newsl 78(79): 44-46.
24. Díaz LM, Blair MW (2006) Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers. Theor Appl Genet 114: 143-154.
25. Evano 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.
26. Freyre R, Ríos R, Guzmán L, Debouck DG, Gepts P (1996) Ecogeographic distribution of Phaseolus spp. (Fabaceae) in Bolivia. Econ Bot 50: 195-215.
27. Freyre R, Skroch P, Geffroy V, Adam-Blondon A-F, Shirmohamadali A, Johnson W, Llaca V, Nodari R, Pereira P, Tsai S-M, Tohme J, Dron M, Nienhuis J, Vallejos C, Gepts P (1998) Towards an integrated linkage map of common bean. 4. Development of a core linkage map and alignment of RFLP maps. Theor Appl Genet 97: 847-856.
28. Gaitán-Sólis E, Duque MC, Edwards K, Tohme J (2002) Microsatellite repeats in common bean (Phaseolus vulgaris L.): isolation, characterization, and cross-species amplification in Phaseolus spp. Crop Sci 42: 2128-2136.
29. Geffroy V, Sicard D, de Oliveira JCF, Sevgnac M, Cohen S, Gepts P, Neema C, Langin T, Dron M (1999) Identification of an ancestral resistance gene cluster involved in the co-evolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum lindemuthianum. Mol Plant Microb Interact 12: 774-784.
30. Gepts P (1988) Phaseolin as an evolutionary marker. In: Resources of Phaseolus beans. Kluwer, Dordtrecht, pp 215-241.
31. Gepts P (2004) Domestication as a long-term selection experiment. Plant Breed Rev 24(part 2): 1-44.
32. Gepts P, Bliss FA (1985) F1 hybrid weakness in the common bean: differential geographic origin suggests two gene pools in cultivated bean germplasm. J Hered 76: 447-450.
33. Gepts P, Bliss FA (1988) Dissemination pathways of common bean (Phaseolus vulgaris, Fabaceae) deduced from phaseolin electrophoretic variability. II. Europe and Africa. Econ Bot 42: 86-104.
34. Gepts P, Osborn T, Rashka K, Bliss F (1986) Phaseolin-protein variability in wild forms and landraces of the common bean (Phaseolus vulgaris L.): evidence for multiple centers of domestication. Econ Bot 40: 451-468.
35. Guerra-Sanz JM (2004) Short communication - New SSR markers of Phaseolus vulgaris from sequence databases. Plant Breed 123: 87-89.
36. Guzmán P, Gilbertson RL, Nodari R, Johnson WC, Temple SR, Mandela D, Mkandawire ABC, Gepts P (1995) Characterization of variability in the fungus Phaseoisariopsis griseola suggests coevolution with the common bean (Phaseolus vulgaris). Phytopathology 85: 600-607.
37. Huang XQ, Börner A, Röder MS, Ganal MW (2002) Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers. Theor Appl Genet 105: 699-707.
38. Innes NL, Conway J, Taylor JD (1984) Resistance to halo blight in the Cambridge accessions V4604 and V4058 of Phaseolus beans. Ann Appl Biol 104: 307-314.
39. Islam FMA, Basford KE, Redden RJ, Gonzalez AV, Kroonenberg PM, Beebe SE (2002) Genetic variability in cultivated common bean beyond the two major gene pools. Genet Resour Crop Evol 49: 271-283.
40. Jarvis DI, Hodgkin T (1999) Wild relatives and crop cultivars: detecting natural introgression and farmer selection of new genetic combinations in agro-ecosystem. Mol Ecol 8: S159-S173.
41. Khairallah M, Sears B, Adams M (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.
42. Koenig R, Gepts P (1989) Allozyme diversity in wild Phaseolus vulgaris: further evidence for two mayor centers of genetic diversity. Theor Appl Genet 78: 809-817.
43. Koinange EMK, Singh SP, Gepts P (1996) Genetic control of the domestication syndrome in common bean. Crop Sci 36: 1037-1045.
44. Kornegay J, White JW, Ortíz de la Cruz O (1992) Growth habit and gene pool effects on inheritance of yield in common bean. Euphytica 62: 171-180.
45. Kwak M, Gepts P (2009) Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor Appl Genet 118: 979-992.
46. Li Z, Nelson RL (2001) Genetic diversity among soybean ac cessions from three countries measured by RAPDs. Crop Sci 41: 1337-1347.
47. Liu K, Muse S (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics Appl Note 21(9): 2128-2129.
48. Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci USA 103: 9578-9583.
49. Luikart G, England PR, Tallmon D (2003) The power and promise of population genomics: From genotyping to genome typing. Nat Rev Genet 4(12): 981-994.
50. Masi G, Logozzo P, Donini P, Spagnoletti Z (2009) Analysis of genetic structure in widely distributed common bean landraces with different plant growth habits using SSR and AFLP markers. Crop Sci 49: 187-199.
51. McClean PE, Lee RK, Miklas PN (2004) Sequence diversity analysis of dihydrofl avonol 4-reductase intron1 in common bean. Genome 47: 266-280.
52. Metais I, Hamon B, Jalouzot R, Peltier D (2002) Structure and level of genetic diversity in various bean types evidenced with microsatellite markers isolated from a genomic enriched library. Theor Appl Genet 104: 1346-1352.
53. Mitchell SE, Kresovich S, Jester CA, Hernandez CJ, Szewc-McFadden AK (1997) Application of multiplex PCR and fluorescence-based, semi-automated allele sizing technology for genotyping plant genetic resources. Crop Sci 37: 617-624.
54. Nei M (1978) Estimation of average heterozygocity and genetic distance from a small number of individuals. Genetics 89: 583-590.
55. Nielsen R (2005) Molecular signatures of natural selection. Annu Rev Genet 39: 197-218.
56. Pañeda A, Rodríguez-Suárez C, Campa A, Ferreira JJ, Giraldez R (2008) Molecular markers linked to the fin gene controlling determinate growth habit in common bean. Euphytica 162: 241-248.
57. 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.
58. Paredes OM, Gepts P (1995) Extensive introgression of Middle American germplasm into Chilean common bean landraces. Genet Resour Crop Evol 42: 29-41.
59. Pastor-Corrales MA (1991) Estandarización de variedades diferenciales y de designación de razas de Colletotrichum lindemuthianum. Phytopathology 81: 694.
60. Pastor-Corrales MA, Jara C, Singh SP (1998) Pathogenic variation in sources of and breeding for resistance to Phaeoisariopsis griseola causing angular leaf spot in common bean. Euphytica 103: 161-171.
61. Peakall R, Smouse PE (2006) GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295.
62. Piergiovanni A, Taranto G, Losavio FP, Pignone D (2006) Common bean (Phaseolus vulgaris L.) landraces from Abruzzo and Lazio regions (Central Italy). Genet Resour Crop Evol 53: 313-322.
63. Pritchard JK, Wen W (2004) Documentation for the STRUCTURE software Version 2. Chicago. http://www. pritch. bsd. uchicagoedu/software/structure2_1. html.
64. Pritchard JK, Stephens M, Donnelly P (2000) Inference of landrace structure using multilocus genotype data. Genetics 155: 945-959.
65. Rick CM, Holle M (1990) Andean Lycopersicon esculentum var. cerasiformie. Genetic variation and its evolutionary significance. Econ Bot 44: 69-78.
66. Rodiño P, Santalla M, González AM, De Ron AM, Singh SP (2006) Novel genetic variation in common bean from the Iberian Peninsula. Crop Sci 46: 2540-2546.
67. Rosales-Serna R, Hernandez-Delgado S, Gonzalez-Paz M, Acosta-Gallegos JA, Mayek-Perez N (2005) Genetic relationships and diversity revealed by AFLP markers in Mexican common bean bred cultivars. Crop Sci 45: 1951-1957.
68. Rossi M, Bitocchi E, Bellucci E, Nanni L, Rau D, Attene G, Papa R (2009) Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L. Evol Appl. doi: 10. 1111/j. 1752-4571. 2009. 00082. x.
69. Sánchez E, Sifres A, Casañas F, Nuez F (2008) The endangered future of organoleptically prestigious European landraces: Ganxet bean (Phaseolus vulgaris L.) as an example of a crop originating in the Americas. Genet Resour Crop Evol 55: 45-52.
70. Santalla M, Rodiño AP, De Ron AM (2002) Allozyme evidence supporting southwestern Europe as a secondary center of genetic diversity for common bean. Theor Appl Genet 104: 934-944.
71. Schlötterer C (2003) Hitchhiking mapping-functional genomics from the population genetics perspective. Trends Genet 19: 32-38.
72. Sicard D, Nanni L, Porfiri O, Bulfon D, Papa R (2005) Genetic diversity of Phaseolus vulgaris L. and Phaseolus coccineus L. landraces in central Italy. Plant Breed 124: 464-472.
73. Singh SP (1995) Selection for seed yield in Middle American versus Andean x Middle American interracial common bean landraces. Plant Breed 114: 269-271.
74. Singh SP, Gutiérrez JA (1990) Effect of plant density on selection for seed yield in two landrace types of Phaseolus vulgaris L. Euphytica 51: 173-178.
75. Singh SP, Gepts P, Debouck DG (1991a) Races of common bean (Phaseolus vulgaris, Fabaceae). Econ Bot 45: 379-396.
76. Singh SP, Gutiérrez JA, Molina A, Urrea C, Gepts P (1991b) Genetic diversity in cultivated common bean: II. Marker-based analysis of morphological and agronomic traits. Crop Sci 31: 23-29.
77. Singh S, Nodari R, Gepts P (1991c) Genetic diversity in cultivated common bean. I. Allozymes. Crop Sci 31: 19-23.
78. Singh SP, Terán H, Germán Muñoz C, Takegami JC (1999) Two cycles of recurrent selection for seed yield in common bean. Crop Sci 39: 391-397.
79. Slatkin M, Barton N (1989a) A comparison of three indirect methods for estimating average levels of gene flow. Evolution 43: 1349-1368.
80. Slatkin M, Barton NH (1989b) A comparison of three indirect methods for estimating the average level of gene flow. Evolution 43: 1349-1368.
81. Storz JF (2005) Using genome scans of DNA polymorphism to infer adaptive landrace divergence. Mol Ecol 14: 671-688.
82. Tohme J, González DO, Beebe S, Duque MC (1996) AFLP analysis of gene pools of a wild bean core collection. Crop Sci 36: 1375-1384.
83. CIAT (Centro Internacional de Agricultura Tropical) (1987) Standard Voysest O. 2000. Mejoramiento genético del frijol (Phaseolus vulgaris system for the evaluation of bean germplasm. van Schoohoven L.): Legado de variedades de América Latina 1930-1999. Pastor- Corrales (compilers). CIAT. Cali, Colombia.
84. van Schoonhoven A, Pastor-Corrales MA (1987) Standard system for the evaluation of bean germplasm. CIAT, Cali, Colombia.
85. Vasemägi A, Nilsson J, Primmer CR (2005) Expressed sequence tag (EST) linked microsatellites as a source of gene associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Mol Biol Evol 22: 1067-1076.
86. Vavilov NI (1951) The origin, variation, immunity and breeding of cultivated plants. Chron Bot 13: 1-366 Translated by K. Start.
87. Vigouroux Y, MacMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J (2002) Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci USA 99: 9650-9655.
88. Vitalis R, Dawson K, Boursot P (2001) Interpretation of variation across marker loci as evidence of selection. Genetics 158: 1811-1823.
89. Vitalis R, Dawson K, Boursot P, Belkhir K (2003) DetSel 1. 0: a computer program to detect markers responding to selection. J Hered 94: 429-431.
90. Vitte C, Ishii T, Lamy F, Brar D, Panaud O (2004) Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol Genet Genom 272: 504-511.
91. Wang L, Guan R, Zhangxiong L, Chang R, Qiu L (2006) Genetic Diversity of Chinese Cultivated Soybean Revealed by SSR Markers. Crop Sci 46: 1032-1038.
92. Weir BS, Cockerman C (1984) Estimating F-statistics for the analysis of landrace structure. Evolution 38: 1358-1370.
93. White JW, Singh SP, Pino C, Rios MJ, Buddenhagen I (1992) Effects of seed size and photoperiod response on crop growth and yield of common bean. Field Crops Res 23: 159-175.
94. Xu P, Tao DY, Hu FY, Zhou JW, Deng XN (2005) Interspecific hybridization of cultivated rice for breeding japonica rice in Yunnan province. Chin J Rice Sci 19(1): 41-46.
95. n microsatellite sequences and description of a predicted MADS-box sequence isolated from common bean (Phaseolus vulgaris L.). Genet Mol Biol 26: 337-342.
96. Yu K, Park J, Poysa V, Gepts P (2000) Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.). J Hered 91: 429-434.
97. Zizumbo-Villarreal D, Colunga-García Marín P, De la Cruz E, Payró Delgado-Valerio P, Gepts P (2005) Landrace structure and evolutionary dynamics of wild-weedy-domesticated complexes of common bean in a Mesoamerican region. Crop Sci 45: 1073-1083.