A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.)

Theoretical and Applied Genetics

Volumn 126, Issue 2, 2013, Pages 535-548

  Blair, Matthew W ^a,b   Cortés, Andrés J ^c   Penmetsa, R Varma ^d   Farmer, Andrew ^e   Carrasquilla Garcia, Noelia ^d   Cook, Doug R ^d  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSIDAD NACIONAL DE COLOMBIA   (Colombia)

^c UPPSALA UNIVERSITY   (Sweden)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e National Center for Genomic Research   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYMORPHISM;

DIVERSITY ANALYSIS; GENE SEQUENCES; GENETIC DIVERSITY; HIGH THROUGHPUT; MICROSATELLITE MARKERS; PHASEOLUS VULGARIS; SINGLE NUCLEOTIDE POLYMORPHISM DETECTIONS; VARIOUS TECHNOLOGIES;

GENES;

PHASEOLUS VULGARIS;

EID: 84873085566     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-012-1999-z     Document Type: Article

References (29)

1. Afanador LK, Hadley SD, Kelly JD (1993) Adoption of a mini-prep DNA extraction method for RAPD marker analysis in common bean. Bean Improv Coop 35: 10-11.
2. Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36: 181-186.
3. Benchimol LL, de Campos T, Carbonell SAM, Colombo CA, Chioratto AF, Formighieri EF, Gouvêa LRL, de Souza AP (2007) Structure of genetic diversity among common bean (Phaseolus vulgaris L.) varieties of Mesoamerican and Andean origins using new develop microsatellite markers. Genet Resour Crop Evol 54: 1747-1762.
4. Blair MW, Giraldo MC, Buendia HF, Tovar E, Duque MC, Beebe SE (2006a) Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 113: 100-109.
5. Blair MW, Iriarte G, Beebe S (2006b) QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean × wild common bean (Phaseolus vulgaris L.) cross. Theor Appl Genet 112: 1149-1163.
6. Blair M, Diaz LM, Buendía HF, Duque MC (2009) Genetic diversity, seed size associations and population structure of a core collection of common beans (Phaseolus vulgaris L.). Theor Appl Genet 119: 955-972.
7. Broughton WJ, Hernández G, Blair MW, Beebe S, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.) model food legumes. Plant Soil 55: 55-128.
8. Chagné D, Batley J, Edwards D, Forster JW (2007) Single nucleotide polymorphism genotyping in plants. In: Oraguzie NC, Rikkerink EHA, Gardiner SE, Silva HNd (eds) Association mapping in plants, pp 77-94.
9. Cortés A, Chavarro C, Blair MW (2011) SNP marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet. doi: 10. 1007/s00122-011-1630-8.
10. Cortés AJ, This D, Chavarro MC, Madriñan S, Blair MW (2012) Nucleotide diversity patterns at the drought related DREB encoding genes in wild and cultivated common bean (Phaseolus vulgaris L.). Theor Appl Genet 125(5): 1069-1085.
11. Deulvot C, Charrel H, Marty A, Jacquin F, Donnadieu C, Lejeune-Hénaut I, Burstin J, Aubert G (2010) Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea. BMC Genomics 11: 468.
12. 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.
13. Galeano CH, Fernández AC, Gómez M, Blair MW (2009a) Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.). BMC Genomics 10: 629.
14. Galeano CH, Gomez M, Rodriguez LM, Blair MW (2009b) CEL I nuclease for SNP discovery and marker development in common bean (Phaseolus vulgaris L.). Crop Sci 49: 381-394.
15. Gepts P, Aragao F, Barros E, Blair MW, Brondani R, Broughton W, Hernández G, Kami J, Lariguet P, McClean P, Melotto M, Miklas P, Pedrosa-Harand A, Porch T, Sánchez F (2008) Genomics of Phaseolus beans, a major source of dietary protein and micronutrients in the tropics. In: Moore PH, Ming R (eds) Genomics of tropical crops, chap 5. Springer, Berlin, pp 113-143.
16. Hyten DL, Song Q, Choi IY, Yoon MS, Specht JE, Matukumalli LK, Nelson RL, Shoemaker RC, Young ND, Cregan PB (2008) High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor Appl Genet 116(7): 945-952.
17. Hyten DL, Song Q, Fickus EW, Quigley CV, Lim J-S, Choi I-Y, Hwang E-Y, Pastor-Corrales M, Cregan PB (2010) High-throughput SNP discovery and assay development in common bean. BMC Genomics 11: 475.
18. 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.
19. Liu K, Muse SVB (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21: 2128-2129.
20. McConnell M, Mamidi S, Lee R, Chikara S, Rossi M, Papa R, McClean P (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.
21. Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottor M, Hearne S, Cisse N, Fatokun C, Ehlers JD, Roberts PA, Close TJ (2009) A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proc Natl Acad Sci USA 106: 18159-18164.
22. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small numbers of individuals. Genetics 89: 583-590.
23. Oliphant A, Barker DL, Stuelpnagel JR, Chee MS (2002) BeadArray technology: enabling an accurate, cost-effective approach to high throughput genotyping. Biotechniques Suppl 5: 6-58.
24. Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield Science Publishers, Montpellier, pp 43-76.
25. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2): 945-959.
26. Singh SP, Gepts P, Debouck DG (1991) Races of common bean (Phaseolus vulgaris, Fabaceae). Econ Bot 45: 379-396.
27. Yan JB, Shah T, Warburton M, Buckler ES, McMullen MD, Crouch J (2009) Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS ONE 4(12): e8451.
28. Yan JB, Yang XH, Shah T, Sanchez-Villeda H, Li JS, Warburton M, Zhou Y, Crouch JH, Xu YB (2010) High-throughput SNP genotyping with the GoldenGate assay in maize. Mol Breed 25: 441-451.
29. Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Liakat Ali ML, Tung C-W, Reynolds A, Bustamante CD, McCouch SR (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS ONE 5(5): e10780.