A Phaseolus vulgaris diversity panel for andean bean improvement

Crop Science

Volumn 55, Issue 5, 2015, Pages 2149-2160

  Cichy, Karen A ^a,e   Porch, Timothy G ^a   Beaver, James S ^b   Cregan, Perry ^a   Fourie, Deidre ^c   Glahn, Raymond P ^a   Grusak, Michael A ^d   Kamfwa, Kelvin ^e   Katuuramu, Dennis N ^e   McClean, Phil ^f   Mndolwa, Eninka ^g   Nchimbi Msolla, Susan ^h   Pastor Corrales, Marcial A ^a   Miklas, Phillip N ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b UNIVERSITY OF PUERTO RICO   (Puerto Rico)

^c ARC GRAIN CROPS INSTITUTE   (South Africa)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

^e MICHIGAN STATE UNIVERSITY   (United States)

^f NORTH DAKOTA STATE UNIVERSITY   (United States)

^g WASHINGTON STATE UNIVERSITY   (United States)

^h SOKOINE UNIVERSITY OF AGRICULTURE   (Tanzania)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); PHASEOLUS VULGARIS; VACCINIUM MACROCARPON;

EID: 84931585444     PISSN: 0011183X     EISSN: 14350653     Source Type: Journal    
DOI: 10.2135/cropsci2014.09.0653     Document Type: Article

References (61)

1. Abawi, G.S., and M.A. Pastor-Corrales. 1990. Root rots of beans in Latin America and Africa: Diagnosis, research methodologies, and management strategies. CIAT, Cali, Colombia.
2. Aggarwal, V., M. Pastor-Corrales, R. Chirwa, and R. Buruchara. 2004. Andean beans (Phaseolus vulgaris L.) with resistance to the angular leaf spot pathogen (Phaeoisariopsis griseola) in southern and eastern Africa. Euphytica 136:201–210. doi:10.1023/B:EUPH.0000030678.12073.a9
3. Akibode, S., and M. Maredia. 2011. Global and regional trends in production, trade and consumption of food legume crops. Department of Agricultural, Food and Resource Economics, Michigan State Univ., East Lansing, MI.
4. Angioi, S.A., D. Rau, G. Attene, L. Nanni, E. Bellucci, G. Logozzo, et al. 2010. Beans in Europe: Origin and structure of the European landraces of Phaseolus vulgaris L. Theor. Appl. Genet. 121:829–843. doi:10.1007/s00122-010-1353-2
5. Asfaw, A., M. Blair, and C. Almekinders. 2009. Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) landraces from the East African highlands. Theor. Appl. Genet. 120:1–12. doi:10.1007/s00122-009-1154-7
6. Beaver, J.S., T.G. Porch, and M. Zapata. 2008. Registration of ‘Verano’ White Bean. J. Plant Reg. 2:187-189.
7. Beaver, J.S., T. G. Porch, and M. Zapata. 2010. Registration of ‘Badillo’ Light Red Kidney Bean. J. Plant Reg. 4:1-4.
8. Beebe, S. 2012. Common bean breeding in the tropics. Plant Breeding Rev. 36:357–426.
9. Beebe, S., A.V. Gonzalez, and J.A.V. Rengifo. 2000. Research on trace minerals in the common bean. Food Nutr. Bull. 21:387–391.
10. Beebe, S., J. Rengifo, E. Gaitan, M.C. Duque, and J. Tohme. 2001. Diversity and origin of Andean landraces of common bean. Crop Sci. 41:854–862. doi:10.2135/cropsci2001.413854x
11. Bellucci, E., E. Bitocchi, D. Rau, M. Rodriguez, E. Biagetti, A. Giardini, et al. 2014. Genomics of origin, domestication and evolution of Phaseolus vulgaris. In: R. Tuberosa, A. Graner, and E. Frison, editors, Genomics of plant genetic resources. Springer, Netherlands. p. 483–507.
12. Bitocchi, E., E. Bellucci, A. Giardini, D. Rau, M. Rodriguez, E. Biagetti, et al. 2013. Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes. New Phytol. 197:300–313. doi:10.1111/j.1469-8137.2012.04377.x
13. Bitocchi, E., L. Nanni, E. Bellucci, M. Rossi, A. Giardini, P.S. Zeuli, et al. 2012. Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. Proc. Natl. Acad. Sci. USA 109:E788–E796. doi:10.1073/pnas.1108973109
14. Blair, M., L. González, P. Kimani, and L. Butare. 2010. Genetic diversity, inter-gene pool introgression and nutritional quality of common beans (Phaseolus vulgaris L.) from Central Africa. Theor. Appl. Genet. 121:237–248. doi:10.1007/s00122-010-1305-x
15. Blair, M.W., C. Astudillo, M.A. Grusak, R. Graham, and S.E. Beebe. 2009. Inheritance of seed iron and zinc concentrations in common bean (Phaseolus vulgaris L.). Mol. Breed. 23:197–207. doi:10.1007/s11032-008-9225-z
16. Blair, M.W., P. Izquierdo, C. Astudillo, and M.A. Grusak. 2013. A legume biofortification quandry: Variability and genetic control of seed coat micronutrient accumulation in common beans. Front. Plant Sci. 4:275. doi:10.3389/fpls.2013.00275
17. Botstein, D., R.L. White, M. Skolnick, and R.W. Davis. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32:314.
18. Bradbury, P.J., Z. Zhang, D.E. Kroon, T.M. Casstevens, Y. Ramdoss, and E.S. Buckler. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635. doi:10.1093/bioinformatics/btm308
19. Copeland, L.O., and M.H. Erdmann. 1977. Montcalm and Mecosta: Halo blight (Pseudomonas phaseolicola) tolerant kidney bean varieties for Michigan. Ext. Bull. 957. Michigan State Univ., East Lansing, MI.
20. Earl, D., and B. vonHoldt. 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4:359–361. doi:10.1007/s12686-011-9548-7
21. Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of clusters of individuals using the software structure: A simulation study. Mol. Ecol. 14:2611–2620. doi:10.1111/j.1365-294X.2005.02553.x
22. Farnham, M.W., A.P. Keinath, and M.A. Grusak. 2011. Mineral concentration of broccoli florets in relation to year of cultivar release. Crop Sci. 51:2721–2727. doi:10.2135/cropsci2010.09.0556
23. Gepts, P., and F.A. Bliss. 1988. Dissemination pathways of common bean (Phaseolus vulgaris, Fabaceae) deduced from phaseolin electrophoretic variability. II. Europe and Africa. Econ. Bot. 42:86–104. doi:10.1007/BF02859038
24. Gepts, P., K. Kmiecik, P. Pereira, and F.A. Bliss. 1988. Dissemination pathways of common bean (Phaseolus vulgaris, Fabaceae) deduced from phaseolin electrophoretic variability. I. The Americas. Econ. Bot. 42:73–85. doi:10.1007/BF02859036
25. Glahn, R.P., O.A. Lee, A. Yeung, M.I. Goldman, and D.D. Miller. 1998. Caco-2 cell ferritin formation predicts non-radiolabelled food iron availability in an in vitro digestion/Caco-2 cell culture model. J. Nutr. 128:1555–1561.
26. Graham, P.H., J.C. Rosas, C. Estevez de Jensen, E. Peralta, B. Tlusty, J. Acosta-Gallegos, et al. 2003. Addressing edaphic constraints to bean production: The Bean/Cowpea CRSP project in perspective. Field Crops Res. 82:179–192. doi:10.1016/S0378-4290(03)00037-6
27. Hill, W.G., and A. Robertson. 1968. Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38:226–231. doi:10.1007/BF01245622
28. Hillocks, R.J., C.S. Madata, R. Chirwa, E.M. Minja, and S. Msolla. 2006. Phaseolus bean improvement in Tanzania, 1959–2005. Euphytica 150:215–231. doi:10.1007/s10681-006-9112-9
29. Kelly, J.D., and K.A. Cichy. 2012. Dry bean breeding and production technologies. In: M. Siddiq, M.A. Uebersax, editors, Dry beans and pulses production, processing and nutrition. John Wiley & Sons, Inc., Ames, IA. p. 23–54.
30. Kelly, J.D., G.L. Hosfield, G.V. Varner, M.A. Uebersax, R.A. Long, and J. Taylor. 1998. Registration of ‘Red Hawk’ dark red kidney bean. Crop Sci. 38:280–281 10.2135/cropsci1998.0011183X003800010056x.
31. Kimani, P.M., R. Buruchara, K. Ampofo, M. Pyndji, R.M. Chirwa, and R. Kirkby. 2001. Breeding beans for smallholder farmers in Eastern, Central, and Southern Africa: Constraints, achievements, and potential. Pan-African Bean Research Network (PABRA) Millennium Workshop, Novotel Mount Meru, Arusha, Tanzania. 28 May–1 June 2005. CIAT, Kampala.
32. Kwak, M., D. Velasco, and P. Gepts. 2008. Mapping homologous sequences for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris). J. Hered. 99:283–291 10.1093/jhered/esn005 doi:10.1093/jhered/esn005
33. Liebenberg, M.M., A.J. Liebenberg, and Z.A. Pretorius. 2005. Breeding for rust resistance increases dry bean productivity in South Africa. S. Afr. J. Plant Soil 22(2):129–139. doi:10.1080/02571862.2005.10634695
34. Liebenberg, M.M., and Z.A. Pretorius. 2010. Common bean rust: Pathology and control. In: J. Janik, editor, Horticultural reviews, vol. 37. Wiley-Blackwell, Hoboken, NJ. p. 1–99.
35. Liu, K., and S.V. Muse. 2005. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129. doi:10.1093/bioinformatics/bti282
36. Logozzo, G., R. Donnoli, L. Macaluso, R. Papa, H. Knüpffer, and P. Zeuli. 2007. Analysis of the contribution of Mesoamerican and Andean gene pools to European common bean (Phaseolus vulgaris L.) germplasm and strategies to establish a core collection. Genet. Resour. Crop Evol. 54:1763–1779. doi:10.1007/s10722-006-9185-2
37. Mamidi, S., Rossi, M., Annam, D., Moghaddam, S., Lee, R., Papa, R., et al. 2011. Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data. Funct. Plant Biol. 38(12), 953–967.
38. McClean, P., J. Terpstra, M. McConnell, C. White, R. Lee, and S. Mamidi. 2012. Population structure and genetic differentiation among the USDA common bean (Phaseolus vulgaris L.) core collection. Genet. Resour. Crop Evol. 59:499–515. doi:10.1007/s10722-011-9699-0
39. McClean, P.E., J.R. Myers, and J.J. Hammond. 1993. Coefficient of parentage and cluster analysis of North American dry bean cultivars. Crop Sci. 33:190–197. doi:10.2135/cropsci1993.0011183X003300010034x
40. Miklas, P.N., J.R. Smith, and S.P. Singh. 2006. Registration of common bacterial blight resistant white kidney bean germplasm line USWK-CBB-17. Crop Sci. 46:2338–2339. doi:10.2135/cropsci2006.04.0246
41. Porch, T.G., J.S. Beaver, G. Abawi, C. Estévez de Jensen, and J.R. Smith. 2014a. Registration of a small-red dry bean germplasm, TARS-LFR1, with multiple disease resistance and superior performance in low nitrogen soils. J. Plant Reg. 8:177–182. doi:10.3198/jpr2013.03.0015crg
42. Porch, T.G., S. Valentin, C. Estevez de Jensen, and J.S. Beaver. 2014b. Identification of soil-borne pathogens in a common bean root rot nursery in Isabela, Puerto Rico. J. Agric. UPR 98:1–14.
43. Pritchard, J.K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–959.
44. Rambaut, A. 2012. FigTree. Institute of Evolutionary Biology, University of Edinburgh, http://tree.bio.ed.ac.uk/ (accessed 18 May 2015).
45. Repinski, S.L., M. Kwak, and P. Gepts. 2012. The common bean growth habit gene PvTFL1y is a functional homolog of Arabidopsis TFL1. Theor. Appl. Genet. 124:1539–1547. doi:10.1007/s00122-012-1808-8
46. Rogers, S., and A. Bendich. 1985. Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol. Biol. 5:69–76. doi:10.1007/BF00020088
47. Rosenberg, N.A. 2004. Distruct: A program for the graphical display of population structure. Mol. Ecol. 4:137–138. doi:10.1046/j.1471-8286.2003.00566.x
48. Schmutz, J., P.E. McClean, S. Mamidi, G.A. Wu, S.B. Cannon, J. Grimwood, et al. 2014. A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet. 46:707–713. doi:10.1038/ng.3008
49. Shii, C., M. Mok, S. Temple, and D. Mok. 1980. Expression of developmental abnormalities in hybrids of Phaseolus vulgaris L. Interaction between temperature and allelic dosage. J. Hered. 71:218–222.
50. Singh, N., D.R. Choudhury, A.K. Singh, S. Kumar, K. Srinivasan, R.K. Tyagi, et al. 2013. Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties. PLoS ONE 8:E84136. doi:10.1371/journal.pone.0084136
51. Singh, S., P. Gepts, and D. Debouck. 1991a. Races of common bean (Phaseolus vulgaris, Fabaceae). Econ. Bot. 45:379–396. doi:10.1007/BF02887079
52. Singh, S., J.A. Gutiérrez, A. Molina, C. Urrea, and P. Gepts. 1991b. Genetic diversity in cultivated common bean: II. Markerbased analysis of morphological and agronomic traits. Crop Sci. 31:23–29. doi:10.2135/cropsci1991.0011183X003100010005x
53. Song, Q., G. Jia, D.L. Hyten, J. Jenkins, E.Y. Hwang, S. Schroeder et al. 2015. SNP marker development for linkage map construction. Anchoring of the common bean whole genome sequence and genetic research. PLoS ONE (in review).
54. Sonnante, G., T. Stockton, R.O. Nodari, V.L. Becerra Velásquez, and P. Gepts. 1994. Evolution of genetic diversity during the domestication of common-bean (Phaseolus vulgaris L.). Theor. Appl. Genet. 89:629–635. doi:10.1007/BF00222458
55. van Berloo, R. 2008. GGT 2.0: Versatile software for visualization and analysis of genetic data. J. Hered. 99:232–236 10.1093/jhered/esm109.doi:10.1093/jhered/esm109
56. Vandemark, G.J., M.A. Brick, J.M. Osorno, J.D. Kelly, and C.A. Urrea. 2014. Edible grain legumes. In: S. Smith, B. Diers, J. Specht, and B. Carver, editors, Yield gains in major U.S. field crops. ASA, CSSA, SSSA, Madison, WI. p. 87–124.
57. van Schoonhoven, A., and M.A. Pastor-Corrales. 1987. Standard system for the evaluation of bean germplasm. CIAT, Cali, Colombia.
58. Voysest, O., M.C. Valencia, and M.C. Amezquita. 1994. Genetic diversity among Latin American Andean and Mesoamerican common bean cultivars. Crop Sci. 34:1100–1110. doi:10.2135/cropsci1994.0011183X003400040049x
59. Wang, N., and J.K. Daun. 2005. Determination of cooking times of pulses using an automated Mattson cooker apparatus. J. Sci. Food Agric. 85:1631–1635. doi:10.1002/jsfa.2134
60. Weir, B.S., and C. Cockerham. 1996. Genetic data analysis 2: Methods for discrete population genetic data. Sinauer Assoc., Sunderland, MA.
61. Wells, H.F., J.K. Bond, and S. Thornsbury. 2014. Vegetable and pulses outlook no. (VGS-354). USDA Economic Research Service, Washington DC.