James Kelly, Ph.D.

James Kelly


Department of Plant, Soil and Microbial Sciences

Saginaw Valley Research and Extension Center

University Distinguished Professor

Telephone: 517-353-0169

Plant and Soil Sciences Building
1066 Bogue Street, Room 370
East Lansing, MI 48824

Area of Expertise:

Dry bean breeding and genetics with emphasis on the use of molecular markers to assist in selection for yield, plant architecture, processing quality, drought tolerance and disease resistance; participation in international agricultural activities related to genetic improvement in beans through the Legume Innovation Lab.


B.S., Queens University of Belfast, N. Ireland, 1968, Botany
B. Agr. (Hons.), Queens University of Belfast, N. Ireland, 1969, Agricultural Botany
M.S., 1971, University of Wisconsin, 1971, Plant Breeding & Genetics
Ph.D., 1974, University of Wisconsin, 1974, Plant Breeding & Genetics, Minor: Botany


 Recent Publications: In print:

  1. Alladassi, B.M.E., S.T. Nkalubo, C. Mukankusi, H.N. Kayaga, P. Gibson, R. Edema, C.A. Urrea, J.D. Kelly, and P.R. Rubaihayo. 2018. Identification of common bean genotypes with dual leaf and pod resistance to common bacterial blight disease in Uganda. African Crop Science Journal 26:63-77.
  2. Cappa, C., J. D. Kelly, and P. K.W. Ng. 2018. Seed characteristics and physicochemical properties of powders of 25 edible dry bean varieties. Food Chemistry 253:305–313. doi.org/10.1016/j.foodchem.2018.01.048
  3. Kelly, J.D., G.V. Varner, P. N. Miklas, K. A. Cichy and E.M. Wright. 2018. Registration of ‘Cayenne’ small red bean. J. Plant Regist. 12:194–198: doi:10.3198/jpr2017.05.0033crc
  4. Kelly, J.D., G.V. Varner, M.I. Chilvers, K. A. Cichy and E.M. Wright. 2018. Registration of ‘Red Cedar’ dark red kidney bean. J. Plant Regist. 12:199–202 doi:10.3198/jpr2017.05.0034crc
  5. Mendoza, F.A., K.A. Cichy, C. Sprague, A. Goffnett, R. Lu, and J.D. Kelly. 2018. Prediction of canned black bean texture (Phaseolus vulgaris L.) from intact dry seeds using visible/near-infrared spectroscopy and hyperspectral imaging data. J. Sci. Food Agric. 98: 283–290. doi: 10.1002/jsfa.8469
  6. Wang, W., J.L. Jacobs, M.I. Chilvers, C. M. Mukankusi, J.D. Kelly, and K.A. Cichy. 2018. QTL analysis of Fusarium root rot resistance in an Andean x Middle American RIL population. Crop Sci. 58:1166–1180. doi:10.2135/cropsci2017.10.0608
  7. Ai, Y., Y. Jin, J. D. Kelly, and P. K.W. Ng. 2017. Composition, functional properties, starch digestibility, and cookie-baking performance of dry bean powders from 25 Michigan-grown varieties.  Cereal Chemistry 94:400-408. doi: 10.1094/cchem-04-16-0089-r
  8. Alladassi, B.M.E.,  S.T. Nkalubo, C. Mukankusi, E. S. Mwale, P. Gibson, R. Edema, C.A. Urrea, J. D. Kelly, and P. R. Rubaihayo. 2017. Inheritance of resistance to common bacterial blight in four selected common bean (Phaseolus vulgaris L.) genotypes. J. Plant Breed. Crop Sci. 9:71-78. doi: 10.5897/JPBCS2017.0644
  9. Heilig, J.A. J. S. Beaver, E. M. Wright, Q. Song, and J. D. Kelly. 2017. QTL analysis of symbiotic nitrogen fixation in a black bean population. Crop Sci. 57: 118-129. doi:10.2135/cropsci2016.05.0348
  10. Heilig, J.A., E.M. Wright, and J.D. Kelly. 2017. Symbiotic N fixation of black and navy beans under organic production systems. Agron. J.109:1-8. doi: 10.2134/agronj2017.01.0051
  11. Kamfwa, K., D. Zhao, J. D. Kelly and K. A. Cichy. 2017. Transcriptome analysis of two recombinant inbred lines of common bean contrasting for symbiotic nitrogen fixation. PLoS ONE 12(2):e0172141. doi:10.1371/journal.pone.0172141
  12. McClean, P.E., S.M. Moghaddam, A-F. Lopez-Millan, M. A. Brick,  J. D. Kelly, P. N. Miklas, J. M. Osorno, T. G. Porch, C.A. Urrea, A. Soltani and M. A. Gruzak. 2017. Phenotypic diversity for seed element concentration in North American dry bean germplasm of Middle American Ancestry. Crop Sci. 57:3129-3144. doi:10.2135/cropsci2017.04.0244
  13. Mendoza, F.A., J.D. Kelly, and K.A. Cichy. 2017. Automated prediction of sensory scores for color and appearance in canned black beans (Phaseolus vulgaris L.) using a color imaging technique.  International Journal of Food Properties 20:83-99. doi:10.1080/10942912.2015.1136939
  14. Odogwu, B.A., S. T. Nkalubo, C. Mukankusi, T. Odong, H. E. Awale, P. Rubaihayo, and J. D. Kelly. 2017. Phenotypic and genotypic screening for rust resistance in common bean germplasm in Uganda. Euphytica 213:49. doi: 10.1007/s10681-016-1795-y
  15. Padder, B.A., P.N. Sharma, H.E. Awale, and J.D. Kelly. 2017. Colletotrichum lindemuthianum, the causal agent of bean anthracnose. J. Plant Pathology 99: 317-330. doi: 10.4454/jpp.v99i2.3867
  16. Rossman, D.R., A. Rojas, J.L. Jacobs, C. Mukankusi, J.D. Kelly, and M.I. Chilvers. 2017. Pathogenicity and virulence of soilborne oomycetes on dry bean (Phaseolus vulgaris). Plant Disease101:1851-1859. doi.org/10.1094/PDIS-02-17-0178-RE
  17. Traub, J., J. D. Kelly, and W. Loescher. 2017. Early metabolic and photosynthetic responses to drought stress in common and tepary bean. Crop Sci. 57:1-17.  doi:10.2135/cropsci2016.09.0746 
  18. Ai, Y., K A. Cichy, J. B. Harte, J. D. Kelly, and P. K.W. Ng. 2016. Effects of extrusion cooking on the chemical composition and functional properties of dry bean powders. Food Chemistry 211:538–545. doi:10.1016/j.foodchem.2016.05.095
  19. Hoyos-Villegas, V., E. M. Wright and J.D. Kelly. 2016. GGE biplot analysis of yield associations with root traits in a Mesoamerican bean diversity panel. Crop Sci. 56:1081-1094. doi:10.2135/cropsci2015.10.0609
  20. Hoyos-Villegas, V., Q. Song, J.D. Kelly. 2016. Genomewide association analysis for drought tolerance and associated traits in common bean. The Plant Genome 9: doi:10.3835/plantgenome2015.12.0122
  21. Hoyos-Villegas, V., Q. Song, E.M. Wright, S. E. Beebe and J.D. Kelly. 2016. Joint linkage QTL mapping for yield and agronomic traits in a composite map of three common bean RIL populations. Crop Sci. 56:2546–2563. doi:10.2135/cropsci2016.01.0063.
  22. Isaacs, K.B., S.S. Snapp, J.D. Kelly and K. R. Chung. 2016. Farmer knowledge identifies competitive bean ideotype for maize-bean intercrop systems in Rwanda. Agriculture & Food Security 5:15. doi 10.1186/s40066-016-0062-8
  23. Kelly, J.D., G.V. Varner, S. Hooper, K.A. Cichy, and E.M. Wright. 2016. Registration of ‘Samurai’ otebo bean. J. Plant Registrations 10:109-114. doi:10.3198/jpr2015.09.0051crc.
  24. Mendoza, F.A, J. D. Kelly, and K. A. Cichy. 2016. Automated prediction of sensory scores for color and appearance in canned black beans (Phaseolus vulgaris L.) using machine vision. International Journal of Food Properties, doi:10.1080/10942912.2015.1136939.
  25. Moghaddam, S.M., S. Mamidi, J. M. Osorno, R. Lee, M. Brick, J. Kelly, P. Miklas, C. Urrea, Q. Song, P. Cregan, J. Grimwood, J. Schmutz, and P. E. McClean. 2016. Genome-wide association study identifies candidate loci underlying agronomic traits in a Middle American diversity panel of common bean. The Plant Genome 9: doi: 10.3835/plantgenome2016.02.0012
  26. Nakedde, T., F. J. Ibarra-Perez, C. Mukankusi, J. G. Waines, and J. D. Kelly. 2016. Mapping of QTL associated with Fusarium root rot resistance and root architecture traits in black beans. Euphytica 212: 51-63. doi: 10.1007/s10681-016-1755-6
  27. Odogwu, B.A., S. T. Nkalubo, C. Mukankusi, P. Paparu, P. Rubaihayo, J. D. Kelly, and J. Steadman. 2016. Prevalence and variability of the common bean rust in Uganda. African Journal of Agricultural Research. 11: 4990-4999. doi: 10.5897/AJAR2016.11600
  28. Padder, B.A., K. Kamfwa, H.E. Awale and J. D. Kelly. 2016. Transcriptome profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum pathosystem. PLoS ONE 11(11): e0165823.doi:10.1371/journal.pone.0165823.
  29. Zuiderveen, G.H., B. A. Padder, K. Kamfwa, Q. Song and J. D. Kelly. 2016. Genome-wide association study of anthracnose resistance in Andean beans. PLoS ONE 11(6): e0156391doi:10.1371/journal.pone.0156391
  30. Hoyos-Villegas, V., W. Mkwaila, P.B. Cregan and J.D. Kelly. 2015. QTL analysis of white mold avoidance in pinto bean (Phaseolus vulgaris). Crop Sci. 55:2116-2129. doi:10.2135/cropsci2015.02.0106.
  31. Kamfwa, K., K.A. Cichy and J.D. Kelly. 2015. Genome-wide association study of agronomic traits in common bean. The Plant Genome 8: doi:10.3835/plantgenome2014.09.0059.
  32. Kamfwa, K., K.A. Cichy and J.D. Kelly. 2015. Genome-wide association analysis of symbiotic nitrogen fixation in common bean. Theor. Appl. Genet. 128:1999-2017. doi. 10.1007/s00122-015-2562-5.
  33. Kelly, J.D., G.V. Varner, K.A. Cichy, and E.M. Wright. 2015. Registration of ‘Alpena’ navy bean. J. Plant Registrations 9:10-14. doi:10.3198/jpr2014.04.0025crc.
  34. Kelly, J.D., G.V. Varner, K.A. Cichy, and E.M. Wright. 2015. Registration of ‘Zenith’ black bean. J. Plant Registrations 9:15-20. doi:10.3198/jpr2014.05.0035crc.
  35. Kelly, J.D., J. Trapp, P.N. Miklas, K.A. Cichy, and E.M. Wright. 2015. Registration of ‘Desert Song’ Flor de Junio and ‘Gypsy Rose’ Flor de Mayo common bean cultivars J. Plant Registrations 9:133-137. 
  36. Sousa, L.L., A. O. Gonçalves, M. C. Gonçalves-Vidigal, G. F. Lacanallo, A. C. Fernandez, H. Awale and J. D. Kelly. 2015. Genetic characterization and mapping of anthracnose resistance of Corinthiano common bean landrace cultivar. Crop Sci. 55:1900-1910. doi:10.2135/cropsci2014.09.0604.
  37. Burt, A.J., H. M. William, G. Perry, R. Khanal, K. P. Pauls, J. D. Kelly, A. Navabi. 2015.  Candidate gene identification with SNP marker-based fine mapping of anthracnose resistance gene Co-4 in common bean. PLoS ONE 10(10): e0139450. doi:10.1371/journal.pone.0139450.
  38. Brisco, E.I., T.G. Porch, P.B. Cregan, and J.D. Kelly. 2014 Quantitative trait loci associated with resistance to Empoasca in common bean. Crop Sci. 54: 2509-2519. doi: 10.2135/cropsci2014.02.0159.
  39. Cichy, K.A., A. Fernandez, A. Kilian, J.D. Kelly, C.H. Galeano, S. Shaw, M. Brick, D. Hodkinson and E. Troxtell. 2014. QTL analysis of canning quality and color retention in black beans (Phaseolus vulgaris L.). Molecular Breeding 33:139-154. doi: 10.1007/s11032-013-9940-y.
  40. Kelly, J.D., G.V. Varner, K.A. Cichy, and E.M. Wright. 2014. Registration of ‘Powderhorn’ great northern bean. J. Plant Registrations 8:1-4. doi:10.3198/jpr2013.05.0020crc.
  41. Mendoza, F.A., K. Cichy, R. Lu and J.D. Kelly. 2014. Evaluation of canning quality traits in black beans (Phaseolus vulgaris L.) by visible/near-infrared spectroscopy. Food Bioprocess Technol. 7:2666-2678.
  42. Miklas, P.N., J. D. Kelly, J. R. Steadman and S. McCoy. 2014. Registration of Partial White Mold Resistant Pinto Bean Germplasm Line USPT-WM-12. J. Plant Registrations 8:183–186.
  43. Mukeshimana, G., L. Butare, P.B. Cregan, M. W. Blair and J. D. Kelly. 2014. Quantitative Trait Loci associated with drought tolerance in common bean. Crop Sci. 54: 923-938. doi: 10.2135/cropsci2013.06.0427.
  44. Mukeshimana, G., A.L. Lasley, W.H. Loescher and J.D. Kelly. 2014. Identification of shoot traits related to drought tolerance in common bean seedlings. J. Amer. Soc. Hort. Sci. 139:299–309.   
  45. Oblessuc, P.R., R. M. Baroni, G. da Silva Pereira, A. F. Chioratto, S.A.M. Carbonell, B. Briñez, L. Da Costa E Silva, A. A. F. Garcia, L.E.A. Camargo, J. D. Kelly, and L. L. Benchimol-Reis. 2014. Quantitative analysis of race-specific resistance to Colletotrichum lindemuthianum in common bean. Molecular Breeding 34:1313-1329.
  46. Schmutz, J., P. McClean…J.D. Kelly... S.A. Jackson. 2014. A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics.46:707-713. doi:10.1038/ng.3008. [41 authors:  J.D. Kelly  no. 26].
  47. Sousa, L.L.,  A. S. Cruz, P. S. Vidigal Filho, V. A. Vallejo, J. D. Kelly and M.C. Gonçalves-Vidigal. 2014. Genetic mapping of the resistance allele Co-52 to Colletotrichum lindemuthianum in the common bean MSU 7-1 line.  Aust. J. Crop Science 8:317-323.