01/05/2026

Adegbola, R. and Brown, J.K. 2024. Genome characterization of seed-transmitted bean common mosaic virus tepary bean isolates. American Phytopathological Society, Memphis TN July 27-30, 2024 (poster; abstract). [Full manuscript in preparation.]

Beaver, J. S., González, A., Mateo, B., Lutz, G. G., Miranda, A., Rosas, J. C., & Porch, T. G. 2024. Release of multiple virus and bruchid resistant Mesoamerican bean germplasm lines PR1303-129 and PR1743-44. Journal of Plant Registrations, 18, 149–156.

Berlingeri, J., Fuentes, A., Ranario, E. et al. (2025). Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance. Theor Appl Genet 138: 205. https://doi.org/10.1007/s00122-025-04984-y

Bolt, T.M., Riggs, M., Sun, W., Yu, S., Lerno, L., Tian, L., Gepts, P., Palkovic, A., Parker, T.A., Bornhorst, G.M. and Diepenbrock, C.H. (2025), Comparison of simulated gastrointestinal digestion platforms with varying complexity and sample mass requirements, using common bean (Phaseolus vulgaris L.) as a model. As of the end of review period, a revised manuscript was under review at J Sci Food Agric.

Chiaravallotti, I., & Hoyos‐Villegas, V. (2025). Simulations of genomic selection implementation pathways in common bean (Phaseolus vulgaris L.) using parametric and nonparametric models. The Plant Genome, 18(4), e70142.

Chiaravallotti, I., Pauptit, O., & Hoyos‐Villegas, V. (2025). Environment ensemble models for genomic prediction in common bean (Phaseolus vulgaris L.). The Plant Genome, 18(2), e70057.

Chipandwe, S., Hamabwe, S., Mwense, B., Kuwabo, K., Lungu, D., Chiaravallotti, I., ... & Kamfwa, K. (2025). GGE biplot and QTL analyses for seed yield in an Andean population of common bean. Euphytica, 221(5), 1-11.

Cordoba-Novoa, H. A., & Hoyos-Villegas, V. (2025). Genetic architecture of ideotype-related traits in middle American beans through single trait, multi-trait and epistatic genome-wide analyses. Theoretical and Applied Genetics, 138(6), 131.

Cordoba-Novoa, H., & Hoyos-Villegas, V. (2025). Prioritization of Deleterious Mutations Improves Genomic Prediction and Increases the Rate of Genetic Gain in Common Bean (Phaseolus vulgaris L.), a Simulation Study. bioRxiv, 2025-05.

Cordoba-Novoa, H., Buckler, E. S., Romay, C. M., Berthel, A., Johnson, L., Balasubramanian, P., & Hoyos-Villegas, V. (2025). Phylogenetic Analysis and Machine Learning Identify Signatures of Selection and Predict Deleterious Mutations in Common Bean. bioRxiv, 2025-05.

Cordoba-Novoa, H., Zhang, B., Guo, Y., Aslam, M. M., Fritschi, F. B., & Hoyos-Villegas, V. (2025). Whole plant transpiration responses of common bean (Phaseolus vulgaris L.) to drying soil: Water channels and transcription factors. Plant Physiology and Biochemistry, 222, 109759.

Cordoba-Novoa, H.A., Sadohara, R., Gali, K.K., Zhou, J., Hart, J., Alexandre, A.C.S., Cichy, K., Wilker, J., Dohle, S., Mukankusi, C., Warkentin, T.D., Rajcan, I., Eskandari, M., Marsolais, F., Vandemark, G., von Wettberg, E., Palanichamy, D., Thomassin, P., Diepenbrock, C.H., Nickerson, M., Orsat, V., Osorno, J.M.,

Hoyos-Villegas, V. 2025. Breeding for plant-based proteins in pulse and legume crops: perspectives, challenges and opportunities. Crop Science, 65, e70137. https://doi.org/10.1002/csc2.70137.

Craine EB, Murray-Nalbandian E†, Richter J†, Ganjyal GM, Barriball S, Peters TE, Schlautman B. 2025. Physicochemical Characterization of Whole and Split Perennial Baki Bean Flours. Legume Science. 7(3): e70046.

Erfatpour, M., Simons, K.J., Roy, J., Figueroa-Cerna, J.C., Lee, R., Beaver, J., McClean, P.E. and Osorno, J.M., 2025. Fine mapping and identification of causal alleles at the Ur-11 locus controlling rust resistance in common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics, 138(3), pp.1-14.

Esquivel Garcia, L., Zaleski-Cox, M., Chatterton, S., Calder, B., Derbyshire, M. D., Newman, T. E., & Hoyos-Villegas, V. (2025). Classifying aggressiveness on common bean (Phaseolus vulgaris L.) of a Canadian collection of Sclerotinia sclerotiorum L. de Bary isolates. Canadian Journal of Plant Pathology, 1-17.

Fashakin, O.O., Cichy, K. and Medina-Meza, I.G. (2025), Enhancing phytochemical composition and nutritional profiles in dry bean varieties through roasting. Journal of the Science of Food and Agriculture, 105: 8694-8705. https://doi.org/10.1002/jsfa.70106

Glick AA, Winham DM, Heer MM, Hutchins AM, Shelley MC. Nutrition Knowledge Varies by Food Group and Nutrient Among Adults. Foods. 2025 Feb 12;14(4):606.

Hooper, S., Peplinski, H., Akariza, A.P., Burtovoy, S., Jeffery, H., Osorno, J.M., Miklas, P., McClean, P. and Cichy, K. (2025), Protein content and flour viscosity predict pasta quality in pinto bean germplasm. Journal of the Science of Food and Agriculture, 105: 8400-8411. https://doi.org/10.1002/jsfa.70084

Irvin, M. J., Chilvers, M. I., Wright, E. M., Jacobs, J. L., Hoyos‐Villegas, V., & Gomez, F. E. (2025). Response of Elite Dry Bean (Phaseolus vulgaris) Genotypes to Fusarium oxysporum and Rhizoctonia solani Root Rot. Plant Pathology, 74(9), 2682-2696.

Ivey, C. B., Hahn, P., Vallad, G. V., Soto-Adames, F. N., Hochmuth, R. C., Beuzelin, J. M., Jean-Louis, A., & Smith, H. A. (2025). Abundance of Megalurothrips usitatus (Bagnall) (Thysanoptera: Thripidae) and other thrips in commercial snap bean fields in the Homestead Agricultural Area (HAA). Florida Entomologist, 108(1). https://doi.org/10.1515/FLAENT-2024-0075

Izquierdo, P., Wright, E.M., Cichy, K. (2025) GWAS-assisted and multitrait genomic prediction for improvement of seed yield and canning quality traits in a black bean breeding panel, G3 Genes|Genomes|Genetics, Volume 15, Issue 3, jkaf007, https://doi.org/10.1093/g3journal/jkaf007 

Luong RH, Winham DM, Shelley MC, Glick AA. Plant-Based Meat Alternatives Predicted by Theory of Planned Behavior among Midwest Undergraduates. Foods. 2024 Nov 26;13(23):3801.

Mugovo, I., M. Chinji, R. Thole, S.M. Hamabwe, K. Kuwabo, M. Nkandela, K. Zimba, C. Jochua, C. Urrea, P. McClean, J.M. Osorno, and K. Kamfwa. 2025. Genome-wide association analysis for weevil resistance in the Andean gene pool of common bean. Euphytica 221, 13.

Myers JR , Kean D, Kawai S, Davis J, Landgraver E, Heitholt J, Keith J, Meints B, Miles C, Ganjyal GM, Rezaey M†, Karasev AV, Orellana GE, Hernández J, Cichy K. 2025. Release of ‘Poporito’ and ‘Noche Nuña’ Novel Popping Bean (Phaseolus vulgaris L.) Cultivars. HortScience. 60 (12), 2254-2260.

Osorno, J.M., De Oliveira, M., Figueroa‐Cerna, J.C., Khan, N. and Maisonneuve, M., 2025. Registration of ‘ND Galaxy’: A black bean cultivar with intermediate resistance to common bacterial blight and resistance to bean common mosaic virus. Journal of Plant Registrations, 19(3), p.e70023.

Osorno, J.M., Khan, N., Figueroa‐Cerna, J.C. and Maisonneuve, M., 2025. A new pink bean cultivar with improved agronomic performance: Registration of ‘ND Rosalind’. Journal of Plant Registrations, 19(1), p.e20427.

Palkovic, A., Bolt, T., Berlingeri, J. Riggs, M., Adaskaveg, J., Lo, S., Diepenbrock, C. (2025). Summary of activities ongoing in the UC Davis Plant Sciences bean/grain legume breeding program. Annual Report of the Bean Improvement Cooperative 68: 54-55.

Ponskhe, K., DuBois, A., Beaudry, R., Hooper, S., Cichy, K., Mayhew, E. Effect of processing, cultivar, and crop year on volatile composition in pulses and pulse flours analyzed by headspace-solid phase microextraction gas chromatography-mass spectrometry. Journal of Food Science 90, no. 10: e70608. https://doi.org/10.1111/1750-3841.70608 

Ponskhe, K., DuBois, A., Beaudry, R., Hooper, S., Cichy, K., Mayhew, E. Evaluating the impact of cultivar and processing on pulse off-flavor through descriptive analysis, GC-MS, and e-nose. Journal of Food Science 90, no. 10: e70610. https://doi.org/10.1111/1750-3841.70610 

Sadohara, R., Wiesinger, J. A., Thompson, H. J., Glahn, R. P., & Cichy, K. (2025). Yellow bean (Phaseolus vulgaris L.) germplasm with less dietary fiber have shorter cooking times and more bioavailable iron. Current Research in Food Science, 10, 100942. https://doi.org/10.1016/j.crfs.2024.100942

Tay, K., N. Zapata, C.A. Urrea, A. Elazab, M. Garriga, and L. León. 2025. Screening terminal drought tolerance in dry bean genotypes and commercial bean cultivars in Chile. Agronomy, 15(7), 1499; https://doi.org/10.3390/agronomy15071499

Thomas, L., Dlamini, N.N., Cichy, K., Swada, J., Mayhew, E.J. (2025) Toward Sustainable Food and Packaging Choices: Consumer Perception of Quality and Sustainability of Pulses Packaged in Metal, Glass, and Plastic. Journal of Food Science 90, no. 10: e70585. https://doi.org/10.1111/1750-3841.70585 

Thomas, L., Cichy, K., Swada, J. (2025) Evaluation of Cooking Time and Impact of Retort Processing, Packaging Material, and Calcium Chloride Additive on Pulse (Phaseolus vulgaris, Phaseolus coccineus, and Cicer arietinum) Quality Attributes, Journal of Food Processing and Preservation,1164668, https://doi.org/10.1155/jfpp/1164668

Urrea, C.A., and C. Kaarstad. 2025. 2024 Nebraska dry bean variety trials. The Bean Bag 43(1): 12-19.

Van Haute, M.J.S., Q. Yang, N. Korth, M.M. Happ, C.R. Kok, C. Miao, J.L. Clarke, K. Karnik, K.M. Eskridge, C.A. Urrea, D.L. Hyten, J.C. Schnable, D.J. Rose, and A.K. Benson. 2025. Genetic variation and historical breeding patterns in common bean (Phaseolus vulgaris L.) affect fermentation patterns by the human gut microbiome. Commun Biol 8, 1690. https://doi.org/10.1038/s42003-025-09089-2

Wang, W., Dolan, K., Cichy, K. (2025) Effect of Calcium on Pouch Processing Quality in Organic Dry Beans and Comparison of Processing Quality in Cans and Pouches. International Journal of Food Properties Volume 60, Issue 1, vvae085, https://doi.org/10.1093/ijfood/vvae085

Whyte, M., Jackson, M., Volpato, L., Wright, E. M., Hoyos‐Villegas, V., & Gomez, F. E. (2025).Prediction of symbiotic nitrogen fixation in common bean (Phaseolus vulgaris L.) using unmanned aerial system remote sensing. The Plant Phenome Journal, 8(1), e70031.

Winham DM, Camacho-Arriola M, Glick AA, Hall CA, Shelley MC. Pea and Lentil Flours Increase Postprandial Glycemic Response in Adults with Type 2 Diabetes and Metabolic Syndrome. Foods. 2025 May 29;14(11):1933.

Kachapulula, J S., K. Kuwabo, S. M. Hamabwe, M. Nkandela, C. Mukuma, A. Soler-Garzón, P. N. Miklas, and K. Kamfwa. 2025. Quantitative trait loci analysis for anthracnose resistance in a population derived from Andean varieties Bukoba and Kijivu of common bean (Phaseolus vulgaris L.). Plant Breeding 144:432-439. https://doi.org/10.1111/pbr.13264

Soler-Garzón, A., J. Hart, and P. N. Miklas. 2025. Snap bean diversity for resistance to bean common mosaic and necrosis viruses examined using new and existing candidate gene-linked markers. Molecular Breeding 45:98 https://doi.org/10.1007/s11032-025-01605-w

Soler-Garzón, A., F. S. Lopes, J. Roy, J. Clevenger, Z. Myers, W. Korani, W. A. Pereire, Q. Song, T. Porch, P. E. McClean, and P. N. Miklas. 2025. Genetic mapping resistance to white mold in two pinto bean recombinant inbred line populations. The Plant Genome 18: e20538. https: //doi.org/10.1002/tpg2.20538

Soler-Garzón, A., and P. N. Miklas. 2025. An RNase H-Like gene complements resistance to Bean common mosaic necrosis virus in Phaseolus vulgaris. The Plant Genome 18: e70046. https://doi.org/10.1002/tpg2.70046 

Publication - Ready to Submit (authors in italics are students and/or postdoctoral co-authors)

Bhawna, L., J. Trapp, I. Ahmad, D.B. Dola, J. Heitholt, P.N. Miklas, D.K. Harris.  Assessing

drought tolerance in the Durango diversity panel (DDP) of dry beans (Phaseolus

vulgaris): insights from multi-location field experiment using drought tolerance indices. 

To be submitted to PLoS One.