Publications

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2025

Classifying aggressiveness on common bean (Phaseolus vulgaris L.) of a Canadian collection of Sclerotinia sclerotiorum L. de Bary isolates. L Esquivel Garcia, M Zaleski-Cox, S Chatterton, B Calder, MD Derbyshire, TE Newman, V Hoyos-Villegas. 

The future role of regional research infrastructures and networks toward the global plant phenotyping community. S Dhondt, R Dickman, S Fahrner, R Pieruschka, V Hoyos-Villegas, S Robinson, P von Gillhaussen.

Simulations of genomic selection implementation pathways in common bean (Phaseolus vulgaris L.) using parametric and nonparametric models. I Chiaravallotti, V Hoyos-Villegas.

Response of Elite Dry Bean (Phaseolus vulgaris) Genotypes to Fusarium oxysporum and Rhizoctonia solani Root Rot. MJ Irvin, MI Chilvers, EM Wright, JL Jacobs, V Hoyos-Villegas, FE Gomez.

Affordable phenomics: Expanding access to enhancing genetic gain in plant breeding. V Hoyos-Villegas, M Jackson, M Vargas-Cedeño, EE Farmer, M Hanneman, A Mazis, KD Singh, W Sangjan, M McNair, S Sankaran, S Tirado Tolosa, MA Gore, TW Rife. 

Prediction of symbiotic nitrogen fixation in common bean (Phaseolus vulgaris L.) using unmanned aerial system remote sensing. M Whyte, M Jackson, L Volpato, EM Wright, V Hoyos‐Villegas, FE Gomez.  

Use of arduino‐based potentiometric sensors to measure changes in leaf apoplastic pH in common bean (Phaseolus vulgaris L.). R McGee, J Lin, R Dahiya, V Hoyos‐Villegas. 

Breeding for quantitative disease resistance: Case studies, emerging approaches, and exploiting pathogen variation. R McGee, M Zaleski‐Cox, MA Jayawardana, BL Tillman, O Wally, L Esquivel‐Garcia, WGD Fernando, H Raman, HS Bariana, T Copley, AH Carter, V Hoyos‐Villegas. 

Adapting SAM with Dynamic Similarity Graphs for Few-Shot Parameter-Efficient Small Dense Object Detection: A Case Study of Chickpea Pods in Field Conditions. X Jiang, Y Liu, M Debbagh, Y Tian, V Hoyos-Villegas, V Adamchuk, S Sun.  

Prioritization of Deleterious Mutations Informs Genomic Prediction and Increases the Rate of Genetic Gain in Common Bean (Phaseolus vulgaris L.), a Simulation Study. HA Cordoba, V Hoyos-Villegas. 

Breeding for plant‐based proteins in pulse and legume crops: Perspectives, challenges and opportunities. HA Cordoba, R Sadohara, KK Gali, J Zhou, J Hart, AC Silveira Alexandre, K Cichy, J Wilker, S Dohle, C Mukankusi, TD Warkentin, I Rajcan, M Eskandari, F Marsolais, G Vandemark, E von Wettberg, D Palanichamy, P Thomassin, CH Diepenbrock, M Nickerson, V Orsat, JM Osorno, V Hoyos‐Villegas.

Environment ensemble models for genomic prediction in common bean (Phaseolus vulgaris L.). I Chiaravallotti, O Pauptit, V Hoyos‐Villegas.

Genetic architecture of ideotype-related traits in middle American beans through single trait, multi-trait and epistatic genome-wide analyses. HA Cordoba-Novoa, V Hoyos-Villegas.

Phylogenetic Analysis and Machine Learning Identify Signatures of Selection and Predict Deleterious Mutations in Common Bean. HA Cordoba-Novoa, ES Buckler, CM Romay, A Berthel, L Johnson, P Balasubramanian, V Hoyos-Villegas.

GGE biplot and QTL analyses for seed yield in an Andean population of common bean. S Chipandwe, S Hamabwe, B Mwense, K Kuwabo, D Lungu, I Chiaravallotti, V Hoyos-Villegas, K Kamfwa.    

GWAS-Assisted and multi-trait genomic prediction for improvement of seed yield and canning quality traits in a black bean breeding panel. Izquierdo, P., Wright, E.M., Cichy, K.

Whole plant transpiration responses of common bean (Phaseolus vulgaris L.) to drying soil: Water channels and transcription factors. HA Cordoba-Novoa, B Zhang, Y Guo, M Muhammad Aslam, FB Fritschi, V Hoyos-Villegas.

Assessment of the phenotypic diversity and agronomic performance of a Mediterranean lentil collection under rainfed conditions: towards efficient use in breeding programs for adaptation to Mediterranean-type environment. A Zeroual, M Mitache, A Baidani, B Abdallah Abderemane, N Benbrahim, H Ouhemi, E Çakır, V Hoyos-Villegas, A Gadaleta, E Mazzucotelli, H Özkan, O Idrissi.

2024

Cultivating success: Bridging the gaps in plant breeding training in Australia, Canada, and New Zealand. LM Egan, RW Hofmann, WN Stiller, V Hoyos‐Villegas.

Simulations of multiple breeding strategy scenarios in common bean for assessing genomic selection accuracy and model updating. Isabella Chiaravallotti, Jennifer Lin, Vivi Arief, Zulfi Jahufer, Juan M. Osorno, Phil McClean, Diego Jarquin, Valerio Hoyos-Villegas.

Probing Biological Nitrogen Fixation in Legumes Using Raman Spectroscopy. A Jafari, K Seth, A Werner, S Shi, R Hofmann, V Hoyos-Villegas. Sensors 24 (15), 4944

Drone-Based Digital Phenotyping to Evaluating Relative Maturity, Stand Count, and Plant Height in Dry Beans (Phaseolus vulgaris L.). Leonardo Volpato, Evan M. Wright, and Francisco E. Gomez.

A retrospective analysis of historical data of multi‐environment trials for dry bean (Phaseolus vulgaris L.) in Michigan. Leonardo Volpato, Evan M. Wright, Scott Bales, Francisco E. Gomez.

K‐mer genome‐wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel. Andrew T. Wiersma, John P. Hamilton, Brieanne Vaillancourt, Julia Brose, Halima E. Awale, Evan M. Wright, James D. Kelly, C. Robin Buell. 

Anthracnose and bean common mosaic necrosis virus resistance in wild and landrace Phaseolus vulgaris (L.) genetic stocks. Halima E Awale, Andrew T Wiersma, Evan M Wright, C Robin Buell, James D Kelly, Karen A Cichy, Miranda J Haus. 

2023

Automating high-throughput screening for anthracnose resistance in common bean using allele specific PCR. M Zaleski-Cox, PN Miklas, A Soler-Garzón, V Hoyos-Villegas

Eff-3dpseg: 3d organ-level plant shoot segmentation using annotation-efficient deep learning. L Luo, X Jiang, Y Yang, ERA Samy, M Lefsrud, V Hoyos-Villegas, S Sun

Simulations of rate of genetic gain in dry bean breeding programs. Jennifer Lin, Vivi Arief, Zulfi Jahufer, Juan Osorno, Phil McClean, Diego Jarquin, Valerio Hoyos-Villegas

Digital Phenotyping in Plant Breeding: Evaluating Relative Maturity, Stand Count, and Plant Height in Dry Beans (Phaseolus vulgaris L.) via RGB Drone-Based Imagery and Deep Learning Approaches. L Volpato, EM Wright, FE Gomez. 

2022

Advances in Breeding for Quantitative Disease Resistance. V Hoyos-Villegas, J Chen, AM Mastrangelo, H Raman

Development of a Nuclear Magnetic Resonance Method and a Near Infrared Calibration Model for the Rapid Determination of Lipid Content in the Field Pea (Pisum sativum). Philip Wiredu Addo, Philip Ossowski, Sarah MacPherson, Andrée E Gravel, Rajvinder Kaur, Valerio Hoyos-Villegas, Jaswinder Singh, Valérie Orsat, Marie-Josée Dumont, Mark Lefsrud.

A pilot‐scale dry bean canning and evaluation protocol. Weijia Wang, Evan M. Wright, Mark A. Uebersax, Karen Cichy. 

2021

Deterministic and stochastic modelling of impacts from genomic selection and phenomics on genetic gain for perennial ryegrass dry matter yield. MZZ Jahufer, Sai Krishna Arojju, Marty J Faville, Kioumars Ghamkhar, Dongwen Luo, Vivi Arief, Wen-Hsi Yang, Mingzhu Sun, Ian H DeLacy, Andrew G Griffiths, Colin Eady, Will Clayton, Alan V Stewart, Richard M George, Valerio Hoyos-Villegas, Kaye E Basford, Brent Barrett.

Prospects for Trifolium improvement through germplasm characterization and pre-breeding in New Zealand and beyond. LM Egan, RW Hofmann, K Ghamkhar, V Hoyos-Villegas

Transpiration rate of white clover (Trifolium repens L.) cultivars in drying soil. L Egan, R Hofmann, S Nichols, J Hadipurnomo, V Hoyos-Villegas

2020

Pedigree analysis of pre-breeding efforts in Trifolium spp. germplasm in New Zealand. LM Egan, RW Hofmann, P Seguin, K Ghamkhar, V Hoyos-Villegas. 

Genotype by Location Effects on Yield and Seed Nutrient Composition of Common Bean. Rosemary Bulyaba, Donna M. Winham, Andrew W. Lenssen, Kenneth J. Moore, James D. Kelly, Mark A. Brick, Evan M. Wright, James B. Ogg. 

Egan, L., Hofmann, R., Ghamkhar, K., Hoyos-Villegas, V. 2019. Identification of founding accessions and patterns of relatedness and inbreeding derived from historical pedigree data in a red clover (Trifolium pratense L.) germplasm collection in New Zealand.

Determining the Soilborne Pathogens Associated with Root Rot Disease Complex of Dry Bean in Michigan. Janette L. Jacobs, James D. Kelly, Evan M. Wright, Gregory Varner, Martin I. Chilvers. 

2018

Hoyos-Villegas, V., J.R. O’Connor, A.D. Heslop, A. Hilditch, M.Z.Z. Jahufer and B.A. Barrett. 2018. Rate of genetic gain for persistence to grazing and dry matter yield in white clover (Trifolium repens L.) across 90 years of cultivar development.

Hoyos-Villegas, V., Arief, V., Yang, W-H., Sun, M., DeLacy, I., Barrett, B., Jahufer, Z., Basford, K. 2018. QuLinePlus: Extending plant breeding strategy and genetic model simulation to cross-pollinated populations – case studies in forage breeding.

2017

QTL analysis of symbiotic nitrogen fixation in a black bean population. Heilig, J.A., Beaver, J.S., Wright, E.M., Song, Q., Kelly, J.D.

2016

Arun Prabhu Dhanapal, Jeffery D Ray, Shardendu K Singh, Valerio Hoyos-Villegas, James R Smith, Larry C Purcell, Felix Fritschi. 2016. Genome-wide association mapping of soybean chlorophyll traits based on canopy spectral reflectance and leaf extracts.

V. Hoyos-Villegas, Song, Q. Kelly, J.D. Genomewide Association Analysis for Drought Tolerance and Associated Traits in Common Bean.

V. Hoyos-Villegas, Kelly, J.D. Joint Linkage QTL Mapping for Yield and Agronomic Traits in a Composite Map of Three Common Bean RIL Populations.

V. Hoyos-Villegas, Wright, E.M. Kelly, J.D. GGE Biplot Analysis of Yield Associations with Root Traits in a Mesoamerican Bean Diversity Panel.

2015

Arun Prabhu Dhanapal, Jeffery D. Ray, Shardendu K. Singh, Valerio Hoyos-Villegas, James R. Smith, Larry C. Purcell, C. Andy King, and Felix B. Fritschi. Genome-Wide Association Analysis of Diverse Soybean Genotypes Reveals Novel Markers for Nitrogen Derived from Atmosphere, Nitrogen Traits

Jeffery D. Ray, Arun Prabhu Dhanapal, Shardendu K. Singh, Valerio Hoyos-Villegas, James R. Smith, Larry C. Purcell, C. Andy King, Debbie Boykin, Perry B. Cregan, Q. Song and Felix B. Fritschi. Genome-Wide Association Study of Ureide Concentration in Diverse Maturity Group IV Soybean [Glycine max (L.) Merr.] Accessions.

V. Hoyos-Villegas, W. Mkwaila, P.B. Cregan. J. Kelly. QTL analysis of white mold avoidance in pinto bean (Phaseolus vulgaris).

Dhanapal, A.P., J.D. Ray, S.K. Singh, V. Hoyos-Villegas, J.R. Smith, L.C. Purcell, C.A. King and F.B. Fritschi. Association mapping of total leaf carotenoids in diverse soybean [Glycine max (L.) Merr.] genotypes based on leaf extracts and canopy spectral reflectance. 

Dhanapal, A.P., J.D. Ray, S.K. Singh, V. Hoyos-Villegas, J.R. Smith, L.C. Purcell, C.A. King, P.B. Cregan, Q. Song and F. Fritschi. 2014. Genome-wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean [Glycine max (L.) Merr.] genotypes.

2014

V. Hoyos-Villegas, JH Houx, SK Singh, FB Fritschi. Ground-Based Digital Imaging as a Tool to Assess Soybean Growth and Yield. 

2013

Hoyos-Villegas, V. Fritschi, F.B. Relationships Among Vegetation Indices Derived from Aerial Photographs and Soybean Growth and Yield. 

Shardendu K Singh, Valerio Hoyos-Villegas, Jeffery D Ray, James R Smith, Felix B Fritschi. Quantification of leaf pigments in soybean (Glycine max (L.) Merr.) based on wavelet decomposition of hyperspectral features. 

2012

Shardendu K. Singh, Valerio Hoyos-Villegas, James Houx III, Felix Fritschi. Influence   of   artificially   restricted   rooting   depth   on  soybean   yield  and   seed  quality. 

2011

Mapping QTL for seed yield and canning quality following processing of black bean (Phaseolus vulgaris L.). Wright, E.M., Kelly, J.D.

2010

Noguera, D. Rondón, M. Kam-Rigne, L. Hoyos, V. Lavelle, P. Cruz de Carvalho, M.H. Barot, S. Contrasted effect of biochar and earthworms on rice growth and resource allocation in different soils.