Publications

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2025

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.

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

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.