Publication

Articles

2024

• Sipowicz, P.; Andrade, MHML.; Fernandes Filho, CC.; Benevenuto, J.; Munoz, P.; Ferrão, LFV.; Resende Jr, MFR; Messina, C.; Rios, E.; Optimization of high-throughput marker systems for genomic prediction in alfalfa family bulks. The Plant Genome. 2024

• Gonçalves, JFC.; Nascimento, GO.; Carvalho, JC.; Santos, AS.; Rodrigues, DP.; Germano, TA.; Nunes, MS.; Souza, DP.; Cavalcanti, JHF.; Ramos, MV.; Ferrão, LFV, Martins, K.; Lipid profiles and DNA barcoding markers reveal the genetic delimitation between species of the Carapa genus native from the Amazon. Biochemical Systematics and Ecology. 2024

• Peixoto, MA.; Amadeu, RR.; Bhering, LL.; Ferrão, LFV.; Munoz, PR.; Resende Jr.; SimpleMating: R-package for prediction and optimization of breeding crosses using genomic selection. The Plant Genome. 2024

• Adunola, P.; Tavares Flores, E.; Azevedo, C.; Casorzo, G.; Ghimere, L.; Ferrão, LFV.; Munoz, PR.; Phenomic-assisted selection: Assessment of the potential of near-infrared spectroscopy for blueberry breeding.The Plant Phenome. 2024

• Ferrão, LFV.; Azevedo, C.; Sim, C.; Munoz, PR.; A consumer-oriented approach to define breeding targets for molecular breeding. New Phytologist. 2024

• Ferrão, LFV.; Azevedo, C.; Benevenuto, J.; Mengist, MF.; Luby, C.; Pottorff, M.; Casorzo, GP.; Mackey, T.; Ann Lila, M.; Giongo, L.; Bassil, N.; Perkins-Veazie, P.; Iorizzo, M.; Munoz, PR.; Inference of the genetic basis of fruit texture in highbush blueberries using genome-wide association analyses. Horticulture Research. 2024

• Canale,s E., Gallardo, RK.; Iorizzo, M.; Muñoz, PR; Ferrão, LFV.; Luby, C.; Bassil, N.; Pottorff, M.; Perkins, P.; Sandefur, P.; Colonna, A.; Sims, C.; Willingness to Pay for Blueberries: Sensory Attributes, Fruit Quality Traits, and Consumers’ Characteristics. HortScience, 2024

• Casorzo, G.; Ferrão, LFV.;.; Adunola, P.; Tavares Flores, E.; Azevedo, C.; Amadeu, R.; Munoz, PR.; Understanding the Genetic Basis of Blueberry Postharvest Traits to Define Better Breeding Strategies. G3- Genes, Genome, Genetics. 2024

• Adunola, P.; Ferrão, LFV.; Benevenuto, J. Azevedo, C.; Munoz, PR.; Genomic selection optimization in blueberry: Data-driven methods for marker and training population design.The Plant Genome. 2024

• Ferrão, MAG.; Riva-Souza, EM.; Azevedo, C.; Volpi, PS; Fonseca, AFA.; Ferrão, RG.; Montagnon, C.; Ferrão, LFV. Robust and smart: Inference on phenotypic plasticity of Coffea canephora reveals adaptation to alternative environments. Crop Science. 2024

• Adunola, P.; Ferrão, LFV.; Azevedo, C.; Nunez, G.; Munoz, PR.; The effect of environmental variables on the genotyping-by-environment interaction in blueberry.Euphytica. 2024

• Adunola, P.; Tavares Flores, E.; Riva-Souza, E.; Ferrão, MGA.; Senra, JF.; Comério, M.; Espindula, MC.; Verdin Filho, AC.; Volpi, PS.; Fonseca, AAF.; Ferrão, RG.; Munoz, PR.; Ferrão, LFV. A comparison of genomic and phenomic selection methods for yield prediction in Coffea canephora. The Plant Phenome. 2024

• Mengist, MF.; Pottorff, M.; Mackey, T.; Ferrão, F,; Casorzo, G.; Ann Lila, M.; Luby, C.; Giongo, L.; Perkins-Veazie, P.; Bassil, N.; Munoz, P.; Iorizzo, M.; Assessing predictability of post-storage texture and appearance characteristics in blueberry at breeding population level. Postharvest Biology and Technology,2024

• Garzón-Martinez, GA.; Azevedo, C; Berdugo-Cely, JA.; Lasso-Paredes, ZL.; Coronel-Ortiz, B.; Ferrão, LFV.; Enciso-Rodriguez, FE. Genetic dissection of yield and quality-related traits in a Colombian Andigenum potato collection, revealed by genome-wide association and genomic prediction analyses. Euphytica. 2024

• Charles, JR.; Dorval, MD.; Durone, JB.; Ferrão, LFV.; Amadeu, RR.; Munoz, PR; Morris, G.; Meru, G.; Pressoir, G.; Genomic prediction of sweet sorghum agronomic performance under drought and irrigated environments in Haiti Crop Science. 2024

• Azevedo, C.; Ferrão, LFV.; Benevenuto, J.; Resende, MD.; Nascimento, M.; Nascimento, AC.; Munoz, PR. Using visual scores for genomic prediction of complex traits in breeding programs. TAG. 2024

• Neves da Silva, M.; Benevenuto, J.; Ferrão, LFV.; Munoz, PR.; Genome-wide association study and transcriptome analysis reveal candidate genes for off-season flowering in blueberry. Scientia Horticulturae. 2024

2023

• Yocca, AE.; Platts, A.; Alger, E.; Teresi, S.; Mengist, MF.; Benevenuto, J.; Ferrão, LFV.;, Jacobs, M.; Babinski, M.; et al. Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts. Horticulture Research. 2023

• Ferrão, LFV.; Dhakal, R.; Dias, R.; Tieman, D.; Whitaker, V.; Gore, MA; Messina, C.; Resende Jr, MFR.; Machine learning applications to improve flavor and nutritional content of horticultural crops through breeding and genetics. Current Opinion in Biotechnology. 2023

• Amadeu, RR.; Garcia, AAF; Munoz, PR; Ferrão, LFV. AGHmatrix: genetic relationship matrices in R . Bioinformatics. 2023

• Adunola, P; Ferrao; MAG; Ferrão, RG; da Fonseca, AFA; Volpi, PS; Comério, M; Verdin Filho, AC; Munoz, PR; Ferrão, LFV. Genomic selection for genotype performance and environmental stability in Coffea canephora. G3 - Genes.Genomics.Genetics. 2023

• Ferrão, MAG; da Fonseca, AFA; Volpi, PS; de Souza, L; Comério, M; Verdin Filho, AC; Riva-Souza, EM; Munoz, PR; Ferrão, RG; Ferrão, LFV. Genomic-assisted breeding for climate-smart coffee.The Plant Genome. 2023

• Carvalho, HF; Ferrão, LFV; Galli, G; Nonato, JVA; Padilha, L; Maluf, MR; Resende Jr, MFR; Fritsche‑Neto, R; Guerreiro-Filho, O; On the accuracy of threshold genomic prediction models for leaf miner and leaf rust resistance in arabica cofee. Tree Genetics & Genomes. 2023

2022

• Dias, RD; Johnsona, TA; Ferrão, LFV, Munoz, PR; de la Mata, P; Harynuk, JJ. Improved sample storage, preparation and extraction of blueberry aroma volatile organic compounds for gas chromatography. Journal of Chromatography Open, 2022

• Ferrão,LFV;Sater, H; Lyrene, P; Amadeu, RR; Sims, CH; Tieman,DM; Munoz, PR Terpene volatiles mediates the chemical basis of blueberry aroma and consumer acceptability.Food International Research,2022.

• Edger, P; Iorizzo M; Bassil, N; Benevenuto, J; Ferrão, LFV et al. There and back again; historical perspective and future directions for Vaccinium breeding and research studies. Horticultural Research, 2022

• Colantonio,V^co; Ferrão, LFV^co; Tieman, D; Bliznyuk, N; Sims, C; Klee, H; Munoz, PR; Resende Jr, MFR. Metabolomic Selection for Enhanced Fruit Flavor, PNAS,2022. ^{co:authors contributed equally}

2021

• Sater, H; Ferrão,LFV; Olmstead, J; Munoz, PR; Bai, J; Hopf, A; Plotto, A. Exploring environmental and storage factors affecting sensory, physical and chemical attributes of six southern highbush blueberry cultivars.Scientia Horticulturae,2021.

• Ferrão, LFV; Amadeu, RR; Benevenuto, J; de Bem Oliveira, I; Munoz, PR. Genomic Prediction In An Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding. Frontiers in Plant Science, 2021.

2020

• Cappai, F^co; Amadeu, RR^co; Benevenuto,J; Cullen, R; Garcia, A; Grossman, A; Ferrão, LFV; Munoz,PR. High-resolution linkage map and QTL analyses of fruit firmness in autotetraploid blueberry. Frontiers in Plant Science, 2020. ^{co:authors contributed equally}

• de Bem Oliveira, I; Amadeu, RR; Ferrão, LFV; Munoz, PR. Optimizing whole-genomic prediction for autotetraploid blueberry breeding. Heredity, 2020

• Carvalho, HF; Galli, G; Ferrão, LFV; Nonato, JVA; Padilha, L; Maluf, MP; Resende Jr, MFR; Guerreiro Filho, O; Fritsche-Neto, R. The effect of bienniality on genomic prediction of yield in arabica coffee. Euphytica, 2020

• Oliveira,AA; Resende Jr, MFR; Ferrão, LFV; Amadeu,RR; Guimarães, LJM; Guimarães,CT; Pastina, MM; Margarido, GRA.Genomic prediction applied to multiple traits and environments in second season maize hybrids. Heredity, 2020

• Ferrão, LFV; Marinho, CD; Munoz, PR; Resende Jr, MFR. Improvement of predictive ability in maize hybrids by including dominance effects and marker × environment models. Crop Science, 2020.\

• Ferrão, LFV; Johnson, TS; Benevenuto, J; Edger, PP; Colquhoun, TA; Munoz, PR. Genome‐wide association of volatiles reveals candidate loci for blueberry flavor. New Phytologist, 2020.

• Zingaretti, LM; Gezan, SG; Ferrão, LFV; Osorio, LF; Monfort, A; Munoz, PR; Whitaker, V; and Perez-Enciso, M. Exploring deep learning for complex trait genomic prediction in polyploid outcrossing species. Frontiers in Plant Science, 2020

2019

• Benevenuto, J; Bhakta, M; Lohr, DA; Ferrão,LFV; Resende Jr, MFR; Kirst,M; Quesenberry, K; Munoz, P. Cost-effective detection of genome-wide signatures for 2,4-D herbicide resistance adaptation in red clover. Scientific Reports. 2019.

• Gerard, D and Ferrão, LFV. Priors for Genotyping Polyploids. Bioinformatics, 2019.

• Amadeu, RR; Ferrão, LFV; de Bem Oliveira,I; Benevenuto, J; Endelman, J; Munoz, PR; Impact of Dominance Effects on Autotetraploid Genomic Prediction. Crop Science, 2019.

• Benevenuto, J; Ferrão, LFV; Amadeu, RR; Munoz, PR; How can a high-quality genome assembly help plant breeders?. GigaScience, 2019

• de Bem Oliveira,I; Resende Jr., MFR; Ferrão, LFV; Amadeu, RR; Endelman, J; Kirst, M; Coelho, ASG; Munoz, PR; Genomic prediction of autotetraploids; influence of relationship matrices, allele dosage, and continuous genotyping calls in phenotype prediction. G3: GENES, GENOMES, GENETIC, 2019

2018

• Gerard, D; Ferrão, LFV; Garcia, AAF; Stephens, M. Genotyping Polyploids from Messy Sequencing Data. Genetics, Vol. 210, 789–807, 2018.

• Cappai F^co; Benevenuto J^co; Ferrão, LFV^co; Munoz, PR. Molecular and Genetic Bases of Fruit Firmness Variation in Blueberry — A Review. Agronomy, 8(9), 174, 2018. ^{co:authors contributed equally}

• Ferrão, LFV; Benevenuto, J; De Bem Oliveira; I; Cellon, C; Olmstead, J; Kirst, M; Resende Jr. MFR; Munoz, PR. Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context. Frontiers Ecology Evolution, 2018

• Ferrão, LFV; Ferrão, RG; Ferrão MAG; Fonseca, A; Carbonetto, P; Stephens, M; Garcia, AAF. Accurate genomic prediction of Coffea canephora in multiple environments using whole-genome statistical models. Heredity, 2018.

• Cellon, C; Amadeu, RR; Olmstead, J; Mattia,M; Ferrão, LFV.; Munoz, PR. Estimation of genetic parameters and prediction of breeding values in an autotetraploid blueberry breeding population with extensive pedigree data. Euphytica, 2018.

2017

• Ferrão, LFV; Ferrão, RG; Ferrão MAG; Fonseca, A.; Garcia, AAF. Mixed model to multiple harvest-location trial applied to genomic prediction in Coffe canephora. Tree Genetics and Genomes 13:95, 2017.

• Perez-Jaramillo, JE; Carrion, VJ; Bosse, M; Ferrão LFV; de Hollander, M; Garcia, AAF; Ramírez, C; Mendes, R; Raaijmakers, JM. Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. The ISME Journal, 2017.

2015

• Ferrão, LFV ; Caixeta, ET; Pena, GF; Maciel-Zambolim, E ; Cruz, CD; Zambolim, L; Ferrão, MAG; Sakiyama, N S. New EST-SSR markers of Coffea arabica: transferability and application to studies of molecular characterization and genetic mapping. Molecular Breeding 35 (1),1-5, 2015.

2014

• Ferrão, LFV ; Caixeta, ET; Cruz, CD; Souza, FF; Ferrão, MAG; Maciel-Zambolim, E ; Zambolim, L; Sakiyama, N S. The effects of encoding data in diversity studies and the applicability of the weighting index approach for data analysis from different molecular markers. Plant Systematics and Evolution, 300 (7):1649-1661, 2014

2013

• Ferrão, LFV ; Caixeta, ET; Souza, FF; Cruz, CD; Maciel-Zambolim, E; Zambolim, L; Sakiyama, NS. Comparative study of different molecular markers for classifying and establishing genetic relationships in Coffea canephora. Plant Systematics and Evolution, 299: 225-238, 2013

• Souza, FF ; Caixeta, ET; Ferrão, LFV; Pena, GF; Sakiyama, NS; Maciel-Zambolim, E; Zambolim, L; Cruz, CD. Molecular diversity in Coffea canephora germplasm conserved and cultivated in Brazil. Crop Breeding and Applied Biotechnology (Online), v. 13, p. 221, 2013

2011

• Ferrão, LFV ; Cecon, PR ; Finger, FL; Silva, FF; Puiatti, M . Genetic divergence among sub-samples of pepper based on morpho-agronomic characters. Horticultura Brasileira, 29: 354-358, 2011

Book Chapter

• Ferrão, M A G.; Ferrão, L F V.; Motta, L B.; Fonseca, A F A.; Souza, E M R.; Ferrão, R G.; Biotechnology Applied to Coffea canephora. Book: Conillon Coffee In: Ferrão, R G.; Fonseca, A F A.; Ferrão, M A G.; De Muner, L H (Ed.). 3ed.: Incaper, 2019

• Ferrão, R G.; Ferrão, M A G.; Fonseca, A F A.; Ferrão, L F V.; Pacova, B E V.; Coffea canephora Breeding. Book: Conillon Coffee. In: Ferrão, R G.; Fonseca, A F A.; Ferrão, M A G.; De Muner, L H (Ed.). 3ed.: Incaper, 2019

• Ferrão, M A G.; Ferrão, L F V.; Motta, L B.; Fonseca, A F A.; Souza, E M R.; Ferrão, R G.; Biotecnologia Aplicada a Coffea canephora. Book: O Café Conilon. In: Ferrão, R G.; Fonseca, A F A.; Ferrão, M A G.; De Muner, L H (Ed.). 2ed.: Incaper, 2017

• Ferrão, R G.; Ferrão, M A G.; Fonseca, A F A.; Ferrão, L F V.; Pacova, B E V.; Melhoramento de Coffea canephora. Book: O Café Conilon. V2. In: Ferrão, R G.; Fonseca, A F A.; Ferrão, M A G.; De Muner, L H (Ed.). 2ed.: Incaper, 2017

• Ferrão, L F V.; Garcia, A A F.; Ortiz, R.Genomic Selection - State of Art. Book: Genetic Improvement of Tropical Species. In: Hugo Campos and Peter D. S Caligari (Ed.). Springer, 2017

• Souza, F F ; Ferrão, L F V.; Caixeta, E T.; Sakiyama, N S.; Pereira,A A.; de Oliveira, A C B; Aspectos Gerais da biologia e diversidade genética de Coffea canephora. Book: Café na Amazônia, Embrapa, Brazil, 2016

• Caixeta, E T. ; Ferrão, L F V. ; Maciel-Zambolim, E; Zambolim, L. . Chapter: Molecular Markers. In: Borém and Fritsche-Neto. (Org.). Book: Biotechnology and Plant Breeding: Applications and Approaches for Developing Improved Cultivars. 1ed.: Elsiever, 1: 1-249, 2014

• Caixeta, E T. ; Ferrão, L F V. ; Maciel-Zambolim, E; Marcadores Moleculares. In: Fritsche-Neto e Borém. (Org.). Book: Biotecnologia Aplicada ao Melhoramento de Plantas. 1ed.Viçosa: UFV, Brazil, 1:32-68, 2012