Cited by 122Genetic and phenotypic traits in livestockGenetics and Plant BreedingGenetic Mapping and Diversity in Plants and Animals

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Improving accuracies of genomic predictions for drought tolerance in maize by joint modeling of additive and dominance effects in multi-environment trials

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Dias, Kaio Olímpio Das Graças, Gezan, Salvador Alejandro, Guimarães, Claudia Teixeira, Nazarian, Alireza, da Costa e Silva, Luciano, Parentoni, Sidney Netto, de Oliveira Guimarães, Paulo Evaristo, de Oliveira Anoni, Carina, Pádua, José Maria Villela, de Oliveira Pinto, Marcos, Noda, Roberto Willians, Ribeiro, Carlos Alexandre Gomes, de Magalhães, Jurandir Vieira, Garcia, Antonio Augusto Franco, de Souza, João Cândido, Guimarães, Lauro José Moreira, Pastina, Maria Marta·2018·Heredity

DOI 10.1038/s41437-018-0053-6PMC PMC5997769

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Abstract

Breeding for drought tolerance is a challenging task that requires costly, extensive, and precise phenotyping. Genomic selection (GS) can be used to maximize selection efficiency and the genetic gains in maize (Zea mays L.) breeding programs for drought tolerance. Here, we evaluated the accuracy of genomic selection (GS) using additive (A) and additive + dominance (AD) models to predict the performance of untested maize single-cross hybrids for drought tolerance in multi-environment trials. Phenotypic data of five drought tolerance traits were measured in 308 hybrids along eight trials under water-stressed (WS) and well-watered (WW) conditions over two years and two locations in Brazil. Hybrids' genotypes were inferred based on their parents' genotypes (inbred lines) using single-nucleotide polymorphism markers obtained via genotyping-by-sequencing. GS analyses were performed using genomic best linear unbiased prediction by fitting a factor analytic (FA) multiplicative mixed model. Two cross-validation (CV) schemes were tested: CV1 and CV2. The FA framework allowed for investigating the stability of additive and dominance effects across environments, as well as the additive-by-environment and the dominance-by-environment interactions, with interesting applications for parental and hybrid selection. Results showed differences in the predictive accuracy between A and AD models, using both CV1 and CV2, for the five traits in both water conditions. For grain yield (GY) under WS and using CV1, the AD model doubled the predictive accuracy in comparison to the A model. Through CV2, GS models benefit from borrowing information of correlated trials, resulting in an increase of 40% and 9% in the predictive accuracy of GY under WS for A and AD models, respectively. These results highlight the importance of multi-environment trial analyses using GS models that incorporate additive and dominance effects for genomic predictions of GY under drought in maize single-cross hybrids.

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Authors: Dias, K. O. D. G., Gezan, S. A., Guimarães, C. T., Nazarian, A., da Costa e Silva, L., Parentoni, S. N., de Oliveira Guimarães, P. E., de Oliveira Anoni, C., Pádua, J. M. V., de Oliveira Pinto, M., Noda, R. W., Ribeiro, C. A. G., de Magalhães, J. V., Garcia, A. A. F., de Souza, J. C., Guimarães, L. J. M., & Pastina, M. M.
Affiliations: Universidade Federal de Lavras (BR)
University of Florida (US)
Embrapa Milho e Sorgo (BR)
Universidade Federal de Viçosa (BR)
ORCID: Dias, Kaio Olímpio Das Graças
Gezan, Salvador Alejandro
Guimarães, Claudia Teixeira
Nazarian, Alireza
Parentoni, Sidney Netto
Pádua, José Maria Villela
Noda, Roberto Willians
Guimarães, Lauro José Moreira
Pastina, Maria Marta
Venue: Heredity
Publisher: Springer Science and Business Media LLC
Published: 2018-02-23
Volume: 121
Issue: 1
Pages: 24-37
ISSN: 0018-067X (ISSN-L)
1365-2540
DOI: 10.1038/s41437-018-0053-6
PMC: PMC5997769
OpenAlex: W2792329433
Cited by: 115
References: 65
Citations by year: 2026: 8 · 2025: 7 · 2024: 13 · 2023: 16 · 2022: 21 · 2021: 23 · 2020: 16 · 2019: 9 · 2018: 2
FWCI: 7.67
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.springer.com/tdm (tdm)
Locations: Heredity (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Fundação de Amparo à Pesquisa do Estado de São Paulo (2016/12977‐7)
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (23038, program PREMIO 2045/2014)
Empresa Brasileira de Pesquisa Agropecuária
Conselho Nacional de Desenvolvimento Científico e Tecnológico
Fundação de Amparo à Pesquisa do Estado de Minas Gerais
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetics and Plant Breeding
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords: genomic selection, drought tolerance, maize, additive and dominance effects, multi-environment trials, prediction accuracy, single-cross hybrids, cross-validation, gene-environment interaction, SNP markers, genotyping-by-sequencing
MeSH terms: Plant Breeding, Adaptation, Biological, Algorithms, Environment, Genetic Markers, Genotype, Models, Genetic, Phenotype, Selection, Genetic, Stress, Physiological, Reproducibility of Results, Genome, Plant, Quantitative Trait, Heritable, Polymorphism, Single Nucleotide, Genomics, Droughts, Gene-Environment Interaction

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Improving accuracies of genomic predictions for drought tolerance in maize by joint modeling of additive and dominance effects in multi-environment trials

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