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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Optimizing Genomic-Enabled Prediction in Small-Scale Maize Hybrid Breeding Programs: A Roadmap Review

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Author(s):
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Fritsche-Neto, Roberto [1] ; Galli, Giovanni [1] ; Borges, Karina Lima Reis [1] ; Costa-Neto, Germano [1] ; Alves, Filipe Couto [2] ; Sabadin, Felipe [1] ; Lyra, Danilo Hottis [3] ; Morais, Pedro Patric Pinho [4] ; Braatz de Andrade, Luciano Rogerio [5] ; Granato, Italo [6] ; Crossa, Jose [7, 8]
Total Authors: 11
Affiliation:
[1] Univ Sao Paulo, Luiz de Queiroz Coll Agr, Genet Dept, Lab Allogamous Plant Breeding, Piracicaba - Brazil
[2] Michigan State Univ, Dept Epidemiol & Biostat, E Lansing, MI 48824 - USA
[3] Rothamsted Res, Dept Computat & Analyt Sci, Harpenden, Herts - England
[4] Univ Fed Vicosa, Dept Agron, Vicosa, MG - Brazil
[5] Brazilian Agr Res Corp EMBRAPA, Cassava & Fruits, Cruz Das Almas - Brazil
[6] Univ Montpellier, Inst Natl Rech Agron INRA, Lab Ecophysiol Plantes Stress Environm LEPSE, SupAgro, Montpellier - France
[7] Int Maize & Wheat Improvement Ctr CIMMYT, Biometr & Stat Unit, Carretera Mexico Veracruz, Texcoco - Mexico
[8] Colegio Posgrad, Montecillo - Mexico
Total Affiliations: 8
Document type: Review article
Source: FRONTIERS IN PLANT SCIENCE; v. 12, JUL 1 2021.
Web of Science Citations: 0
Abstract

The usefulness of genomic prediction (GP) for many animal and plant breeding programs has been highlighted for many studies in the last 20 years. In maize breeding programs, mostly dedicated to delivering more highly adapted and productive hybrids, this approach has been proved successful for both large- and small-scale breeding programs worldwide. Here, we present some of the strategies developed to improve the accuracy of GP in tropical maize, focusing on its use under low budget and small-scale conditions achieved for most of the hybrid breeding programs in developing countries. We highlight the most important outcomes obtained by the University of Sao Paulo (USP, Brazil) and how they can improve the accuracy of prediction in tropical maize hybrids. Our roadmap starts with the efforts for germplasm characterization, moving on to the practices for mating design, and the selection of the genotypes that are used to compose the training population in field phenotyping trials. Factors including population structure and the importance of non-additive effects (dominance and epistasis) controlling the desired trait are also outlined. Finally, we explain how the source of the molecular markers, environmental, and the modeling of genotype-environment interaction can affect the accuracy of GP. Results of 7 years of research in a public maize hybrid breeding program under tropical conditions are discussed, and with the great advances that have been made, we find that what is yet to come is exciting. The use of open-source software for the quality control of molecular markers, implementing GP, and envirotyping pipelines may reduce costs in an efficient computational manner. We conclude that exploring new models/tools using high-throughput phenotyping data along with large-scale envirotyping may bring more resolution and realism when predicting genotype performances. Despite the initial costs, mostly for genotyping, the GP platforms in combination with these other data sources can be a cost-effective approach for predicting the performance of maize hybrids for a large set of growing conditions. (AU)

FAPESP's process: 17/24327-0 - TCGA: an tropical corn germplasm assembly for genomic prediction and high-throughput phenotyping studies
Grantee:Roberto Fritsche Neto
Support type: Regular Research Grants
FAPESP's process: 13/24135-2 - Genome-Wide Association Studies for nitrogen use efficiency and its components in tropical maize lines
Grantee:Roberto Fritsche Neto
Support type: Regular Research Grants