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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.)

Impact of Phenotypic Correction Method and Missing Phenotypic Data on Genomic Prediction of Maize Hybrids

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Author(s):
Galli, Giovanni [1] ; Lyra, Danilo Hottis [2] ; Alves, Filipe Couto [1] ; Correia Granato, Italo Stefanine [1] ; Bandeira e Sousa, Massaine [3] ; Fritsche-Neto, Roberto [1]
Total Authors: 6
Affiliation:
[1] Univ Sao Paulo, Dept Genet, Luiz de Queiroz Coll Agr, Piracicaba, SP - Brazil
[2] Rothamsted Res, Dept Computat & Analyt Sci, Harpenden, Herts - England
[3] Embrapa Cassava & Fruits, Cruz Das Almas, BA - Brazil
Total Affiliations: 3
Document type: Journal article
Source: CROP SCIENCE; v. 58, n. 4, p. 1481-1491, JUL-AUG 2018.
Web of Science Citations: 1
Abstract

Phenotypic datasets in plant breeding are commonly incomplete due to missing phenotypic information. The best approach for correcting these datasets for a stage-wise genomic prediction (GP) is not unanimous in the scientific community. Therefore, this study evaluates a two-step GP based on different methods of phenotypic correction considering complete and incomplete datasets of maize (Zea mays L.) single crosses. The dataset consists of 325 hybrids evaluated for grain yield and plant height in four sites. Sequential levels of data loss were simulated to the original dataset (from 0 to 30%) to assess the impact of missing information. The prediction was performed by an additive genomic best linear unbiased prediction model (GBLUP) using best linear unbiased estimations (BLUEs), best linear unbiased predictions (BLUPs), and deregressed BLUPs as the response variable. Mean reliability and predictive ability slightly decreased as missing phenotypic information increased, irrespective of the response variable. Regarding phenotypic correction, all methods yielded similar results for these parameters over most missing information percentages. The coincidence of selection between single-and two-stage GP was not systematically affected by response variable across multiple selection intensities, and missing data only led to a minor decrease in coincidence. Therefore, from a breeding standpoint, regardless of phenotypic correction method and missing data level, a similar set of genotypes tend to be selected. (AU)

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