Modeling copy number variation in the genomic prediction of maize hybrids

Author(s)

Lyra, Danilo Hottis ^{[1, 2]} ; Galli, Giovanni ^[1] ; Alves, Filipe Couto ^[1] ; Correia Granato, Italo Stefanine ^[1] ; Vidotti, Miriam Suzane ^[1] ; Bandeira e Sousa, Massaine ^[1] ; Morosini, Julia Silva ^[1] ; Crossa, Jose ^[3] ; Fritsche-Neto, Roberto ^[1]

Affiliation

^[1] Univ Sao Paulo, ESALQ, Dept Genet, Luiz de Queiroz Coll Agr, Sao Paulo - Brazil

^[2] Rothamsted Res, Dept Computat & Analyt Sci, Harpenden AL52JQ, Herts - England

^[3] Int Maize & Wheat Improvement Ctr CIMMYT, Biometr & Stat Unit, Texcoco 06600, DF - Mexico

• Document type: Journal article
• Source: THEORETICAL AND APPLIED GENETICS; v. 132, n. 1, p. 273-288, JAN 2019.
• Web of Science Citations: 1

Abstract

Key messageOur study indicates that copy variants may play an essential role in the phenotypic variation of complex traits in maize hybrids. Moreover, predicting hybrid phenotypes by combining additive-dominance effects with copy variants has the potential to be a viable predictive model.AbstractNon-additive effects resulting from the actions of multiple loci may influence trait variation in single-cross hybrids. In addition, complementation of allelic variation could be a valuable contributor to hybrid genetic variation, especially when crossing inbred lines with higher contents of copy gains. With this in mind, we aimed (1) to study the association between copy number variation (CNV) and hybrid phenotype, and (2) to compare the predictive ability (PA) of additive and additive-dominance genomic best linear unbiased prediction model when combined with the effects of CNV in two datasets of maize hybrids (USP and HELIX). In the USP dataset, we observed a significant negative phenotypic correlation of low magnitude between copy number loss and plant height, revealing a tendency that more copy losses lead to lower plants. In the same set, when CNV was combined with the additive plus dominance effects, the PA significantly increased only for plant height under low nitrogen. In this case, CNV effects explicitly capture relatedness between individuals and add extra information to the model. In the HELIX dataset, we observed a pronounced difference in PA between additive (0.50) and additive-dominance (0.71) models for predicting grain yield, suggesting a significant contribution of dominance. We conclude that copy variants may play an essential role in the phenotypic variation of complex traits in maize hybrids, although the inclusion of CNVs into datasets does not return significant gains concerning PA. (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 Opportunities: Regular Research Grants
• FAPESP's process: 14/26326-2 - Accuracy of non-additive models of genomic selection for nitrogen use efficiency in tropical maize hybrids
• Grantee: Danilo Hottis Lyra
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 15/14376-8 - Accuracy of non-additive models and population structure of genomic selection in maize
• Grantee: Danilo Hottis Lyra
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate