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J Appl Genet. 2017 Aug;58(3):393-400. doi: 10.1007/s13353-017-0395-4. Epub 2017 Apr 5.

Using a system of differential equations that models cattle growth to uncover the genetic basis of complex traits.

Author information

1
Department of Veterinary Medicine, GMAB, Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil.
2
Department of Veterinary Medicine, GMAB, Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil. miguel-has@hotmail.com.
3
Centre for Genetic Improvement for Livestock, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
4
Department of Animal Science, Texas A&M University, 230 Kleberg Center, 2471 TAMU, College Station, TX, 77843, USA.

Abstract

The interplay between dynamic models of biological systems and genomics is based on the assumption that genetic variation of the complex trait (i.e., outcome of model behavior) arises from component traits (i.e., model parameters) in lower hierarchical levels. In order to provide a proof of concept of this statement for a cattle growth model, we ask whether model parameters map genomic regions that harbor quantitative trait loci (QTLs) already described for the complex trait. We conducted a genome-wide association study (GWAS) with a Bayesian hierarchical LASSO method in two parameters of the Davis Growth Model, a system of three ordinary differential equations describing DNA accretion, protein synthesis and degradation, and fat synthesis. Phenotypic and genotypic data were available for 893 Nellore (Bos indicus) cattle. Computed values for parameter k1 (DNA accretion rate) ranged from 0.005 ± 0.003 and for α (constant for energy for maintenance requirement) 0.134 ± 0.024. The expected biological interpretation of the parameters is confirmed by QTLs mapped for k1 and α. QTLs within genomic regions mapped for k1 are expected to be correlated with the DNA pool: body size and weight. Single nucleotide polymorphisms (SNPs) which were significant for α mapped QTLs that had already been associated with residual feed intake, feed conversion ratio, average daily gain (ADG), body weight, and also dry matter intake. SNPs identified for k1 were able to additionally explain 2.2% of the phenotypic variability of the complex ADG, even when SNPs for k1 did not match the genomic regions associated with ADG. Although improvements are needed, our findings suggest that genomic analysis on component traits may help to uncover the genetic basis of more complex traits, particularly when lower biological hierarchies are mechanistically described by mathematical simulation models.

KEYWORDS:

Beef cattle; GWAS; Mechanistic modeling; Nellore; Performance

PMID:
28382466
DOI:
10.1007/s13353-017-0395-4
[Indexed for MEDLINE]

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