title: Multi-Trait GWAS and New Candidate Genes Annotation for Growth Curve Parameters in Brahman Cattle.
abstract: Understanding the genetic architecture of beef cattle growth cannot be limited simply to the genome-wide association study (GWAS) for body weight at any specific ages, but should be extended to a more general purpose by considering the whole growth trajectory over time using a growth curve approach. For such an approach, the parameters that are used to describe growth curves were treated as phenotypes under a GWAS model. Data from 1,255 Brahman cattle that were weighed at birth, 6, 12, 15, 18, and 24 months of age were analyzed. Parameter estimates, such as mature weight (A) and maturity rate (K) from nonlinear models are utilized as substitutes for the original body weights for the GWAS analysis. We chose the best nonlinear model to describe the weight-age data, and the estimated parameters were used as phenotypes in a multi-trait GWAS. Our aims were to identify and characterize associated SNP markers to indicate SNP-derived candidate genes and annotate their function as related to growth processes in beef cattle. The Brody model presented the best goodness of fit, and the heritability values for the parameter estimates for mature weight (A) and maturity rate (K) were 0.23 and 0.32, respectively, proving that these traits can be a feasible alternative when the objective is to change the shape of growth curves within genetic improvement programs. The genetic correlation between A and K was -0.84, indicating that animals with lower mature body weights reached that weight at younger ages. One hundred and sixty seven (167) and two hundred and sixty two (262) significant SNPs were associated with A and K, respectively. The annotated genes closest to the most significant SNPs for A had direct biological functions related to muscle development (RAB28), myogenic induction (BTG1), fetal growth (IL2), and body weights (APEX2); K genes were functionally associated with body weight, body height, average daily gain (TMEM18), and skeletal muscle development (SMN1). Candidate genes emerging from this GWAS may inform the search for causative mutations that could underpin genomic breeding for improved growth rates.
authors.affiliation: Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
authors.forename: Aline Camporez
authors.initials: AC
authors.lastname: Crispim
authors.affiliation: Queensland Alliance for Agriculture & Food Innovation University of Queensland, Brisbane, Queensland, Australia.
authors.forename: Matthew John
authors.initials: MJ
authors.lastname: Kelly
authors.affiliation: Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
authors.forename: Simone Eliza Facioni
authors.initials: SE
authors.lastname: Guimarães
authors.affiliation: Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
authors.forename: Fabyano
authors.initials: F
authors.lastname: Fonseca e Silva
authors.affiliation: School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, Queensland, Australia.
authors.forename: Marina Rufino Salinas
authors.initials: MR
authors.lastname: Fortes
authors.affiliation: Animal Science Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Raphael Rocha
authors.initials: RR
authors.lastname: Wenceslau
authors.affiliation: Queensland Alliance for Agriculture & Food Innovation University of Queensland, Brisbane, Queensland, Australia.
authors.forename: Stephen
authors.initials: S
authors.lastname: Moore
mesh_terms: D000818:Animals; D001835:Body Weight / Q000235:genetics*; D002417:Cattle; D004720:Endonucleases / Q000235:genetics; D016678:Genome; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes; D007376:Interleukin-2 / Q000235:genetics; D008565:Membrane Proteins / Q000235:genetics; D009154:Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D055533:Survival of Motor Neuron 1 Protein / Q000235:genetics; D020691:rab GTP-Binding Proteins / Q000235:genetics
chemical_list: D007376:Interleukin-2; D008565:Membrane Proteins; D055533:Survival of Motor Neuron 1 Protein; D004720:Endonucleases; D020691:rab GTP-Binding Proteins