Multi-Trait GWAS and new candidate genes annotation for growth curve parameters in Brahman cattle

Camporez Crispim, Aline, Kelly, Matthew John, Facioni Guimarães, Simone Eliza, Fonseca e Silva, Fabyano, Rufino Salinas Fortes, Marina, Rocha Wenceslau, Raphael and Moore, Stephen (2015) Multi-Trait GWAS and new candidate genes annotation for growth curve parameters in Brahman cattle. PLoS ONE, 10 10: e0139906.1-e0139906.19. doi:10.1371/journal.pone.0139906

Author Camporez Crispim, Aline
Kelly, Matthew John
Facioni Guimarães, Simone Eliza
Fonseca e Silva, Fabyano
Rufino Salinas Fortes, Marina
Rocha Wenceslau, Raphael
Moore, Stephen
Title Multi-Trait GWAS and new candidate genes annotation for growth curve parameters in Brahman cattle
Journal name PLoS ONE   Check publisher's open access policy
ISSN 1932-6203
Publication date 2015-10-07
Sub-type Article (original research)
DOI 10.1371/journal.pone.0139906
Open Access Status DOI
Volume 10
Issue 10
Start page e0139906.1
End page e0139906.19
Total pages 19
Place of publication San Francisco, CA, United States
Publisher Public Library of Science
Language eng
Subject 2700 Medicine
1300 Biochemistry, Genetics and Molecular Biology
1100 Agricultural and Biological Sciences
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.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2016 Collection
School of Chemistry and Molecular Biosciences
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Created: Fri, 16 Oct 2015, 19:28:18 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences