Haplotype-Based Single-Step GWAS for Yearling Temperament in American Angus Cattle.

Andre C Araujo,Hinayah R Oliveira,Luiz F Brito,Amanda B Alvarenga,Kelli Retallick,Stephen P Miller,Paulo L S Carneiro

doi:10.3390/genes13010017

Andre C Araujo, Hinayah R Oliveira + Show 5 more

Open Access

https://doi.org/10.3390/genes13010017

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Abstract

Behavior is a complex trait and, therefore, understanding its genetic architecture is paramount for the development of effective breeding strategies. The objective of this study was to perform traditional and weighted single-step genome-wide association studies (ssGWAS and WssGWAS, respectively) for yearling temperament (YT) in North American Angus cattle using haplotypes. Approximately 266 K YT records and 70 K animals genotyped using a 50 K single nucleotide polymorphisms (SNP) panel were used. Linkage disequilibrium thresholds (LD) of 0.15, 0.50, and 0.80 were used to create the haploblocks, and the inclusion of non-LD-clustered SNPs (NCSNP) with the haplotypes in the genomic models was also evaluated. WssGWAS did not perform better than ssGWAS. Cattle YT was found to be a highly polygenic trait, with genes and quantitative trait loci (QTL) broadly distributed across the whole genome. Association studies using LD-based haplotypes should include NCSNPs and different LD thresholds to increase the likelihood of finding the relevant genomic regions affecting the trait of interest. The main candidate genes identified, i.e., ATXN10, ADAM10, VAX2, ATP6V1B1, CRISPLD1, CAPRIN1, FA2H, SPEF2, PLXNA1, and CACNA2D3, are involved in important biological processes and metabolic pathways related to behavioral traits, social interactions, and aggressiveness in cattle. Future studies should further investigate the role of these candidate genes.

Highlights

Behavior is a complex trait influenced by multiple factors and the interaction among group-housed individuals and the environment [1]
We have investigated the genomic architecture of yearling temperament (YT) using large phenotypic and genomic datasets from American Angus cattle
Our results show important genes and quantitative trait loci (QTL) for YT would not be considered without the inclusion of non-LD-clustered SNPs (NCSNP), and using both haplotypes and NCSNP accounts for most relevant genes and QTL found based on haplotypes only

Summary

Introduction

Behavior is a complex trait influenced by multiple factors (e.g., age, health status, life experiences, genetics) and the interaction among group-housed individuals and the environment [1]. Animals presented different behavior characteristics compared to domesticated populations, indicating that behavioral traits can be genetically modified through selective breeding [1]. Livestock behavior is important due to its impact in several other relevant traits for the industry, including production, reproduction, and both animal and handler’s welfare and health [3–5]. Docile temperament is a desired behavior in cattle because it facilitates the handling process and it has been proven to be favorably associated with meat quality, productive efficiency, and welfare traits [6]. A previous study has shown that YT is heritable (heritability ~0.38), suggesting genetic progress can be achieved through direct selection [5]. A multi-species systematic review reported 797 genomic regions and 383 candidate genes associated with behavioral traits in cattle [8]. Six genes (GRM5, MAML3, C8B, RUSC2, POMC, MIPOL1, and SLC18A2) were in overlap among trait definitions and populations [8], suggesting a natural particularity of each population and measurement definition

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