Tag‐SNP selection using Bayesian genomewide association study for growth traits in Hereford and Braford cattle

• Published in: Journal of animal breeding and genetics (1986) Vol. 137; no. 5; pp. 449 - 467
• Main Authors: Campos, Gabriel Soares, Sollero, Bruna Pena, Reimann, Fernando Antonio, Junqueira, Vinicius Silva, Cardoso, Leandro Lunardini, Yokoo, Marcos Jun Iti, Boligon, Arione Augusti, Braccini, José, Cardoso, Fernando Flores
• Format: Journal Article
• Language: English
• Published: Germany Blackwell Publishing Ltd 01.09.2020
• Subjects: Animals; Bayes Theorem; Bayesian analysis; Bayesian theory; beef cattle; Birth weight; Body Weight - genetics; Breeding - methods; Cattle; Cattle Diseases - genetics; Cattle Diseases - pathology; Cluster Analysis; Clustering; Density; Gene mapping; Gene polymorphism; genes; Genome - genetics; Genome-Wide Association Study - statistics & numerical data; genomic prediction; Genomics; Genomics - methods; Genotype; Genotypes; GWAS; Hereford; low‐density panel; Mapping; Marker panels; Medical Subject Headings-MeSH; Nucleotides; Phenotype; Polymorphism; Polymorphism, Single Nucleotide - genetics; prediction; Predictions; Single-nucleotide polymorphism; variance; Weaning; Weight; yearlings; beef cattle; low-density panel; GWAS; genomic prediction
• ISSN: 0931-2668; 1439-0388; 1439-0388
• DOI: 10.1111/jbg.12458

The aim of this study was to perform a Bayesian genomewide association study (GWAS) to identify genomic regions associated with growth traits in Hereford and Braford cattle, and to select Tag‐SNPs to represent these regions in low‐density panels useful for genomic predictions. In addition, we propose candidate genes through functional enrichment analysis associated with growth traits using Medical Subject Headings (MeSH). Phenotypic data from 126,290 animals and genotypes for 131 sires and 3,545 animals were used. The Tag‐SNPs were selected with BayesB (π = 0.995) method to compose low‐density panels. The number of Tag‐single nucleotide polymorphism (SNP) ranged between 79 and 103 SNP for the growth traits at weaning and between 78 and 100 SNP for the yearling growth traits. The average proportion of variance explained by Tag‐SNP with BayesA was 0.29, 0.23, 0.32 and 0.19 for birthweight (BW), weaning weight (WW205), yearling weight (YW550) and postweaning gain (PWG345), respectively. For Tag‐SNP with BayesA method accuracy values ranged from 0.13 to 0.30 for k‐means and from 0.30 to 0.65 for random clustering of animals to compose reference and validation groups. Although genomic prediction accuracies were higher with the full marker panel, predictions with low‐density panels retained on average 76% of the accuracy obtained with BayesB with full markers for growth traits. The MeSH analysis was able to translate genomic information providing biological meanings of more specific gene products related to the growth traits. The proposed Tag‐SNP panels may be useful for future fine mapping studies and for lower‐cost commercial genomic prediction applications.