Genomic wide association study of body conformation traits in crossbred dairy cattle using Bayesian approaches

Mohammadi, hOSSEIN; Shamsollahi, Mohammad

Volume 19, Issue 1 (5-2024) MGj 2024, 19(1): 61-73 | Back to browse issues page

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Mohammadi H, Shamsollahi M. Genomic wide association study of body conformation traits in crossbred dairy cattle using Bayesian approaches. MGj 2024; 19 (1) : 6
URL: http://mg.genetics.ir/article-1-1827-en.html

Genomic wide association study of body conformation traits in crossbred dairy cattle using Bayesian approaches

HOSSEIN Mohammadi

, Mohammad Shamsollahi ^*

Illam university

Abstract: (447 Views)

Using the appropriate statistical method in genome wide association studies is one of the main factors for identifying genomic regions related to important economic traits. Therefore, the purpose of the present study was to calculate the explained genetic variance of Bayesian multi-step methods including BayesA, BayesB and BayesCπ for traits related to body conformation traits in crossbreed dairy cattle that were genotyped with 50K cattle chips. For each animal, five traits, body length, wither height, chest depth, chest circumference, and hip width, were collected. The analyses were performed using package hibayes in R software by fitting covariates for either SNPs alleles in Bayes A, Bayes B, or Bayes Cπ models. The lowest and highest amount of explained variance was obtained for chest circumference (12.5%) and body length (21.7%), respectively. The markers obtained from BayesA with the highest additive genetic variance were located in the chromosomes 4, 5, 6, 7, 10, 11, 16 and 23. In the present study, the genes related to body conformations traits in our study included PRDX6, ATF3, ARAP2, PDE1B, CHCHD3, TBPL2, SYN3, and PTBP1. The functional aspects of these candidate genes suggested their potential role in body growth. Moreover, pleiotropic effects were observed for some SNPs for conformation traits. The present results show when the genetic architecture of quantitative traits follows infinitesimal model assumptions, BayesA method usually performs better than Bayes. Moreover, considering the identification of new genome regions and the key role of the mentioned genes in development of body conformation, the Bayes A method can be validated for GWAS in body conformation traits.

Article number: 6

Keywords: Body size, Candidate gene, Genome scan, Model statistic, SNP.

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Type of Study: Applicable | Subject: Subject 02
Received: 2023/06/22 | Accepted: 2024/06/7 | Published: 2024/08/25