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Genome-wide association study identifies significant SNP and related genes associated with body size in Yorkshire pigs using latent variable modelling

Published online by Cambridge University Press:  07 September 2023

Elahe Sanjari Banestani ,
Ali Esmailizadeh ,
Mehdi Momen ,
Ahmad Ayatollahi Mehrgardi  and
Morteza Mokhtari Open the ORCID record for Morteza Mokhtari [Opens in a new window]
Elahe Sanjari Banestani
Affiliation:
Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
Ali Esmailizadeh
Affiliation:
Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
Mehdi Momen
Affiliation:
Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
Ahmad Ayatollahi Mehrgardi
Affiliation:
Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
Morteza Mokhtari*
Affiliation:
Department of Animal Science, Faculty of Agriculture, University of Jiroft, P.O. Box 7867155311, Jiroft, Iran
*
Corresponding author: Morteza Mokhtari; Email: msmokhtari@ujiroft.ac.ir
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Abstract

This study aimed to quantify a latent variable for body size (BS) in pigs by using five linear body measurements including body length (BL), body height (BH), chest width (CW), chest girth (CG) and tube girth (TG), and also to identify the most associated single nucleotide polymorphisms (SNP) and related genes with BS by using the genomic best linear unbiased prediction (GBLUP) based genome-wide association study (GWAS) or GBLUP-GWAS methodology. To perform a GWAS on the BS latent trait, we used a mixed linear model and identified a total of 53 significant SNPs. Additionally, we found that nine genes, including Rho GTPase activating protein 12 (ARHGAP12), transmembrane protein 108 (TMEM108), T-cell lymphoma invasion and metastasis inducing factor 1 (TIAM1), ras homologue gene family member B (RHOB), POU class 4 homeobox 1 (POU4F1), follistatin-related protein 4 (FSTL4), cellular communication network factor 2 (CCN2), beaded filament structural protein 2 (BFSP2) and attractin-like protein 1 (ATRNL1) were associated with the BS trait in pigs. These genes are involved in several biological processes, including the regulation of anatomical structure, morphogenesis, the regulation of cell size and growth. The results suggest that the identified SNP and related genes may play important roles in regulating the growth and development of pigs. The results imply that these genes could be promising candidates for further exploration of the underlying mechanisms of body size variation. Furthermore, the findings have significant practical implications for enhancing the efficiency and profitability of pig farming through genetic selection.

Keywords

body measurementscandidate genesfactor analysisstructural equation model
Type
Animal Research Paper
Information
The Journal of Agricultural Science , Volume 161 , Issue 4 , August 2023 , pp. 599 - 605
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Copyright
Copyright © The Author(s), 2023. Published by Cambridge University Press

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