Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle

Abstract

Bone weight is critical to affect body conformation and stature in cattle. In this study, we conducted a genome-wide association study for bone weight in Chinese Simmental beef cattle based on the imputed sequence variants. We identified 364 variants associated with bone weight, while 350 of them were not included in the Illumina BovineHD SNP array, and several candidate genes and GO terms were captured to be associated with bone weight. Remarkably, we identified four potential variants in a candidate region on BTA6 using Bayesian fine-mapping. Several important candidate genes were captured, including LAP3, MED28, NCAPG, LCORL, SLIT2, and IBSP, which have been previously reported to be associated with carcass traits, body measurements, and growth traits. Notably, we found that the transcription factors related to MED28 and LCORL showed high conservation across multiple species. Our findings provide some valuable information for understanding the genetic basis of body stature in beef cattle.

Identify Candidate Genes Associated with the Weight and Egg Quality Traits in Wenshui Green Shell-Laying Chickens by the Copy Number Variation-Based Genome-Wide Association Study

“…The MED28 gene is a protein-coding gene involved in cell proliferation and cycle regulation. In cattle, the MED28 gene was found to be associated with body weight and intramuscular fat content [ 44 , 45 , 46 ]. In sheep, the MED28 gene was found to be associated with prenatal and postnatal body weights [ 47 , 48 ].…”

Genome‐wide association study of growth traits and validation of key mutations (MSTN c.C861T) associated with the muscle mass of meat pigeons

“…LCORL has been associated with height in humans (Horikoshi et al., 2013; Soranzo et al., 2009). Meanwhile, the NCAPG / LCORL region has been associated with the height and size of dogs (Vaysse et al., 2011), cows (Niu et al., 2021), horses (Tetens et al., 2013), donkeys (Liu et al., 2022), pigs (Rubin et al., 2012), sheep (Posbergh & Huson, 2021) and chickens (Liu et al., 2021). NCAPG is a subunit of the condensed protein I complex, which is crucial for maintenance of chromosome structure (Kimura et al., 2001).…”

Genetic Bases and Molecular Breeding of Key Economic Traits in China Dairy Cattle: A Progress Report

“…A total of 364 variants were found by GWAS to influence bone weight in Chinese Simmental cattle. Genes, such as LAP3, MED28, NCAPG, LCORL, SLIT2 and IBSP, previously reported to be associated with animal carcass characteristics, body measurements and growth characteristics were more precisely identified as being involved with bone weight [41]. Further GWAS, based on a random regression model, revealed 37 SNPs associated with body weight, including FGF4, ANGPT4, PLA2G4A and ITGA5 [42].…”