Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Abstract

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

Genome-Wide Association Study Based on Random Regression Model Reveals Candidate Genes Associated with Longitudinal Data in Chinese Simmental Beef Cattle

“…Body weight was measured for each individual at 0, 6, 12, and 18 months after birth, respectively. Here, the body weight data were consistent with the data in the study by Duan et al [ 24 ].…”

“…Notably, intramuscular fat becomes an important component of maturing muscles, and the mass of skeletal muscle accounts for 40% of total body weight in animals [ 32 ], thus it could be speculated that ANGPTL4 might regulate BW trait by influencing the formation of adipose tissue. Additionally, previous studies have reported ANGPTL2 , a homologous family gene of ANGPTL4 , influences the development of the bovine BW trait [ 24 ]. Taken together, ANGPTL4 could be recognized as the candidate gene regulating the BW trait for further research.…”

“…Previous studies have demonstrated that SHISA9 affected the growth and development traits such as pre-weaning gain in sheep and BW in beef cattle [ 24 , 64 ]. Protein shisa-2 homolog 2 ( SHISA2 ) identified in this study belongs to the same family as SHISA9 , which encodes an endoplasmic reticulum protein against both Wnt and FGF signaling to affect the development of Chicken and Xenopus embryos [ 65 , 66 ].…”

“…In agreement, the high expression of PDE1C was screened in proliferating human arterial SMCs in primary culture, but not in the quiescent SMCs [ 74 ], which indicated this gene was an indicator of cell proliferation. Notably, the previous study by Duan et al found PDE1C might be the candidate gene affecting bovine BW trait through signal-trait GWAS [ 24 ]. However, many studies of PDE1C mainly rely on human and mouse SMCs, with less research on beef cattle, thus the functions of PDE1C in beef cattle should be further investigated.…”

“…Here, we performed a principal component analysis (PCA) by PLINK v1.9 [ 25 ]. Our previous work demonstrated the first two principal components had been selected as covariances to eliminate the influence of population stratification [ 24 ].…”