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

Qunhao Niu,Bo Zhu,Xue Gao,Tianliu Zhang,Lingyang Xu,Huijiang Gao,Lupei Zhang,Junya Li,Tianzhen Wang,Yan Chen,Zezhao Wang,Ling Xu

doi:10.3389/fgene.2021.750746

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.

Highlights

Cattle, as one of the most important farm animals, provide numerous meat products for high-quality protein
We found that the heritability for bone weight estimated by Illumina BovineHD SNP array and the imputed sequence variants were 0.43 ± 0.07 and 0.44 ± 0.08, respectively
Using association analysis based on the imputed sequence variants, we totally identified 145 candidate variants for bone weight under the significant threshold

Summary

Introduction

As one of the most important farm animals, provide numerous meat products for high-quality protein. Bone weight can reflect the size of stature and the skeleton frame (Berg and Butterfield 1966; Chumlea et al, 2002; Conroy et al, 2010) and is involved in the respiratory disease and feed efficiency in cattle (Snowder et al, 2007; Mader et al, 2009). Many economically important traits (carcass weight, meat yield, etc.) were significantly associated with bone weight (Pabiou et al, 2012). Several QTLs relevant to stature, body size, growth, and carcass traits have been revealed in many previous studies, including PLAG1 (stature) (Karim et al, 2011; Bouwman et al, 2018) and NCAPG-LCORL (body size, carcass weight and feed efficiency) (Lindholm-Perry et al, 2011; Zhang et al, 2016; Chen et al, 2020)

Methods

Results

Conclusion