Identification of muscle-specific candidate genes in Simmental beef cattle using imputed next generation sequencing.

Farhad Bordbar,Huijiang Gao,Lupei Zhang,Bo Zhu,Zezhao Wang,Tianpeng Chang,Min Du,Just Jensen,Lingyang Xu,Ling Xu,Lei Xu,Junya Li,Julio Cesar De Souza

doi:10.1371/journal.pone.0223671

Abstract

Genome-wide association studies (GWAS) have commonly been used to identify candidate genes that control economically important traits in livestock. Our objective was to detect potential candidate genes associated mainly with muscle development traits related to dimension of hindquarter in cattle. A next generation sequencing (NGS) dataset to imputed to 12 million single nucleotide polymorphisms (SNPs) (from 1252 Simmental beef cattle) were used to search for genes affecting hindquarter traits using a linear, mixed model approach. We also used haplotype and linkage disequilibrium blocks to further support our identifications. We identified 202 significant SNPs in the bovine BTA4 chromosome region associated with width of hind leg, based on a stringent statistical threshold (p = 0.05/ effective number of SNPs identified). After exploring the region around these SNPs, we found candidate genes that were potentially related to the associated markers. More importantly, we identified a region of approximately 280 Kb on the BTA4 chromosome that harbored several muscle specific candidate genes, genes to be in a potential region for muscle development. However, we also found candidate gene SLC13A1 on BTA4, which seems to be associated with bone disorders (such as chondrodysplasia) in Simmental beef cattle.

Highlights

Cattle and other livestock species are economically important in almost all regions of the world [1]
To identify more reliable QTLs and candidate genes, we set a stringent threshold to each segment (p = 0.05/ effective number of single nucleotide polymorphisms (SNPs)) [i.e., Segment 1 (p = 8.58×10−9), Segment 2 (p = 1.24×10−8), and Segment 3 (p = 1.95×10−8)]
We identified three candidate genes (IQUB, NDUFA5, and ASB15) for Sub-section 1, which spanned with a range of about 322 kb

Summary

Introduction

Cattle and other livestock species are economically important in almost all regions of the world [1]. Cattle breeds are continuously being developed to optimize the efficiency of meat production [2] and meat-production traits, controlled by a variety of genes, are among the most important traits selected for in various beef cattle breeding programs [3]. Cattle breeders desire cattle with more rapid lean muscle growth. The focus on lean muscle is important because consumers today demand leaner meat [4], making muscle growth an important economic factor in the beef industry.

Objectives

Methods

Results

Conclusion