Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle

Lingyang Xu,Huijiang Gao,Liu Yang,Bo Zhu,Lei Wang,Xue Gao,Junya Li,George E Liu,Lupei Zhang,Yan Chen

doi:10.1186/s12864-018-5403-5

Abstract

BackgroundAverage daily gain (ADG) is an important trait that contributes to the production efficiency and economic benefits in the beef cattle industry. The molecular mechanisms of ADG have not yet been fully explored because most recent association studies for ADG are based on SNPs or haplotypes. We reported a systematic CNV discovery and association analysis for ADG in Chinese Simmental beef cattle.ResultsOur study identified 4912 nonredundant CNVRs with a total length of ~ 248.7 Mb, corresponding to ~ 8.9% of the cattle genome. Using probe-based CNV association, we identified 24 and 12 significant SNP probes within five deletions and two duplications for ADG, respectively. Among them, we found one common deletion with 89 kb imbedded in LHFPL Tetraspan Subfamily Member 6 (LHFPL6) at 22.9 Mb on BTA12, which has high frequency (12.9%) dispersing across population. CNV selection test using VST statistic suggested this common deletion may be under positive selection in Chinese Simmental cattle. Moreover, this deletion was not overlapped with any candidate SNP for ADG compared with previous SNPs-based association studies, suggesting its important role for ADG. In addition, we identified one rare deletion near gene Growth Factor Receptor-bound Protein 10 (GRB10) at 5.1 Mb on BTA4 for ADG using both probe-based association and region-based approaches.ConclusionsOur results provided some valuable insights to elucidate the genetic basis of ADG in beef cattle, and these findings offer an alternative perspective to understand the genetic mechanism of complex traits in terms of copy number variations in farm animals.

Highlights

Average daily gain (ADG) is an important trait that contributes to the production efficiency and economic benefits in the beef cattle industry
These Copy number variation (CNV) were merged into 4912 nonredundant copy number variation regions (CNVRs) with a total length of ~ 248.7 Mb, corresponding to ~ 8.9% of the cattle genome
CNVs overlap with Quantitative trait locus (QTL) associated with ADG trait We explored the overlap of QTLs on CNV regions

Summary

Introduction

Average daily gain (ADG) is an important trait that contributes to the production efficiency and economic benefits in the beef cattle industry. We reported a systematic CNV discovery and association analysis for ADG in Chinese Simmental beef cattle. Genomic structural variants mainly comprised of copy number variations (CNVs) in the form of large-scale insertions and deletions, as well as inversions and translocations [1]. High-throughput SNP genotyping arrays have been widely used in genome-wide studies While these arrays have limited capacity to assess the effects of rare single-site variants, they can be readily used to identify large copy number variations, even if they occur in only a few subjects [6]. There are tremendous evidences showing that other genetic variants like copy number variations may affect complex traits, including short stature and anthropometric traits in human [7, 8]. Previous study identified several genes (e.g., MC4R, FIBIN, and FMO5), harboring both common and rare variants which may affect body

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