Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus.

Yang Zhou,Steven G Schroeder,Derek M Bickhart,Roberto Carvalheiro,Tad S Sonstegard,Jose Fernando Garcia,El Hamidi Abdel Hay,José Bento Sterman Ferraz,Pamela Almeida Alexandre,Heidge Fukumasu,Benjamin D Rosen,George E Liu,Lingyang Xu,Curtis P Van Tassell,Yuri T Utsunomiya,Haroldo Henrique De Rezende Neves

doi:10.1186/s12864-016-2461-4

Abstract

BackgroundApart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. To date, no genome-wide association study (GWAS) for CNV and body traits in beef cattle has been reported, so the present study aimed to investigate this type of association in one of the most important cattle subspecies: Bos indicus (Nellore breed).ResultsWe have used intensity data from over 700,000 SNP probes across the bovine genome to detect common CNVs in a sample of 2230 Nellore cattle, and performed GWAS between the detected CNVs and nine growth traits. After filtering for frequency and length, a total of 231 CNVs ranging from 894 bp to 4,855,088 bp were kept and tested as predictors for each growth trait using linear regression analysis with principal components correction. There were 49 significant associations identified among 17 CNVs and seven body traits after false discovery rate correction (P < 0.05). Among the 17 CNVs, three were significant or marginally significant for all the traits. We have compared the locations of associated CNVs with quantitative trait locus and the RefGene database, and found two sets of 9 CNVs overlapping with either known QTLs or genes, respectively. The gene overlapping with CNV100, KCNJ12, is a functional candidate for muscle development and plays critical roles in muscling traits.ConclusionThis study presents the first CNV-based GWAS of growth traits using high density SNP microarray data in cattle. We detected 17 CNVs significantly associated with seven growth traits and one of them (CNV100) may be involved in growth traits through KCNJ12.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2461-4) contains supplementary material, which is available to authorized users.

Highlights

Apart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle
The results showed that birth weight (BW) and post weaning gain (PWG) had low correlation (R = 0.09), and they were both positively correlated with weaning gain (WG) showing R values of 0.22 and 0.47, respectively
For the other seven traits, we found 7, 5, 5, 9, 8, 7 and 8 CNVs significantly associated with WG, conformation at weaning (CW), conformation at yearling (CY), muscling at weaning (MW), muscling at yearling (MY), precocity at weaning (PW) and precocity at yearling (PY), respectively (Fig. 3 and Table 1)

Summary

Introduction

Apart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. Growth traits can directly affect production of beef cattle, which is an economically important sector of global agriculture. Both body weight measurements and visual trait scores of conformation, precocity and muscling are used to select calves and steers for breeding and to predict carcass parameters. We have reported and characterized 34 significantly associated CNVs with milk production traits in Holsteins [6] and found one deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle [18]. No systematic study of the relationship between CNVs and beef growth traits using SNP microarray data with high resolution has been published

Methods

Results

Conclusion