Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle

Abstract

Brazil is one of the largest beef producers and exporters in the world with the Nelore breed representing the vast majority of Brazilian cattle (Bos taurus indicus). Despite the great adaptability of the Nelore breed to tropical climate, meat tenderness (MT) remains to be improved. Several factors including genetic composition can influence MT. In this article, we report a genome-wide analysis of copy number variation (CNV) inferred from Illumina® High Density SNP-chip data for a Nelore population of 723 males. We detected >2,600 CNV regions (CNVRs) representing ≈6.5% of the genome. Comparing our results with previous studies revealed an overlap in ≈1400 CNVRs (>50%). A total of 1,155 CNVRs (43.6%) overlapped 2,750 genes. They were enriched for processes involving guanosine triphosphate (GTP), previously reported to influence skeletal muscle physiology and morphology. Nelore CNVRs also overlapped QTLs for MT reported in other breeds (8.9%, 236 CNVRs) and from a previous study with this population (4.1%, 109 CNVRs). Two CNVRs were also proximal to glutathione metabolism genes that were previously associated with MT. Genome-wide association study of CN state with estimated breeding values derived from meat shear force identified 6 regions, including a region on BTA3 that contains genes of the cAMP and cGMP pathway. Ten CNVRs that overlapped regions associated with MT were successfully validated by qPCR. Our results represent the first comprehensive CNV study in Bos taurus indicus cattle and identify regions in which copy number changes are potentially of importance for the MT phenotype.

Pakistan’da Bazı Sığır Irklarında Kopya Sayısı Değişikliklerinin Genetik Özellikleri

“…Seventy two percent of the CNVs were identified, which were marked by flanking SNPs as reported by Xu et al [8] . However, the results of this investigation were not efficiently capable to distinguish recent divergent populations of common geographic origin, such as Cholistani and Bhagnari cattle breeds and also reported by Silva et al [7] and Xu et al [8] in Holstein and Angus cattle breeds. Human published data also revealed that the CNVs based on population genetic properties can only be investigated with large data set of continent population level [10] .…”

“…Previous studies in some species, including Human, Dog, Zebra fish, Stickleback fish and some worldwide cattle breeds have identified CNVs, based on population genetic properties, within and between population [6][7][8] .…”

“…1) which is similar as reported by previously SNPs based studies in different cattle population worldwide, including taurine, indicus or sanga etc. [7] . Seventy two percent of the CNVs were identified, which were marked by flanking SNPs as reported by Xu et al [8] .…”

Applications of genomic copy number variations on livestock: A review

“…In the works of , Ben Sassi et al (2016), Jiang et al (2016) and Upadhyay et al (2017), CNVs were significantly associated with milk production traits. In addition, CNVs of the genes are associated with reproduction and milk phenotype in cattle (Durán Aguilar et al, 2017;Da Silva et al, 2016b;McCarthy et al, 2012;Prinsen et al, 2017;Sermyagin et al, 2016;Shin et al, 2014;Xu et al, 2016;Yue et al, 2013;Zhou et al, 2018). In chickens, novel CNV of the TGFβ3 gene is associated with duration of fertility traits (Gu et al, 2017).…”

CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes

“…Such regions are denoted as CNV calls and are the starting point for subsequent downstream analysis. In previous work, we developed, described, and applied functionality for analyzing CNVs across a population, including association analysis with gene expression and quantitative phenotypes (da Silva et al, 2016(da Silva et al, , 2018Geistlinger et al, 2018). To allow straightforward application to similar datasets, we generalize these concepts and provide refined implementations in the CNVRanger R/Bioconductor package.…”