Copy number variation regions in Nellore cattle: Evidences of environment adaptation

Abstract

The aim of the present study was to analyze the distribution of CNV regions (CNVRs) as well as to address hypothesis about the natural/artificial selection process in Nellore cattle. A total of 399,361 CNVs were identified, using the PennCNV algorithm, in 3794 Nellore cattle (Bos taurus indicus) genotyped with the Bovine HD BeadChip array. The default quality control was applied and 2902 samples and 195,873 CNVs remained. The medium CNV length size was 54,744 bp with a maximum of 870,000 bp and a minimum of 3000 bp. The CNVRs were generated by overlapping the 195,873 identified CNVs using the CNVRuler program. There was a higher incidence of CNVRs on BTA19 (24.26%), BTA23 (18.68%), and BTA25 (18.05%). The chromosomes that showed a lower incidence of CNVR were BTA29 (1.63%), BTA13 (9.72%), and BTA8 (9.72%). According to the type, 38.5%, 28.5% and 33.0% of the CNVRs were characterized as insertion, deletion and mixed (insertion and deletion in the same region), respectively. The 9805 CNVR estimated in the present study covered approximately 13.05% of the cattle genome (UMD_3.1, 2,649,685,063 bp) and overlapped with 5495 genes. These genes have functions described as involved in biological processes that might be related to the environmental adaptation of the subspecies to tropical areas, such as regulation of vasodilatation, immune system response, hair follicle morphogenesis, among others. This study confirms the existence of large structural variations in the Nellore cattle genome and contributes to understanding the differences between cattle subspecies. Besides, it can also work as a guideline for future studies in which structural variations are present.

Genome-wide detection of copy number variation in American mink using whole-genome sequencing

“…In total, we identified 164,733 CNV events (144,517 deletions and 20,216 duplications) with the average number of 1647.3 per mink. Similar results were reported in other livestock species e.g., dairy cattle (182,823 CNVs) [ 70 ], yak (98,441 CNVs) [ 39 ], Nellore cattle (195,873 CNVs) [ 71 ], and goat (208,649 CNVs) [ 26 ]. Some other studies reported a wide range of CNVs from 12 CNVs in chicken [ 72 ] to 1,747,604 CNVs in sheep [ 23 ].…”

“…The results showed that 5378 CNVR covered around 47.3 Mb (1.9%) of the mink genome, which falls within the range of several studies reported in other species, such as pig (1.72%) [ 75 ], cattle (2.5%) [ 42 ], chicken (1%) [ 32 ], quail (1.6-1.9%) [ 76 ], horse (1.3%) [ 77 ], and buffalo (2%) [ 37 ]. The CNVR covered the genome in different ranges in other species, including cat (0.3%) [ 78 ], pig (0.9%) [ 57 ], yak (6.2%) [ 38 ], [ 78 ] goat (10.8%) [ 26 ], chicken (12.8%) [ 69 ], and cattle (13%) [ 71 ]. Several reasons might affect the quantity of CNVR detection such as the detection algorithm, population size, genetic background, the quality of applied technology, and the differences in genome size [ 73 , 79 ].…”

Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole‐genome re‐sequencing data

“…The sizes of the identified CNVs mostly ranged from 10 to 30 kb for all breeds, with a few outliers having a size greater than 500 kb. Such results are consistent with those based on SNP array (Bae et al, 2010;Lemos et al, 2018;Wu et al, 2015;Zhang et al, 2015) on diverse cattle breeds; however, it differed from NGS data (da Silva et al, 2016) in which CNVs were most frequent between 100 and 200 kb. Nevertheless, it is worth underscoring that the CNVR size range distribution concurred with those described in the literature for both SNP array-based and NGS data (Ben Sassi et al, 2016;da Silva et al, 2016;Gao et al, 2017;Lemos et al, 2018).…”

Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

“…Recently, CNVs have been increasingly shown to affect cattle traits of economic interest to humans, such as milk production (Xu et al, 2014), milk composition (Gao et al, 2017), residual feed intake (Zhou et al, 2018), body size (Zhou et al, 2016a), meat quality (Silva et al, 2016), and reproduction (Liu et al, 2019). Additionally, emerging evidence demonstrates that CNVs have been implicated in the adaptation of Nellore cattle to the tropical environment (Lemos et al, 2018). These findings indicate that artificial and natural selection may have shaped the landscape of CNVs in cattle genomes, thereby contributing to adaptive evolution, diversity, and breed differentiation.…”