A genome wide association study between CNVs and quantitative traits in Brown Swiss cattle

Prinsen, R.T.M.M.; Rossoni, Attilio; Gredler, Birgit; Bieber, Anna; Bagnato, A.; Strillacci, M.G.

doi:10.1016/j.livsci.2017.05.011

Cited by 35 publications

(35 citation statements)

References 27 publications

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“…In cattle, serial translocation of the KIT gene was related to a colour-sidedness phenotype [16]. Moreover, CNVs were shown to be associated with quantitative traits that are economically important in livestock breeding, in various cattle populations [17][18][19]. One study investigated whether trait associated CNVs are in linkage disequilibrium (LD) with, and thus are tagged by, SNP markers, and revealed that2 5% of CNVs were not in LD with SNP markers [17].…”

Section: Introductionmentioning

confidence: 99%

“…Holstein Friesian (HOL) and Jersey (JER) are the two main commercial dairy cattle breeds that have been bred under different breeding schemes. Although there have been studies investigating the link between CNVs and individual production traits [17][18][19][20][21], in-depth assessment of functional impacts of CNVs in cattle genomes has been limited. Also, whether CNVs that have an impact on phenotypes are captured in genomic evaluation, in other words, whether CNVs are in sufficient LD with SNPs, is largely unexplored.…”

Section: Introductionmentioning

confidence: 99%

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Functional and population genetic features of copy number variations in two dairy cattle populations

et al. 2020

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Background: Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features.Results: We discovered 14,272 autosomal CNVs, which were aggregated into 1755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (MAF ≥ 0.05). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes, which are related to starch digestion and body size, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF ≥ 0.05) showed slightly higher LD (r 2 =~0.1 at 10 kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD (r 2 =~0.5 at 10 kb distance). Conclusions:Our analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17, which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Functional and population genetic features of copy number variations in two dairy cattle populations

et al. 2020

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“…CNVs are known to be associated with gene expression, phenotypic variation, adaption, and the development of various diseases [2,3]. In cattle, the CNV is associated with resistance or susceptibility to gastrointestinal nematodes [4], production traits [5,6], and muscle [7]. Studies showed that the CNV also plays a key role in the coat color in goat [8], pig [9], and horse [10].…”

Section: Introductionmentioning

confidence: 99%

Copy Number Variations of Four Y-Linked Genes in Swamp Buffaloes

Sun

Hanif

Chen

et al. 2019

Animals

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Copy number variation (CNV), a significant source of genetic diversity in the mammalian Y chromosome, is associated with the development of many complex phenotypes, such as spermatogenesis and male fertility. The contribution of Y-linked CNVs has been studied in various species, however, water buffalo has not been explored in this area and the genetic information still remains unknown. The aim of the current study was to investigate the CNVs of four Y-linked genes, including, sex determining Region of Y-Chromosome (SRY), ubiquitously transcribed tetratricopeptide repeat gene protein on the chromosome Y (UTY), DEAD-box helicase 3 Y-linked (DDX3Y, also known as DBY), and oral-facial-digital syndrome 1 Y-linked (OFD1Y) in 254 swamp buffaloes from 15 populations distributed across China, Vietnam, and Laos using quantitative real-time PCR (qPCR). Our results revealed the prevalence of a single-copy UTY gene in buffaloes. The DBY and OFD1Y represented CNVs among and within different buffalo breeds. The SRY showed CNVs only in Vietnamese and Laotian buffaloes. In conclusion, this study indicated that DBY, OFD1Y, and SRY showed CNVs, while the UTY was a single-copy gene in swamp buffaloes.

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“…In the human genome, CNVs contribute approximately 4.8-9.5% of variations, including the creation of evident phenotypic effects from the deletion of approximately 100 genes (Zarrei et al 2015). Strikingly, in cattle, milk production is associated with CNVs (Xu, Cole, et al 2014;Prinsen et al 2017). Further studies performed in Chinese cattle revealed that CNVs of the leptin receptor (LEPR) (Shi et al 2016), myosin heavy chain 3 (MYH3) (Xu, Shi, et al 2014), potassium voltage-gated channel subfamily J member (KCNJ12) , mitogen-activated protein kinase 10 (MAPK10) ), MICAL-like 2 (MICAL-L2) , and phospholipase A2 group IID (PLA2G2D) (Zhang, Jia, et al 2014) genes are associated with growth traits.…”

Section: Introductionmentioning

confidence: 99%

Association study and expression analysis of GPC1 gene copy number variation in Chinese Datong yak (Bos grunniens) breed

Goshu

Chen

et al. 2019

Italian Journal of Animal Science

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Copy number variations (CNVs) can cause radical changes in phenotype variation, gene expression and evolutionary adaptation, through gene dosage effects, disruption of transcript arrangement and regulatory polymorphisms. Therefore, the current study was undertaken to investigate the distribution of glypican1 (GPC1) CNVs in five domestic yak breeds, and their association growth traits and gene expression. The data were analysed using real-time quantitative PCR (qPCR). Loss and normal copy number types had a significant (p < .05) associated with body height, weight and length and chest girth than gain of copy number types. Population studies indicated that loss of copy number was more frequently observed in the Tianzhu, Gannan and Plateau yaks than the Polled and Datong yaks. We elucidated a moderately negative and highly significant (p < .005) correlation among DNA copy numbers and mRNA transcription levels of GPC1. From these results, we hypothesise that GPC1 CNVs could alter mRNA transcription levels of skeletal muscles which impact on quantitative of growth traits. Our study makes data available for breeders and genomics studies focussing on the fundamental function of GPC1 CNVs in gene expression and growth traits and presents the foundation for future molecular marker application in designing yak breeding programmes. HIGHLIGHTSThe GPC1 gene encompasses within CNVRs of yak individuals that overlap with growth traits. The copy number types of GPC1 had a significant associated with growth traits of yak breeds Negative and highly significant correlation among DNA copy numbers and mRNA transcription levels of GPC1 are obtained ARTICLE HISTORY

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A genome wide association study between CNVs and quantitative traits in Brown Swiss cattle

Cited by 35 publications

References 27 publications

Functional and population genetic features of copy number variations in two dairy cattle populations

Functional and population genetic features of copy number variations in two dairy cattle populations

Copy Number Variations of Four Y-Linked Genes in Swamp Buffaloes

Association study and expression analysis of GPC1 gene copy number variation in Chinese Datong yak (Bos grunniens) breed

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