Identification and Validation of Copy Number Variants in Italian Brown Swiss Dairy Cattle Using Illumina Bovine SNP50 Beadchip<sup>®</sup>

Bagnato, A.; Strillacci, M.G.; Pellegrino, Laura; Schiavini, F.; Frigo, E.; Rossoni, Attilio; Maltecca, Christian; Prinsen, R.T.M.M.; Dolezal, Marlies

doi:10.4081/ijas.2015.3900

Cited by 12 publications

(10 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Comparison with literature findings showed that 78.5% of significant CNVRs (a total of 65) here identified have been already reported in 9 studies (Table S3), providing evidence they are likely true CNVRs (Hou et al 2012;Jiang et al 2013;Xu et al 2014;Zang et al 2015;Wu et al 2015;Bagnato et al 2015;Sasaki et al 2016;Xu et al 2016;Choi et al 2016). Additionally, many of the CNVRs reported by the 9 studies perfectly overlapped those found here and were found among different breeds suggesting that they are CNVRs conserved across populations.…”

Section: Cnv Calling and Association Analysis With Penncnvsupporting

confidence: 79%

Genome‐wide association study for milk somatic cell score in holstein cattle using copy number variation as markers

Aguilar

Ponce

López

et al. 2016

J Animal Breeding Genetics

View full text Add to dashboard Cite

Mastitis, the most common and expensive disease in dairy cows, implies significant losses in the dairy industry worldwide. Many efforts have been made to improve genetic mastitis resistance in dairy populations, but low heritability of this trait made this process not as effective as desired. The purpose of this study was to identify genomic regions explaining genetic variation of somatic cell count using copy number variations (CNVs) as markers in the Holstein population, genotyped with the Illumina BovineHD BeadChip. We found 24 and 47 copy number variation regions significantly associated with estimated breeding values for somatic cell score (SCS_EBVs) using SVS 8.3.1 and PennCNV-CNVRuler software, respectively. The association analysis performed with these two software allowed the identification of 18 candidate genes (TERT, NOTCH1, SLC6A3, CLPTM1L, PPARα, BCL-2, ABO, VAV2, CACNA1S, TRAF2, RELA, ELF3, DBH, CDK5, NF2, FASN, EWSR1 and MAP3K11) that result classified in the same functional cluster. These genes are also part of two gene networks, whose genes share the 'stress', 'cell death', 'inflammation' and 'immune response' GO terms. Combining CNV detection/association analysis based on two different algorithms helps towards a more complete identification of genes linked to phenotypic variation of the somatic cell count.

show abstract

Section: Cnv Calling and Association Analysis With Penncnvsupporting

confidence: 79%

Genome‐wide association study for milk somatic cell score in holstein cattle using copy number variation as markers

Aguilar

Ponce

López

et al. 2016

J Animal Breeding Genetics

View full text Add to dashboard Cite

show abstract

“…There was high variability in the total number and length of the CNVRs identified in the different studies and only a small number of CNVRs identified in the present study were reported in other studies, which has also been reported by Bagnato et al (2015). The greatest coincidence of CNVRs was found with the studies of Hou et al (2011Hou et al ( , 2012a, with 31.1% and 29.9% common CNVRs respectively, and the total lengths of overlapping regions were 7.6 and 7.4 Mb respectively.…”

Section: Cnv and Cnvr Detectionmentioning

confidence: 36%

“…The 41 CNVRs covered 8.2 Mb and 0.32% of the genomic autosomal sequence, with an average length and median size of 200.58 kb and 163.88 kb respectively. The differences in the numbers of CNVs and CNVRs detected in each breed by the two software were probably attributable to the identification of longer CNVs with the univariate approach of SVS (Bagnato et al 2015).…”

Section: Cnv and Cnvr Detectionmentioning

confidence: 99%

Genome-wide detection of copy-number variations in local cattle breeds

et al. 2019

View full text Add to dashboard Cite

Abstract. The aim of the present study was to identify copy-number variations (CNVs) in Cinisara (CIN) and Modicana (MOD) cattle breeds on the basis of signal intensity (logR ratio) and B allele frequency of each marker, using Illumina's BovineSNP50K Genotyping BeadChip. The CNVs were detected with the PennCNV and SVS 8.7.0 software and were aggregated into CNV regions (CNVRs). PennCNV identified 487 CNVs in CIN that aggregated into 86 CNVRs, and 424 CNVs in MOD that aggregated into 81 CNVRs. SVS identified a total of 207 CNVs in CIN that aggregated into 39 CNVRs, and 181 CNVs in MOD that aggregated into 41 CNVRs. The CNVRs identified with the two softwares contained 29 common CNVRs in CIN and 17 common CNVRs in MOD. Only a small number of CNVRs identified in the present study have been identified elsewhere, probably because of the limitations of the array used. In total, 178 and 208 genes were found within the CNVRs of CIN and MOD respectively. Gene Ontology and KEGG pathway analyses showed that several of these genes are involved in milk production, reproduction and behaviour, the immune response, and resistance/susceptibility to infectious diseases. Our results have provided significant information for the construction of more-complete CNV maps of the bovine genome and offer an important resource for the investigation of genomic changes and traits of interest in the CIN and MOD cattle breeds. Our results will also be valuable for future studies and constitute a preliminary report of the CNV distribution resources in local cattle genomes.

show abstract

“…Cattle CNVs have been reported using a variety of platforms, including comparative genomic hybridization arrays (Liu et al, 2008, 2010; Fadista et al, 2010), the Illumina BovineHD BeadChip (Hou et al, 2012a; Wu et al, 2015; Aguilar et al, 2016; Prinsen et al, 2016; Xu et al, 2016), the Illumina BovineSNP50 BeadChip (Matukumalli et al, 2009; Bae et al, 2010; Hou et al, 2011, 2012b; Jiang et al, 2012; Bagnato et al, 2015; Ben Sassi et al, 2016), and next-generation sequencing (NGS) (Stothard et al, 2011; Zhan et al, 2011; Bickhart et al, 2012; Choi et al, 2013; Keel et al, 2016; Ben Sassi et al, 2016). In these studies, it is reported that copy number variable regions comprise ~2–7% of the cattle genome.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome1

2016

View full text Add to dashboard Cite

Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV. We identified and characterized CNV regions by utilizing exome sequence from 175 influential sires used in the Germplasm Evaluation project, representing 10 breeds. We examined various evolutionary and functional aspects of these CNVs, including selective constraint on CNV-overlapped genes, centrality of CNV genes in protein-protein interaction networks, and tissue-specific expression of CNV genes. Patterns of CNV in the Bos taurus genome reveal that reduced functional constraint and mutational bias may play a prominent role in shaping this type of structural variation.

show abstract

Identification and Validation of Copy Number Variants in Italian Brown Swiss Dairy Cattle Using Illumina Bovine SNP50 Beadchip^®

Cited by 12 publications

References 32 publications

Genome‐wide association study for milk somatic cell score in holstein cattle using copy number variation as markers

Genome‐wide association study for milk somatic cell score in holstein cattle using copy number variation as markers

Genome-wide detection of copy-number variations in local cattle breeds

Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome1

Contact Info

Product

Resources

About

Identification and Validation of Copy Number Variants in Italian Brown Swiss Dairy Cattle Using Illumina Bovine SNP50 Beadchip®

Cited by 12 publications

References 32 publications

Genome‐wide association study for milk somatic cell score in holstein cattle using copy number variation as markers

Genome‐wide association study for milk somatic cell score in holstein cattle using copy number variation as markers

Genome-wide detection of copy-number variations in local cattle breeds

Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome1

Contact Info

Product

Resources

About

Identification and Validation of Copy Number Variants in Italian Brown Swiss Dairy Cattle Using Illumina Bovine SNP50 Beadchip^®