Analysis of copy number variants by three detection algorithms and their association with body size in horses

Metzger, Julia; Philipp, Ute; Lopes, M. S.; Machado, Artur da Câmara; Felicetti, Michela; Silvestrelli, Maurizio; Distl, O.

doi:10.1186/1471-2164-14-487

Cited by 56 publications

(85 citation statements)

References 45 publications

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“…In total, 700 CNVs on autosomals were detected (Table 1 and Table S2 in File S1), including 302 gains and 398 losses. And the average number of CNVs per individual was 120, ranging from 82 to 211, slightly less than Doan of 139.3 (2368/17, CGH analysis) [30], while significantly greater than Dupuis of 5.9 (2797/477, SNP analysis) [31] and Metzger of 5.6 (4013/717, SNP analysis) [32]. This might be caused by different experimental samples or detection methods of CNV.…”

Section: Resultsmentioning

confidence: 94%

Genome-Wide Detection of Copy Number Variations among Diverse Horse Breeds by Array CGH

Wang

Hou

et al. 2014

PLoS ONE

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Recent studies have found that copy number variations (CNVs) are widespread in human and animal genomes. CNVs are a significant source of genetic variation, and have been shown to be associated with phenotypic diversity. However, the effect of CNVs on genetic variation in horses is not well understood. In the present study, CNVs in 6 different breeds of mare horses, Mongolia horse, Abaga horse, Hequ horse and Kazakh horse (all plateau breeds) and Debao pony and Thoroughbred, were determined using aCGH. In total, seven hundred CNVs were identified ranging in size from 6.1 Kb to 0.57 Mb across all autosomes, with an average size of 43.08 Kb and a median size of 15.11 Kb. By merging overlapping CNVs, we found a total of three hundred and fifty-three CNV regions (CNVRs). The length of the CNVRs ranged from 6.1 Kb to 1.45 Mb with average and median sizes of 38.49 Kb and 13.1 Kb. Collectively, 13.59 Mb of copy number variation was identified among the horses investigated and accounted for approximately 0.61% of the horse genome sequence. Five hundred and eighteen annotated genes were affected by CNVs, which corresponded to about 2.26% of all horse genes. Through the gene ontology (GO), genetic pathway analysis and comparison of CNV genes among different breeds, we found evidence that CNVs involving 7 genes may be related to the adaptation to severe environment of these plateau horses. This study is the first report of copy number variations in Chinese horses, which indicates that CNVs are ubiquitous in the horse genome and influence many biological processes of the horse. These results will be helpful not only in mapping the horse whole-genome CNVs, but also to further research for the adaption to the high altitude severe environment for plateau horses.

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Section: Resultsmentioning

confidence: 94%

Genome-Wide Detection of Copy Number Variations among Diverse Horse Breeds by Array CGH

Wang

Hou

et al. 2014

PLoS ONE

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“…Similarly, newborn homozygous QQ and heterozygous Qq dairy calves were found to be 18.8 and 10.4% heavier, respectively, compared to homozygous qq calves (Littlejohn et al 2012). Variants of PLAG1 have also been suggested to contribute to body size in European domestic pigs and horses (Rubin et al 2012, Metzger et al 2013, indicating that this role of PLAG1 is likely to be conserved across mammals. It should be emphasized, however, that although PLAG1 was found to be the most plausible candidate on chromosome 14 as the causative gene for stature differences in cattle, other genes in the vicinity of PLAG1, such as RPS20, MOS, RDHE2, SDR16C6, and PENK, some of which having established links with growth, were also differentially expressed in the fetal tissues of QQ and qq animals (Karim et al 2011).…”

Section: Evidence From Genome-wide Association Studiesmentioning

confidence: 97%

Emerging role of PLAG1 as a regulator of growth and reproduction

Juma

Damdimopoulou

Grommen

et al. 2015

Journal of Endocrinology

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Pleomorphic adenoma gene 1 (PLAG1) belongs to the PLAG family of zinc finger transcription factors along with PLAG-like 1 and PLAG-like 2. The PLAG1 gene is best known as an oncogene associated with certain types of cancer, most notably pleomorphic adenomas of the salivary gland. While the mechanisms of PLAG1-induced tumorigenesis are reasonably well understood, the role of PLAG1 in normal physiology is less clear. It is known that PLAG1 is involved in cell proliferation by directly regulating a wide array of target genes, including a number of growth factors such as insulin-like growth factor 2. This is likely to be a central mode of action for PLAG1 both in embryonic development and in cancer. The phenotype of Plag1 knockout mice suggests an important role for PLAG1 also in postnatal growth and reproduction, as PLAG1 deficiency causes growth retardation and reduced fertility. A role for PLAG1 in growth and reproduction is further corroborated by genome-wide association studies in humans and domestic animals in which polymorphisms in the PLAG1 genomic region are associated with body growth and reproductive traits. Here we review the current evidence for PLAG1 as a regulator of growth and fertility and discuss possible endocrine mechanisms involved.

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“…The algorithm (cnvPartition) is optimized for Illumina's data and was shown to be able to detect regions which to a large extent overlap with regions detected by other methods. Additionally, lower number of CNVs can be detected by this algorithm when compared to other available methods, which suggests than cnvPartition may be more prone to detection of false-negatives rather than false-positives (Metzger et al 2013). This is satisfying if the reasonable number of high-quality regions is the point of interest.…”

Section: Discussionmentioning

confidence: 87%

“…Most of them use signal intensity and allelic intensity ratios as well as allele calls (allele frequency spectra analysis) to detect genomic regions showing a loss or gain of copy number. Recently, efforts have been made to compare these methods and indicate the best performing approach (Winchester et al 2009;Koike et al 2011;Metzger et al 2013). However, each method has its strengths and weaknesses, making it difficult to point the best one.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide characteristics of copy number variation in Polish Holstein and Polish Red cattle using SNP genotyping assay

et al. 2015

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Copy number variation (CNV), which results from deletions or amplifications of large fragments of genomic DNA, is widespread in mammalian genomes and apart from its potential pathogenic effect it is considered as a source of natural genetic diversity. In cattle populations, this kind of genetic variability remains still insufficiently elucidated and studies focusing on the detection of new structural genomic variants in different cattle populations may contribute to a better understanding of cattle breeds' diversity and genetic basis of production traits. In this study, by using BovineSNP50 assay and cnvPartition algorithm we identified CNVs in two different cattle breeds: Holstein (859 animals) and Polish Red (301). In Holstein cattle we found 648 CNVs which could be reduced to 91 non-redundant variable genomic regions (CNVRs) covering in total 168.6 Mb of the genomic sequence. In Polish Red cattle we detected 62 CNVs, localized in 37 variable regions encompassing 22.3 Mb of the sequence, corresponding to 0.89 % of the autosomal genome. Within the regions we identified 1,192 unique RefSeq genes which are engaged in a variety of biological processes. High concordance of the regions' distribution was found between the studied breeds, however copy number variants seemed to be more common in Holstein cattle. About 26 % of the regions described in this study could be classified as newly identified. The results of this study will broaden the knowledge of CNVs in genomes of cattle of different breeds and will provide foundations for further research aiming to identify a relationship between this type of genetic variation and phenotypic traits.

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Analysis of copy number variants by three detection algorithms and their association with body size in horses

Cited by 56 publications

References 45 publications

Genome-Wide Detection of Copy Number Variations among Diverse Horse Breeds by Array CGH

Genome-Wide Detection of Copy Number Variations among Diverse Horse Breeds by Array CGH

Emerging role of PLAG1 as a regulator of growth and reproduction

Genome-wide characteristics of copy number variation in Polish Holstein and Polish Red cattle using SNP genotyping assay

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