Copy number variations in high and low fertility breeding boars

Révay, Tamás; Quach, Anh T.; Maignel, Laurence; Sullivan, B. Patrick; King, W. A.

doi:10.1186/s12864-015-1473-9

Cited by 28 publications

(24 citation statements)

References 72 publications

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“…In order to extend the panel of the 21 tested animals, of which we had no specific fertility information available other than their general good reproductive health, 10 additional unrelated boars with known fertility status (five High-fertility and five Low-fertility) were chosen from a separate population [ 23 ]. The fertility indicator parameter was the Direct Boar Effect on litter size (DBE) that is the number of piglets the given boar produces in average per litter ( S3 Table ) as compared to the overall average of the population and corrected for all identified environmental effects and breeding values of their mate [ 24 ].…”

Section: Methodsmentioning

confidence: 99%

The Porcine TSPY Gene Is Tricopy but Not a Copy Number Variant

et al. 2015

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The testis-specific protein Y-encoded (TSPY) gene is situated on the mammalian Y-chromosome and exhibits some remarkable biological characteristics. It has the highest known copy number (CN) of all protein coding genes in the human and bovine genomes (up to 74 and 200, respectively) and also shows high individual variability. Although the biological function of TSPY has not yet been elucidated, its specific expression in the testis and several identified binding domains within the protein suggests roles in male reproduction. Here we describe the porcine TSPY, as a multicopy gene with three copies located on the short arm of the Y-chromosome with no variation at three exon loci among 20 animals of normal reproductive health from four breeds of domestic pigs (Piétrain, Landrace, Duroc and Yorkshire). To further investigate the speculation that porcine TSPY is not a copy number variant, we have included five Low-fertility boars and five boars with exceptional High-fertility records. Interestingly, there was no difference between the High- and Low-fertile groups, but we detected slightly lower TSPY CN at all three exons (2.56-2.85) in both groups, as compared to normal animals, which could be attributed to technical variability or somatic mosaicism. The results are based on both relative quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR). Chromosomal localization of the porcine TSPY was done using fluorescence in situ hybridization (FISH) with gene specific PCR probes.

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Section: Methodsmentioning

confidence: 99%

The Porcine TSPY Gene Is Tricopy but Not a Copy Number Variant

et al. 2015

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“…Genome-wide (autosomal) CNVs were estimated from the normalized signal intensity data (logR ratio) using the SNP and Variation Suite (SVS version 8.4.3., GoldenHelix Inc.), as described earlier in detail [Revay et al, 2015]. Briefly, quality control steps of testing for outlier noise or genomic waves by investigating the derivative logR ratio distribution and batch effects with principal component analysis were followed by the detection of CNVs using the Univariate-CNAM segmentation algorithm in SVS.…”

Section: Methodsmentioning

confidence: 99%

Somatic Mosaicism in Bulls Estimated from Genome-Wide CNV Array and <b><i>TSPY</i></b> Gene Copy Numbers

Oluwole

Révay²,

Mahboubi³

et al. 2016

Cytogenet Genome Res

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Somatic mosaicism has become a focus in human research due to the implications of individual genetic variability in disease. Here, we assessed somatic copy number variations (CNVs) in Holstein bulls in 2 respects. We estimated genome-wide CNVs and assayed CNVs of the TSPY gene, the most variable bovine gene from the Y chromosome. Somatic tissues (blood, lung, heart, muscle, testis, and brain) of 4 bulls were arrayed on the Illumina Bovine SNP50k chip and qPCR tested for TSPY copy numbers. Our results showed extensive copy number divergence in tissues within the same animal as well as significant copy number alterations of TSPY. We detected a mean of 31 CNVs per animal among which 14 were of germline origin, as they were constantly present in all investigated tissues of the animal, while 18 were specific to 1 tissue. Thus, 57% of the total number of detected CNVs was the result of de novo somatic events. Further, TSPY copy number was found to vary significantly among tissues as well as among the same tissue type from different animals in a wide range from 7 to 224% of the calibrator. Our study shows significant autosomal and Y-chromosomal de novo somatic CNV in bulls.

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“…They are also associated with common traits and various diseases such as Crohn's disease, rheumatoid arthritis and diabetes (Fontanesi et al., ; WTCCC, ). The determination of CNV has become increasingly important for the evaluation of genomic traits in domestic animals (Revay, Quach, Maignel, Sullivan, & King, ; Xu et al., ). Our previous study revealed that MTHFSD gene was identified in the CNVs region of Chinese Xiang pig genome by Illumina PorcineSNP60K BeadChip.…”

Section: Introductionmentioning

confidence: 99%

“…2010). The determination of CNV has become increasingly important for the evaluation of genomic traits in domestic animals (Revay, Quach, Maignel, Sullivan, & King, 2015;Xu et al, 2014). Our previous study revealed that MTHFSD gene was identified in the CNVs region of Chinese Xiang pig genome by Illumina PorcineSNP60K…”

Section: Introductionmentioning

confidence: 99%

Copy number variations of MTHFSD gene across pig breeds and its association with litter size traits in Chinese indigenous Xiang pig

Ran

Hua

Huang

et al. 2018

Animal Physiology Nutrition

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Copy number variation (CNV) is a major proportion of genetic variation, which changes the gene structure and dosage and affects gene expression and function. To validate the presence and the function of CNV in pig, we used real-time quantitative polymerase chain reaction (qPCR) method to validate a 496 kb CNV region comprising MTHFSD gene on chromosome 6 of Xiang pig detected by single nucleotide polymorphism (SNP) array. Then we investigated the distribution of the MTHFSD CNV in a total of 545 pigs in four breeds. About 46.2% and 32.7% individuals in the four pig breeds were detected to be types of loss and gain of MTHFSD locus. The relative copy numbers of MTHFSD gene showed the largest variation range (0-55 copies) in the Xiang pig population. The copy numbers of MTHFSD gene presented the positive correlations with the transcript level of MTHFSD gene in adult ovaries. Statistical analysis indicated that CNVs of MTHFSD gene was significantly changed the litter size traits of Xiang pigs, and the individuals with CNV gain showed more litter size than the CNV loss pigs. We have reasons to believe that the MTHFSD as RNA-binding protein play an important role in pig reproduction as a result of regulating MTHFS mRNA metabolism.

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Copy number variations in high and low fertility breeding boars

Cited by 28 publications

References 72 publications

The Porcine TSPY Gene Is Tricopy but Not a Copy Number Variant

The Porcine TSPY Gene Is Tricopy but Not a Copy Number Variant

Somatic Mosaicism in Bulls Estimated from Genome-Wide CNV Array and <b><i>TSPY</i></b> Gene Copy Numbers

Copy number variations of MTHFSD gene across pig breeds and its association with litter size traits in Chinese indigenous Xiang pig

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