Diversity of copy number variation in a worldwide population of sheep

Liu, Yang; Xu, Lingyang; Zhou, Yang; Liu, Mei; Wang, Lei; Kijas, James W.; Zhang, Hongping; Li, Li; Liu, George E.

doi:10.1016/j.ygeno.2017.09.005

Cited by 58 publications

(55 citation statements)

References 34 publications

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“…Compared with SNP, CNVs are longer fragments of variation with more significant effects on the growth traits of sheep. More and more copy number variation studies have been performed on different species, such as human [24], mouse [25], cattle [26,27], chicken [28], monkey [29], and sheep [30,31]. In recent years, with increasing consumer requirements for sheep quality and the development of molecular breeding, there is a need to exploit CNV molecular genetic variation for economic trait selection and disease prevention.…”

Section: Discussionmentioning

confidence: 99%

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Feng

Cheng

et al. 2020

Animals

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Simple Summary:The PIGY (phosphatidylinositol glycan anchor biosynthesis class Y) gene is a member of the PIG gene family and encodes the glycosylphosphatidylinositol-Nacetylglucosaminyltransferase (GPI-GnT) complex. It initiates the biosynthesis of GPI and plays an important role in cell-cell interactions. Sequencing has revealed a 3600 bp copy number variation (CNV) in exon 2 of the PIGY gene in sheep, potentially altering a functional part of the protein. The CNV overlaps 28 quantitative trait loci that are relevant to some economic traits like muscle density and carcass weight. We screened for this CNV of the PIGY gene in 569 individuals, namely, 240 Chaka sheep (CKS), 168 Hu sheep (HS), and 161 small-tailed Han sheep (STHS), and analyzed the association between the presence of this CNV and sheep body size traits. The results showed that the loss-type CNV was more prevalent than other types in these three breeds, and there were significant effects of the PIGY gene CNV on body weight, chest circumference, and circumference of cannon bone of sheep. The results showed that sheep with gain-type CNV had better growth traits than those with other types. The findings reveal the relationship between the CNV of the PIGY gene and growth traits of sheep, suggesting that CNV could be utilized for improved molecular breeding of sheep.Abstract: Copy number variation (CNV) is a type of genomic variation with an important effect on animal phenotype. We found that the PIGY gene contains a 3600 bp copy number variation (CNV) region located in chromosome 6 of sheep (Oar_v4.0 36,121,601-36,125,200 bp). This region overlaps with multiple quantitative trait loci related to phenotypes like muscle density and carcass weight. Therefore, in this study, the copy number variation of the PIGY gene was screened in three Chinese sheep breeds, namely, Chaka sheep (CKS, May of 2018, Wulan County, Qinghai Province, China), Hu sheep (HS, May of 2015, Mengjin County, Henan Province, China), and small-tailed Han sheep (STHS, May of 2016, Yongjing, Gansu Province, China). Association analyses were performed on the presence of CNV and sheep body size traits. We used real-time quantitative PCR (qPCR) to detect the CNV for association analysis. According to the results, the loss-type CNV was more common than other types in the three breeds (global average: loss = 61.5%, normal = 17.5%, and gain = 21.0%). The association analysis also showed significant effects of the PIGY gene CNV on body weight, chest circumference, and circumference of the cannon bone of sheep. Sheep with gain-type CNV had better growth traits than those with other types. The results indicate a clear relationship between the PIGY gene CNV and growth traits of sheep, suggesting the use of CNV as a new molecular breeding marker.

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Section: Discussionmentioning

confidence: 99%

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Feng

Cheng

et al. 2020

Animals

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“…In animal breeding, according to reports, copy number variations can affect the economic traits of animals and lay the foundation for molecular breeding, such as in pig (Fowler et al, 2013), chicken (Lin et al, 2018), sheep (Ma et al, 2017), and cattle (Xu et al, 2014;Zheng et al, 2019). Studies have shown that a comprehensive sheep CNV map has been generated, equivalent to 6.9 % of the sheep genome (Yang et al, 2018b). However, it is necessary to use a large number of experimental individuals from various sheep breeds to identify the existence of gene CNVs and to study whether specific CNVs affect individuals.…”

Section: Discussionmentioning

confidence: 99%

Associations of <i>ORMDL1</i> gene copy number variations with growth traits in four Chinese sheep breeds

et al. 2019

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Copy number variations (CNVs) are gains and losses of genomic sequence of more than 50 bp between two individuals of a species. Also, CNV is considered to be one of the main elements affecting the phenotypic diversity and evolutionary adaptation of animals. ORMDL sphingolipid biosynthesis regulator 1 (ORMDL1) is a protein-coding gene associated with diseases and development. In our study, the polymorphism of ORMDL1 gene copy numbers in four Chinese sheep breeds (abbreviated CK, HU, STH, and LTH) was detected. In addition, we analyzed the transcriptional expression level of ORMDL1 gene in different tissues of sheep and examined the association of ORMDL1 CNV with growth traits. The statistical analysis revealed that ORMDL1 CNV was remarkably correlated with body height, heart girth, and circumference of cannon bone in HU sheep (P<0.05), and there are significant effects on body weight, body height, body length, chest depth, and height of hip cross in STH sheep (P<0.05). In conclusion, our results provide a basis for the relationship between CNV of ORMDL1 gene and sheep growth traits, suggesting that ORMDL1 CNV may be considered a promising marker for the molecular breeding of Chinese sheep.

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“…L1 transposition occurs through reverse transcription and integration [ 10 ]. A number of studies have been carried out to identify the CNV in different species such as cattle [ 11 - 14 ], sheep [ 15 , 16 ], goat [ 17 ], pig [ 18 - 21 ] and chicken [ 22 ].…”

Section: Mechanisms Of Cnv Formationmentioning

confidence: 99%

“…[ 11 ] also identified 368 unique CNV regions from 265 Korean Hanwoo cattle based on 50K SNP array covering 15.8Mb of the genome using PennCNV algorithm without considering the pedigree information and genomic waves. Recent studies on CNV detection using different approaches are given in the Table-1 [ 11 - 14 , 23 , 30 , 34 - 37 , 42 - 46 ] for cattle and Table-2 [ 14 , 16 , 47 - 52 ] for other species.…”

Section: Cnv Identification Studies In Domestic Speciesmentioning

confidence: 99%

Copy number variation in livestock: A mini review

Bhanuprakash¹,

Chhotaray²,

Dr³

et al. 2018

Vet World

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Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between the individuals in a population. It is an important source of genetic variation in an individual which is now being utilized rather than single nucleotide polymorphisms (SNPs), as it covers the more genomic region. CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs). Earlier, researchers extensively utilized SNPs as the main source of genetic variation. But now, the focus is on identification of CNVs associated with complex traits. With the recent advances and reduction in the cost of sequencing, arrays are developed for genotyping which cover the maximum number of SNPs at a time that can be used for detection of CNVRs and underlying quantitative trait loci (QTL) for the complex traits to accelerate genetic improvement. CNV studies are also being carried out to understand the evolutionary mechanism in the domestication of livestock and their adaptation to the different environmental conditions. The main aim of the study is to review the available data on CNV and its role in genetic variation among the livestock.

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Diversity of copy number variation in a worldwide population of sheep

Cited by 58 publications

References 34 publications

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Associations of <i>ORMDL1</i> gene copy number variations with growth traits in four Chinese sheep breeds

Copy number variation in livestock: A mini review

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Diversity of copy number variation in a worldwide population of sheep

Cited by 58 publications

References 34 publications

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Associations of &lt;i&gt;ORMDL1&lt;/i&gt; gene copy number variations with growth traits in four Chinese sheep breeds

Copy number variation in livestock: A mini review

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Associations of <i>ORMDL1</i> gene copy number variations with growth traits in four Chinese sheep breeds