Copy number variations at <i>LEPR</i> gene locus associated with gene expression and phenotypic traits in Chinese cattle

Shi, Tao; Xu, Yao; Yang, Mingjuan; Huang, Yongzhen; Lan, Xianyong; Lei, Chuzhao; Qi, Xinglei; Yang, Xiaoming; Chen, Hong

doi:10.1111/asj.12531

Cited by 34 publications

(43 citation statements)

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“…We found that the PIGY gene in sheep contains a copy number variation region located in exon 2, and it overlaps with 28 QTLs, including carcass weight and muscle density. Previous studies have reported that, in chickens, some QTLs associated with CNV fragments are related to body weight, carcass weight, and pectoral muscle mass [32,33]. Therefore, we focused on the PIGY gene to investigate the association between copy number variation and sheep economic traits.…”

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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“…Third, quantitative PCR (qPCR) was performed to meansure CNVs [28]. Briefly, two pairs of quantitative primer were designed based on TGFβ3 (Gene ID: 396438, NC_006092.3) and PCCA gene sequences (Gene ID: 418774, NC_006088.3).…”

Section: Methodsmentioning

confidence: 99%

Novel copy number variation of the TGFβ3 gene is associated with TGFβ3 gene expression and duration of fertility traits in hens

Sun

Gong

et al. 2017

PLoS ONE

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Improvements in the duration of fertility (DF) could increase the interval between successive artificial inseminations, thereby decreasing the cost associated with production of hatching eggs. The molecular mechanisms involved in DF in hens remains under-explored. In this study, expression levels of the transforming growth factor-β genes (TGFβs: TGFβ1, TGFβ2, TGFβ3) were investigated in utero-vaginal junctions (UVJs) of hens with long DF (Group L, n = 10) and short DF (Group S, n = 10). TGFβ1 and 2 tended to exhibit higher expression levels in UVJs from Group L hens. The expression levels of TGFβ3 mRNA and protein were significantly increased in UVJs of hens from Group L compared to hens in Group S. Consistently, six TGFβs downstream genes (DAXX, MEKK1, T-BET, GATA-3, TAK1, and FOXP3) associated with the immune response were found to be significantly differentially expressed in UVJs of Group L than Group S hens. In addition, four SNPs were identified in intron 1 of TGFβ3, and these SNPs were significantly associated with DF traits (P < 0.05). Furthermore, we identified multi-copy and copy number variants (CNVs) in chicken TGFβ3 and later determined significant associations between TGFβ3 CNVs and DF traits in hens. Specifically, TGFβ3 copy number exhibited a significant positive correlation with its expression (P < 0.05). Collectively, our results suggest that chicken DF traits may be regulated by the expression of TGFβ3 in UVJ. Meanwhile, the copy number variation in the TGFβ3 gene identified in this study seems to be one marker for DF traits.

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“…With the development of genomics, copy number variation has recently been shown to be associated with disease and phenotypic variation (Bujakowska et al, 2017;Keel et al, 2017;Shi et al, 2016). And it had been continuously confirmed to be able to influence individual phenotypic traits through gene dosage or structural variation (Bickhart et al, 2012;Wright et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

Copy number variation (CNV) in the <i>IGF1R</i> gene across four cattle breeds and its association with economic traits

Wen

Cao

et al. 2019

Arch. Anim. Breed.

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The insulin-like growth factor 1 receptor (IGF1R) plays a vital role in immunomodulation and muscle and bone growth. The copy number variation (CNV) is believed to the reason for many complex phenotypic variations. In this paper, we statistically analyzed the copy number and the expression profiling in different tissue types of the IGF1R gene using the 422 samples from four Chinese beef cattle breeds, and the mRNA of IGF1R was widely expressed in nine tissue types of adult cattle (heart, liver, kidney, muscle, fat, stomach, spleen, lung and testis). Results of CNV and growth traits indicated that the IGF1R CNV was significantly associated with body weight and body height of Jinnan (JN) cattle and was significantly associated with body height and hucklebone width of Qinchuan (QC) cattle, making IGF1R CNV a promising molecular marker to improve meat production in beef cattle breeding. Bioinformatics predictions show that the CNV region is highly similar to the human genome, and there are a large number of transcription factors, DNase I hypersensitive sites, and high levels of histone acetylation, suggesting that this region may play a role in transcriptional regulation, providing directions for further study of the role of bovine CNV and economic traits.

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Copy number variations at LEPR gene locus associated with gene expression and phenotypic traits in Chinese cattle

Cited by 34 publications

References 48 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

Novel copy number variation of the TGFβ3 gene is associated with TGFβ3 gene expression and duration of fertility traits in hens

Copy number variation (CNV) in the <i>IGF1R</i> gene across four cattle breeds and its association with economic traits

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Copy number variations at LEPR gene locus associated with gene expression and phenotypic traits in Chinese cattle

Cited by 34 publications

References 48 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

Novel copy number variation of the TGFβ3 gene is associated with TGFβ3 gene expression and duration of fertility traits in hens

Copy number variation (CNV) in the &lt;i&gt;IGF1R&lt;/i&gt; gene across four cattle breeds and its association with economic traits

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Copy number variation (CNV) in the <i>IGF1R</i> gene across four cattle breeds and its association with economic traits