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

Ma, Yihan; Wen, Yifan; Cao, Xiukai; Cheng, Jie; Huang, Yongzhen; Ma, Yun; Hu, Linyong; Lei, Chuzhao; Qi, Xinglei; Cao, Hui; Chen, Hong

doi:10.5194/aab-62-171-2019

Cited by 19 publications

(9 citation statements)

References 52 publications

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“…The knockout mice experiment suggested the positive impact of HMGA2 expression on myoblast growth [ 32 ]. On the other hand, Chinese beef cattles with copy number loss of IGF1R had significantly better growth trait such as body weight, body height and hucklebone width [ 33 ]. In addition, HMGA2 and IGF1R were strongly associated with size differences between dog breeds [ 34 ].…”

Section: Discussionmentioning

confidence: 99%

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

et al. 2021

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Background CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV. Results Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs. Conclusion For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments.

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Section: Discussionmentioning

confidence: 99%

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

et al. 2021

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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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“…The expression level of IGF1R gene in muscle was found through bovine muscle transcriptome sequencing in the early stage of the laboratory, and bioinformatics analysis was conducted on it by animal quantitative trait loci (QTL) Database and NCBI. The previous study found the mRNA of IGF1R was widely expressed in heart, liver, kidney, muscle, fat, stomach, spleen and lung (from female cattle) and testis (from male cattle) in adult cattle, with the highest level of expression in testis and the middle-level expression in muscle (Ma et al ., 2019).…”

Section: Methodsmentioning

confidence: 99%

A novel 28-bp indel inIGF1Rgene associated with growth traits across four Chinese cattle breeds

Tang

Ma²,

Yang

et al. 2021

J. Agric. Sci.

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Insulin-like growth factor 1 receptor (IGF1R) is a cell surface receptor, belonging to the tyrosine kinase receptor superfamily. IGF1R plays a role not only in normal cell development but also in malignant transformation, which has become a candidate therapeutic target for the treatment of human cancer. This study aimed to explore insertions and deletions (indels) in IGF1R gene and investigate their association with growth traits in four Chinese cattle breeds (Xianan cattle, Jinnan cattle, Qinchuan cattle and Nanyang cattle). The current paper identified a 28-bp indel by polymerase chain reaction within IGF1R gene. The analysis showed that there was a significant correlation between the locus and the hucklebone width of Nanyang cattle in four periods, in which it was highly correlated at 6, 12 and 18 months. At the age of 6 months, it was also significantly correlated with body height, body weight and body length. Association analysis showed that the locus in Jinnan cattle was extremely significantly correlated with body slanting length and body weight, and significantly correlated with chest circumference. There was no significant correlation between this locus and growth traits of Xianan cattle and Qinchuan cattle. The detected indel in the IGF1R gene was significantly associated with growth traits in Jinnan and Nanyang cattle, and could be used as a molecular marker for growth trait selection.

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

Cited by 19 publications

References 52 publications

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

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

A novel 28-bp indel inIGF1Rgene associated with growth traits across four Chinese cattle breeds

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