scholarly journals Copy Number Variation of the SHE Gene in Sheep and Its Association with Economic Traits

Animals ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 531 ◽  
Author(s):  
Rui Jiang ◽  
Jie Cheng ◽  
Xiu-Kai Cao ◽  
Yi-Lei Ma ◽  
Buren Chaogetu ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Milk Fat ◽  
Copy Number ◽  
Linear Models ◽  
Copy Number Variation Region ◽  
Copy Number Loss ◽  
Economic Traits ◽  
Fat Percentage ◽  
Association Analyses ◽  
Number Variation

Copy number variation (CNV) caused by gene rearrangement is an important part of genomic structural variation. We found that the copy number variation region of the Src Homology 2 Domain Containing E (SHE) gene correlates with a quantitative trait locus of sheep related to milk fat percentage and bone density. The aim of our study was to detect the copy number variation of the SHE gene in four sheep breeds and to conduct a correlation analysis with economic traits, hoping to provide some reference for sheep breeding. In this study, we examined 750 sheep from four Chinese breeds: Chaka sheep (CKS), Hu sheep (HS), Large Tail Han sheep (LTHS) and Small Tail Han sheep (STHS). We used qPCR to evaluate the copy number of the SHE gene, and then used general linear models to analyze the associations between CNV and economic traits. The results showed that there were more individuals with SHE copy number loss in CKS and HS than in STHS and LTHS individuals. Association analyses showed that gain and normal copy number types were correlated to body length, circumference of cannon bone, heart girth, chest width and high at the cross in CKS, HS and STHS (p < 0.05), but this association was not observed for LTHS. Chi-square values (χ2) found prominent differences in CNV distribution among the studied breeds. Overall, the CNV of the SHE gene may be an important consideration for sheep molecular breeding.

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

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 688 ◽  
Author(s):  
Ziting Feng ◽  
Xinyu Li ◽  
Jie Cheng ◽  
Rui Jiang ◽  
Ruolan Huang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Association Analysis ◽  
Copy Number ◽  
Growth Traits ◽  
Gansu Province ◽  
Genomic Variation ◽  
Association Analyses ◽  
Qinghai Province ◽  
Real Time Quantitative Pcr ◽  
Number Variation

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.

scholarly journals Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1008 ◽  
Author(s):  
Fei Ge ◽  
Congjun Jia ◽  
Min Chu ◽  
Chunnian Liang ◽  
Ping Yan
Keyword(s):  
Body Weight ◽  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Quantitative Polymerase Chain Reaction ◽  
The Body ◽  
Gene Copy ◽  
Common Source ◽  
Economic Traits ◽  
Number Variation

Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.

scholarly journals A comprehensive map of single-base polymorphisms in the hypervariableLPAkringle IV type 2 copy number variation region

2018 ◽  
Vol 60 (1) ◽  
pp. 186-199 ◽  
Author(s):  
Stefan Coassin ◽  
Sebastian Schönherr ◽  
Hansi Weissensteiner ◽  
Gertraud Erhart ◽  
Lukas Forer ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Copy Number Variation Region ◽  
Single Base ◽  
Number Variation

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

2019 ◽  
Vol 62 (1) ◽  
pp. 171-179 ◽  
Author(s):  
Yi-Lei Ma ◽  
Yi-Fan Wen ◽  
Xiu-Kai Cao ◽  
Jie Cheng ◽  
Yong-Zhen Huang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Copy Number Variation ◽  
Copy Number ◽  
Bone Growth ◽  
Body Height ◽  
Meat Production ◽  
Economic Traits ◽  
Adult Cattle ◽  
Cattle Breeds ◽  
Number Variation

Abstract. 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.

scholarly journals Genome-Wide Association Study of Copy Number Variation and QTL for Economic Traits in Holstein Cattle

2010 ◽  
Author(s):  
Eyal Seroussi ◽  
George Liu
Keyword(s):  
Copy Number Variation ◽  
Association Study ◽  
Copy Number ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Holstein Cattle ◽  
Economic Traits ◽  
Genome Wide ◽  
Number Variation

Copy number variation (CNV) has been recently identified in human and other mammalian genomes and increasing awareness that CNV might be a major source for heritable variation in complex traits has emerged. Despite this, little has been published on CNVs in Holsteins. In order to fill this knowledge-gap, we proposed a genome-wide association study between quantitative trait loci (QTL) for economic traits and CNV in the Holstein cattle. The approved feasibility study was aimed at the genome-wide characterization of CNVs in Holstein cattle and at the demonstrating of their possible association with economic traits by performing the activities of preparation of DNA samples, Comparative Genomic Hybridization (CGH), initial association study between CNVs and production traits and characterization of CNVSNP associations. For both countries, 40 genomic DNA samples of bulls representing the extreme sub-populations for economically important traits were CGH analyzed using the same reference genome on a NimbleGen tiling array. We designed this array based on the latest build of the bovine genome (UMD3) with average probe spacing of 1150 bases (total number of probes was 2,166,672). Two CNV gene clusters, PLA2G2D on BTA2 and KIAA1683 on BTA7 revealed significant association with milk percentage and cow fertility, respectively, and were chosen for further characterization and verification in a larger sample using other methodologies including sequencing, tag SNPs and real time PCR (qPCR). Comparison between these four methods indicated that there is under estimation of the number of CNV loci in Holstein cattle and their complexity. The variation in sequence between different copies seemed to affect their functionality and thus the hybridization based methods were less informative than the methods that are based on sequencing. We thus conclude that large scale sequencing effort complemented by array CGH should be considered to better detect and characterize CNVs in order to effectively employ them in marker-assisted selection.

scholarly journals Investigation of a nonsense mutation located in the complex KIV-2 copy number variation region of apolipoprotein(a) in 10,910 individuals

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Silvia Di Maio ◽  
Rebecca Grüneis ◽  
Gertraud Streiter ◽  
Claudia Lamina ◽  
Manuel Maglione ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Nonsense Mutation ◽  
Copy Number ◽  
Copy Number Variation Region ◽  
Apolipoprotein A ◽  
Number Variation

scholarly journals Genome-Wide Copy Number Variation Association Analyses for Age at Menarche

2012 ◽  
Vol 97 (11) ◽  
pp. E2133-E2139 ◽  
Author(s):  
Yao-Zhong Liu ◽  
Jian Li ◽  
Rong Pan ◽  
Hui Shen ◽  
Qing Tian ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Age At Menarche ◽  
Association Analyses ◽  
Genome Wide ◽  
Number Variation

scholarly journals The Association of the Copy Number Variation of the MLLT10 Gene with Growth Traits of Chinese Cattle

Animals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 250
Author(s):  
Peng Yang ◽  
Zijing Zhang ◽  
Jiawei Xu ◽  
Kaixing Qu ◽  
Shijie Lyv ◽  
...  
Keyword(s):  
Correlation Analysis ◽  
Copy Number Variation ◽  
Copy Number ◽  
High Throughput Screening ◽  
Growth Traits ◽  
Gene Copy ◽  
Copy Number Variation Region ◽  
Positive Effects ◽  
Cattle Breeds ◽  
Number Variation

Copy number variation is a part of genomic structural variation and has caused widespread concern. According to the results of high-throughput screening of the MLLT10 gene, we found that the copy number variation region of the MLLT10 gene was correlated with bovine growth traits. We aimed to detect the MLLT10 gene copy number variation and provide materials for the Chinese yellow cattle breed. In this study, the SPSS software was used to analyze the correlation among the copy number type of six different cattle breeds (i.e., Qinchuan, Xianan, Jiaxian, Yanbian, Sinan, Yunling) and the corresponding growth traits. The results showed the following: In Qinchuan cattle, the copy number duplication type was greater than the deletion and normal types; in Xianan cattle, the copy number duplication and normal types were less as compared with the deletion type; and in Yunling cattle, the frequency of the duplication type was dominant among the three types of copy number variants. The correlation analysis result showed that there is a significant correlation between the copy number variation (CNV) of the MLLT10 gene and the growth traits of three cattle breeds. Furthermore, correlation analysis showed that MLLT10 CNV had positive effects on growth traits such as hip width, rump length, hucklebone width, and cannon bone circumference (p < 0.05). This study provides a basis for the molecular-assisted marker breeding of cattle and contributes to the breeding of cattle.

scholarly journals Phenotypic Association Analyses With Copy Number Variation in Recurrent Depressive Disorder

2016 ◽  
Vol 79 (4) ◽  
pp. 329-336 ◽  
Author(s):  
James J.H. Rucker ◽  
Katherine E. Tansey ◽  
Margarita Rivera ◽  
Dalila Pinto ◽  
Sarah Cohen-Woods ◽  
...  
Keyword(s):  
Depressive Disorder ◽  
Copy Number Variation ◽  
Copy Number ◽  
Association Analyses ◽  
Number Variation
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