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.

Association analysis of KMT2D copy number variation as a positional candidate for growth traits

Gene ◽  
2020 ◽  
Vol 753 ◽  
pp. 144799
Author(s):  
Jie Cheng ◽  
Rui Jiang ◽  
Yu Yang ◽  
Xiukai Cao ◽  
Yongzhen Huang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Association Analysis ◽  
Copy Number ◽  
Growth Traits ◽  
Positional Candidate ◽  
Number Variation

Effect of copy number variation of PLA2G2A gene to growth traits in Chinese cattle

Gene ◽  
2021 ◽  
pp. 146014
Author(s):  
Peng Yang ◽  
Cuicui Cai ◽  
Mengxiao Niu ◽  
Xian Liu ◽  
Hongli Wang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Chinese Cattle ◽  
Number Variation

scholarly journals Structural genome analysis in cultivated potato taxa

2019 ◽  
Vol 133 (3) ◽  
pp. 951-966 ◽  
Author(s):  
Maria Kyriakidou ◽  
Sai Reddy Achakkagari ◽  
José Héctor Gálvez López ◽  
Xinyi Zhu ◽  
Chen Yu Tang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Agronomic Traits ◽  
Genomic Variation ◽  
Sequencing Data ◽  
Structural Variations ◽  
Structural Genomic ◽  
Ploidy Levels ◽  
Cultivated Potato ◽  
Number Variation

Abstract Key message Twelve potato accessions were selected to represent two principal views on potato taxonomy. The genomes were sequenced and analyzed for structural variation (copy number variation) against three published potato genomes. Abstract The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X–5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.

Novel copy number variation of the KLF3 gene is associated with growth traits in beef cattle

Gene ◽  
2019 ◽  
Vol 680 ◽  
pp. 99-104 ◽  
Author(s):  
Jia-Wei Xu ◽  
Li Zheng ◽  
Li-Juan Li ◽  
Yu-fei Yao ◽  
He Hua ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Number Variation

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 Population genetics of immune-related multilocus copy number variation in Native Americans

2017 ◽  
Vol 14 (128) ◽  
pp. 20170057 ◽  
Author(s):  
Luciana W. Zuccherato ◽  
Silvana Schneider ◽  
Eduardo Tarazona-Santos ◽  
Robert J. Hardwick ◽  
Douglas E. Berg ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Native American ◽  
Native Americans ◽  
Copy Number Variation ◽  
Copy Number ◽  
Genomic Variation ◽  
Population Subdivision ◽  
Nucleotide Polymorphisms ◽  
Number Variation

While multiallelic copy number variation (mCNV) loci are a major component of genomic variation, quantifying the individual copy number of a locus and defining genotypes is challenging. Few methods exist to study how mCNV genetic diversity is apportioned within and between populations (i.e. to define the population genetic structure of mCNV). These inferences are critical in populations with a small effective size, such as Amerindians, that may not fit the Hardy–Weinberg model due to inbreeding, assortative mating, population subdivision, natural selection or a combination of these evolutionary factors. We propose a likelihood-based method that simultaneously infers mCNV allele frequencies and the population structure parameter f , which quantifies the departure of homozygosity from the Hardy–Weinberg expectation. This method is implemented in the freely available software CNVice, which also infers individual genotypes using information from both the population and from trios, if available. We studied the population genetics of five immune-related mCNV loci associated with complex diseases (beta-defensins, CCL3L1/CCL4L1 , FCGR3A , FCGR3B and FCGR2C ) in 12 traditional Native American populations and found that the population structure parameters inferred for these mCNVs are comparable to but lower than those for single nucleotide polymorphisms studied in the same populations.

The clinical context of copy number variation in the human genome

2010 ◽  
Vol 12 ◽  
Author(s):  
Charles Lee ◽  
Stephen W. Scherer
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Clinical Diagnostics ◽  
Genomic Variation ◽  
Single Nucleotide ◽  
Genomic Changes ◽  
Creative Solutions ◽  
Number Variation ◽  
The Relationship ◽  
Prevalent Form

During the past five years, copy number variation (CNV) has emerged as a highly prevalent form of genomic variation, bridging the interval between long-recognised microscopic chromosomal alterations and single-nucleotide changes. These genomic segmental differences among humans reflect the dynamic nature of genomes, and account for both normal variations among us and variations that predispose to conditions of medical consequence. Here, we place CNVs into their historical and medical contexts, focusing on how these variations can be recognised, documented, characterised and interpreted in clinical diagnostics. We also discuss how they can cause disease or influence adaptation to an environment. Various clinical exemplars are drawn out to illustrate salient characteristics and residual enigmas of CNVs, particularly the complexity of the data and information associated with CNVs relative to that of single-nucleotide variation. The potential is immense for CNVs to explain and predict disorders and traits that have long resisted understanding. However, creative solutions are needed to manage the sudden and overwhelming burden of expectation for laboratories and clinicians to assay and interpret these complex genomic variations as awareness permeates medical practice. Challenges remain for understanding the relationship between genomic changes and the phenotypes that might be predicted and prevented by such knowledge.

Novel copy number variation of the BAG4 gene is associated with growth traits in three Chinese sheep populations

2020 ◽  
pp. 1-9 ◽  
Author(s):  
Zhaoxin Yang ◽  
Xiukai Cao ◽  
Yilei Ma ◽  
Jie Cheng ◽  
Chengchuang Song ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Number Variation

Copy number variation of MYLK4 gene and its growth traits of Capra hircus (goat)

2019 ◽  
Vol 31 (6) ◽  
pp. 532-537 ◽  
Author(s):  
Shu-Yue Shi ◽  
Li-Juan Li ◽  
Zi-Jing Zhang ◽  
Er-Yao Wang ◽  
Jian Wang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Capra Hircus ◽  
Number Variation

scholarly journals Acquired variation outweighs inherited variation in whole genome analysis of methotrexate polyglutamate accumulation in leukemia

Blood ◽  
2009 ◽  
Vol 113 (19) ◽  
pp. 4512-4520 ◽  
Author(s):  
Deborah French ◽  
Wenjian Yang ◽  
Cheng Cheng ◽  
Susana C. Raimondi ◽  
Charles G. Mullighan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Copy Number Variation ◽  
Cell Lines ◽  
Copy Number ◽  
Genomic Variation ◽  
Leukemia Cells ◽  
Whole Genome ◽  
Chromosome 18 ◽  
Number Variation

Abstract Methotrexate polyglutamates (MTXPGs) determine in vivo efficacy in acute lymphoblastic leukemia (ALL). MTXPG accumulation differs by leukemic subtypes, but genomic determinants of MTXPG variation in ALL remain unclear. We analyzed 3 types of whole genome variation: leukemia cell gene expression and somatic copy number variation, and inherited single nucleotide polymorphism (SNP) genotypes and determined their association with MTXPGs in leukemia cells. Seven genes (FHOD3, IMPA2, ME2, RASSF4, SLC39A6, SMAD2, and SMAD4) displayed all 3 types of genomic variation associated with MTXPGs (P < .05 for gene expression, P < .01 for copy number variation and SNPs): 6 on chromosome 18 and 1 on chromosome 10. Increased chromosome 18 (P = .002) or 10 (P = .036) copy number was associated with MTXPGs even after adjusting for ALL subtype. The expression of the top 7 genes in leukemia cells accounted for more variation in MTXPGs (46%) than did the expression of the top 7 genes in normal HapMap cell lines (20%). The top 7 inherited SNPs in patients accounted for approximately the same degree of variation (17%) in MTXPGs as did the top 7 SNP genotypes in HapMap cell lines (20%). We conclude that acquired genetic variation in leukemia cells has a stronger influence on MTXPG accumulation than inherited genetic variation.

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