scholarly journals Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yibin Qiu ◽  
Rongrong Ding ◽  
Zhanwei Zhuang ◽  
Jie Wu ◽  
Ming Yang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Complex Traits ◽  
Copy Number ◽  
Association Studies ◽  
Average Daily Gain ◽  
Genome Wide Association Studies ◽  
Potential Candidate ◽  
Genome Wide ◽  
Number Variation ◽  
Genetic Mechanisms

Abstract Background In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not well understood. Copy number variation (CNV), an important source of genetic diversity, can affect a variety of complex traits and diseases and has gradually been thrust into the limelight. In this study, we reported the genome-wide CNVs of Duroc pigs using SNP genotyping data from 6627 animals. We also performed a copy number variation region (CNVR)-based genome-wide association studies (GWAS) for growth and fatness traits in two Duroc populations. Results Our study identified 953 nonredundant CNVRs in U.S. and Canadian Duroc pigs, covering 246.89 Mb (~ 10.90%) of the pig autosomal genome. Of these, 802 CNVRs were in U.S. Duroc pigs with 499 CNVRs were in Canadian Duroc pigs, indicating 348 CNVRs were shared by the two populations. Experimentally, 77.8% of nine randomly selected CNVRs were validated through quantitative PCR (qPCR). We also identified 35 CNVRs with significant association with growth and fatness traits using CNVR-based GWAS. Ten of these CNVRs were associated with both ADG and AGE traits in U.S. Duroc pigs. Notably, four CNVRs showed significant associations with ADG, AGE, and BFT, indicating that these CNVRs may play a pleiotropic role in regulating pig growth and fat deposition. In Canadian Duroc pigs, nine CNVRs were significantly associated with both ADG and AGE traits. Further bioinformatic analysis identified a subset of potential candidate genes, including PDGFA, GPER1, PNPLA2 and BSCL2. Conclusions The present study provides a necessary supplement to the CNV map of the Duroc genome through large-scale population genotyping. In addition, the CNVR-based GWAS results provide a meaningful way to elucidate the genetic mechanisms underlying complex traits. The identified CNVRs can be used as molecular markers for genetic improvement in the molecular-guided breeding of modern commercial pigs.

scholarly journals Current analysis platforms and methods for detecting copy number variation

2013 ◽  
Vol 45 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Wenli Li ◽  
Michael Olivier
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Genomic Structural Variation ◽  
Disease Phenotypes ◽  
Human Genomes ◽  
Genome Wide ◽  
Number Variation ◽  
Genomic Regions

Copy number variation (CNV), generated through duplication or deletion events that affect one or more loci, is widespread in the human genomes and is often associated with functional consequences that may include changes in gene expression levels or fusion of genes. Genome-wide association studies indicate that some disease phenotypes and physiological pathways might be impacted by CNV in a small number of characterized genomic regions. However, the pervasiveness and full impact of such variation remains unclear. Suitable analytic methods are needed to thoroughly mine human genomes for genomic structural variation, and to explore the interplay between observed CNV and disease phenotypes, but many medical researchers are unfamiliar with the features and nuances of recently developed technologies for detecting CNV. In this article, we evaluate a suite of commonly used and recently developed approaches to uncovering genome-wide CNVs and discuss the relative merits of each.

scholarly journals Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs

2020 ◽  
Author(s):  
Yibin Qiu ◽  
Rongrong Ding ◽  
Zhanwei Zhuang ◽  
Jie Wu ◽  
Ming Yang ◽  
...  
Keyword(s):  
Association Analysis ◽  
Complex Traits ◽  
Large Scale ◽  
Average Daily Gain ◽  
Potential Candidate ◽  
Genome Wide ◽  
Potential Association ◽  
Scale Population ◽  
Number Variation ◽  
Genetic Mechanisms

Abstract Background: In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not well understood. As an essential source of genetic diversity, copy number variation (CNV) that can affect a variety of complex traits and diseases, has gradually been thrust into the limelight. In this study, we reported the genome-wide CNVs of Duroc pigs by SNP genotyping data of 6,627 Duroc pigs. Moreover, we also performed CNV region (CNVR) based association analysis for growth and fatness traits in two Duroc populations.Results: Our study identified a total of 835 nonredundant CNVRs in American and Canadian Duroc pigs, which covered 226.73 Mb (~ 10.00%) of the pig autosomal genome. Among them, we identified 682 CNVRs in the American Duroc pigs and 424 CNVRs in the Canadian Duroc pigs, and 271 CNVRs were detected in both populations. Experimentally, 77.8% of randomly selected CNVRs were validated by quantitative PCR (qPCR). We also identified 24 significant CNVRs for growth and fatness traits though CNVR-based association analysis. Among these, six and three CNVRs in American and Canadian Duroc pigs were found to be associated with both ADG and AGE traits, respectively. Notably, four CNVRs showed both significant in ADG, AGE, and BFT, indicating that these CNVRs may play a pleiotropic role in regulating pig growth and fat deposition. Besides, further bioinformatics analysis determined a subset of potential candidate genes, such as PDGFRB, INSIG1, GPER1, PDGFA, and LPCAT1.Conclusions: The present study provides a necessary supplement to the CNV map of the Duroc genome through a large-scale population genotyping. Also, the CNVR-based association results provide a meaningful way to elucidate the genetic mechanisms of complex traits. The identified CNVRs can be used as molecular markers for genetic improvement in molecular-guided breeding of modern commercial pigs

scholarly journals Copy Number Variation Accuracy in Genome-Wide Association Studies

2011 ◽  
Vol 71 (3) ◽  
pp. 141-147 ◽  
Author(s):  
Peng Lin ◽  
Sarah M. Hartz ◽  
Jen-Chyong Wang ◽  
Robert F. Krueger ◽  
Tatiana M. Foroud ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Number Variation

scholarly journals CONAN: copy number variation analysis software for genome-wide association studies

2010 ◽  
Vol 11 (1) ◽  
pp. 318 ◽  
Author(s):  
Lukas Forer ◽  
Sebastian Schönherr ◽  
Hansi Weissensteiner ◽  
Florian Haider ◽  
Thomas Kluckner ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Variation Analysis ◽  
Analysis Software ◽  
Copy Number Variation Analysis ◽  
Genome Wide ◽  
Number Variation

scholarly journals Transcriptome association studies of neuropsychiatric traits in African Americans implicate PRMT7 in schizophrenia

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7778 ◽  
Author(s):  
Peter N. Fiorica ◽  
Heather E. Wheeler
Keyword(s):  
Bipolar Disorder ◽  
African Americans ◽  
Complex Traits ◽  
Multiple Testing ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Potential Candidate ◽  
Candidate Locus ◽  
Genome Wide ◽  
Multiple Testing Adjustment

In the past 15 years, genome-wide association studies (GWAS) have provided novel insight into the genetic architecture of various complex traits; however, this insight has been primarily focused on populations of European descent. This emphasis on European populations has led to individuals of recent African descent being grossly underrepresented in the study of genetics. With African Americans making up less than 2% of participants in neuropsychiatric GWAS, this discrepancy is magnified in diseases such as schizophrenia and bipolar disorder. In this study, we performed GWAS and the gene-based association method PrediXcan for schizophrenia (n = 2,256) and bipolar disorder (n = 1,019) in African American cohorts. In our PrediXcan analyses, we identified PRMT7 (P = 5.5 × 10−6, local false sign rate = 0.12) as significantly associated with schizophrenia following an adaptive shrinkage multiple testing adjustment. This association with schizophrenia was confirmed in the much larger, predominantly European, Psychiatric Genomics Consortium. In addition to the PRMT7 association with schizophrenia, we identified rs10168049 (P = 1.0 × 10−6) as a potential candidate locus for bipolar disorder with highly divergent allele frequencies across populations, highlighting the need for diversity in genetic studies.

scholarly journals The genetics of neuropsychiatric disorders

2018 ◽  
Vol 2 ◽  
pp. 239821281879927 ◽  
Author(s):  
Nicholas J. Bray ◽  
Michael C. O’Donovan
Keyword(s):  
Copy Number ◽  
Genetic Architecture ◽  
Recent Progress ◽  
Association Studies ◽  
Neuropsychiatric Disorders ◽  
Review Article ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Number Variation

Neuropsychiatric disorders are complex conditions with poorly defined neurobiological bases. In recent years, there have been significant advances in our understanding of the genetic architecture of these conditions and the genetic loci involved. This review article describes historical attempts to identify susceptibility genes for neuropsychiatric disorders, recent progress through genome-wide association studies, copy number variation analyses and exome sequencing, and how these insights can inform the neuroscientific investigation of these conditions.

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