Characterization of Copy Number Variation’s Potential Role in Marek’s Disease

Xu, Lingyang; He, Yanghua; Ding, Yi; Sun, Guirong; Carrillo, José A.; Li, Yaokun; Ghaly, Mona M.; Ma, Li; Zhang, Huanmin; Liu, George E.; Song, Jiuzhou

doi:10.3390/ijms18051020

Cited by 13 publications

(27 citation statements)

References 79 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, our study explored the genetic structure based on CNV in different inbred chicken lines. The PCA analysis showed clearly that the rst two PCs can divide all chickens into four unique groups, which is similar to the results of Xu et al [22]. Therefore, our study further con rms that CNV markers can be used to study the genetic variability in diverse chicken lines, which could possibly contribute to lineagespeci c phenotypes.…”

Section: Discussionsupporting

confidence: 89%

“…We eventually obtained 585 CNVRs in the present study for comparison. Our results were then compared to 12 previous reports on chicken genomic CNV ( [22] results that also involved in MD were validated in our study.…”

Section: Comparison With Other Studies On Cnv In Chickenssupporting

confidence: 61%

“…In the present study, we performed comparisons with the previous CNV studies, especially three researches also involved in MD. We found 247 CNVRs covering 93.9 Mb length overlapped with these three MD studies, where only 7 (1.2%) and 15 (2.6%) CNVRs shared with Luo et al's [20] and Xu et al's [22] results using SNP chip data, which may be, in part, related to limited sample sizes, different platforms, different analysis methods, and different chicken genome references (although we converted the genome positions from two previous genome assemblies (galGal2 and galGal3) to a newer one (galGal4) with the help of LiftOver based on UCSC, some information may still be missed). More importantly, we also used different chicken lines, especially the selected RCSs from a total of 19 RCSs (Figure 1).…”

Section: Discussionmentioning

confidence: 50%

“…Following the rst two genome-wide scans for CNVs in human genome [7,8], an large number of CNV detection studies have been performed, which revealed that CNVs are ubiquitously distributed in the genome and can in uence the phenotype via regulations of gene expression and gene dosage [9][10][11]. Besides, numerous studies in other species have also shown that CNVs contributed to phenotypic variation of complex diseases and traits [12][13][14][15][16][17][18][19], including MD in chicken [20][21][22]. Two major traditional platforms employed in CNV detection are based on SNP chips, one is known as comparative genomic hybridization (CGH) array, and the other is SNP genotyping array.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing

Bai

Ding

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Marek’s disease (MD) is a highly neoplastic disease primarily affecting chickens, and remains as a chronic infectious disease that threatens the poultry industry. Copy number variation (CNV) has been examined in many species and is recognized as a major source of genetic variation that directly contributes to phenotypic variation such as resistance to infectious diseases. Two highly inbred chicken lines 63 (MD-resistant) and 72 (MD-susceptible), as well as their F1 generation and six recombinant congenic strains (RCSs) with varied susceptibility to MD, are considered as ideal models to identify the complex mechanisms of genetic and molecular resistance to MD.Results: In the present study, to unravel the potential genetic mechanisms underlying resistance to MD, we performed a genome-wide CNV detection using next generation sequencing on the inbred chicken lines with the assistance of CNVnator. As a result, a total of 1,649 CNV regions (CNVRs) were successfully identified after merging all the nine datasets, of which 90 CNVRs were overlapped across all the chicken lines. Within these shared regions, 1,360 harbored genes were identified. In addition, 55 and 44 CNVRs with 62 and 57 harbored genes were specifically identified in line 63 and 72, respectively. Bioinformatics analysis showed that the nearby genes were significantly enriched in 36 GO terms and 6 KEGG pathways including JAK/STAT signaling pathway. Ten CNVRs (nine deletions and one duplication) involved in 10 disease-related genes were selected for validation by using qRT-PCR, all of which were successfully confirmed. Finally, qRT-PCR was also used to validate two deletion events in line 72 that were definitely normal in line 63. One high-confidence gene, IRF2 was identified as the most promising candidate gene underlying resistance and susceptibility to MD in view of its function and overlaps with data from previous study.Conclusions: Our findings provide valuable insights for understanding the genetic mechanism of resistance to MD and the identified gene and pathway could be considered as the subject of further functional characterization.

show abstract

Section: Discussionsupporting

confidence: 89%

Section: Comparison With Other Studies On Cnv In Chickenssupporting

confidence: 61%

Section: Discussionmentioning

confidence: 50%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing

Bai

Ding

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…; Xu et al . ). Two major platforms—comparative genomic hybridization (CGH) array and SNP genotyping arrays—are traditionally used for CNV detection.…”

Section: Introductionmentioning

confidence: 97%

Genome‐wide detection ofCNVs associated with beak deformity in chickens using high‐density 600KSNParrays

et al. 2018

View full text Add to dashboard Cite

Beak deformity (crossed beaks) is found in several indigenous chicken breeds including Beijing-You studied here. Birds with deformed beaks have reduced feed intake and poor production performance. Recently, copy number variation (CNV) has been examined in many species and is recognized as a source of genetic variation, especially for disease phenotypes. In this study, to unravel the genetic mechanisms underlying beak deformity, we performed genome-wide CNV detection using Affymetrix chicken high-density 600K data on 48 deformed-beak and 48 normal birds using penncnv. As a result, two and eight CNV regions (CNVRs) covering 0.32 and 2.45 Mb respectively on autosomes were identified in deformed-beak and normal birds respectively. Further RT-qPCR studies validated nine of the 10 CNVRs. The ratios of six CNVRs were significantly different between deformed-beak and normal birds (P < 0.01). Within these six regions, three and 21 known genes were identified in deformed-beak and normal birds respectively. Bioinformatics analysis showed that these genes were enriched in six GO terms and one KEGG pathway. Five candidate genes in the CNVRs were further validated using RT-qPCR. The expression of LRIG2 (leucine rich repeats and immunoglobulin like domains 2) was lower in birds with deformed beaks (P < 0.01). Therefore, the LRIG2 gene could be considered a key factor in view of its known functions and its potential roles in beak deformity. Overall, our results will be helpful for future investigations of the genomic structural variations underlying beak deformity in chickens.

show abstract

circRUNX2.2, highly expressed in Marek's disease tumor tissues, functions in cis to regulate parental gene RUNX2 expression

Wang,

Zheng,

Yuan

et al. 2024

Poultry Science

View full text Add to dashboard Cite

Characterization of Copy Number Variation’s Potential Role in Marek’s Disease

Cited by 13 publications

References 79 publications

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing

Genome‐wide detection ofCNVs associated with beak deformity in chickens using high‐density 600KSNParrays

circRUNX2.2, highly expressed in Marek's disease tumor tissues, functions in cis to regulate parental gene RUNX2 expression

Contact Info

Product

Resources

About