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

Authors: BAI, HAO - Yangzhou University; HE, YANGHUA - University Of Maryland; DING, YI - University Of Maryland; CHU, QIN - University Of Maryland; LIAN, LING - China Agricultural University; HEIFETZ, ELIYAHU - Jerusalem College Of Technology; YANG, NING - Institute Of Animal Science (CAAS); Cheng, Hans; Zhang, Huanmin; CHEN, JILAN - Chinese Academy Of Agricultural Sciences; SONG, JIUZHOU - University Of Maryland

Submitted to: BMC Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/5/2020
Publication Date: 7/16/2020
Citation: Bai, H., He, Y., Ding, Y., Chu, Q., Lian, L., Heifetz, E.M., Yang, N., Cheng, H.H., Zhang, H., Chen, J., Song, J. 2020. Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing. BMC Genetics. 21:77. https://doi.org/10.1186/s12863-020-00884-w.
DOI: https://doi.org/10.1186/s12863-020-00884-w

Interpretive Summary: Marek's disease (MD) can result in higher mortality in commercial chicken flocks and is currently controlled by widespread vaccination. However, Marek's disease virus (MDV) has repeatedly evolved to overcome vaccinal protection suggesting that additional MD control measures are needed, such as enhancing MD genetic resistance. In this study, the genomes of birds that MD resistant and MD susceptible were examined for structural variation. Over 90 regions were identified that included genes that likely account for some of the observed genetic differences. If validated in commercial lines, this should aid in the breeding of birds with superior MD resistance, which will result in more productive poultry farms and enhanced chicken welfare.

Technical Abstract: 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 quantitative real-time PCR (qPCR), all of which were successfully confirmed. Finally, qPCR 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.