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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Avian Disease and Oncology Research » Research » Publications at this Location » Publication #323659

Research Project: GENETIC AND BIOLOGICAL DETERMINANTS OF AVIAN TUMOR VIRUS PATHOGENICITY, TRANSMISSION, AND EVOLUTION

Location: Avian Disease and Oncology Research

Title: Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek’s disease

Author
item YAN, YIYUAN - China Agriculture University
item YANG, NING - China Agricultural University
item Cheng, Hans
item SONG, JIIZHOU - University Of Maryland
item QU, LUJIANG - China Agricultural University

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/13/2015
Publication Date: 10/23/2015
Citation: Yan, Y., Yang, N., Cheng, H.H., Song, J., Qu, L. 2015. Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek’s disease. Biomed Central (BMC) Genomics. 16(843):1-10.

Interpretive Summary: Identifying genes conferring resistance to Marek’s disease (MD), a T cell lymphoma of chickens caused by the highly oncogenic Marek’s disease virus (MDV), is highly relevant for the poultry breeding industry. Using a genome-wide sequencing screen and two experimental chicken lines that differ greatly in genetic resistance to MD, we identified a number of candidate genes. The results provide the basis to look for similar genes in commercial lines, which may result in the selection of superior birds. If found to be valid, this information will yield healthier and more sustainable birds as well as safer and more economical poultry products.

Technical Abstract: Background: Copy number variation (CNV) is a major source of genome polymorphism that directly contributes to phenotypic variation such as resistance to infectious diseases. Lines 63 and 72 are two highly inbred experimental chicken lines that differ greatly in susceptibility to Marek’s disease (MD), and have been used extensively in efforts to identify the genetic and molecular basis for genetic resistance to MD. Using next generation sequencing, we present a genome-wide assessment of CNVs that are potentially associated with genetic resistance to MD. Methods: Three chickens randomly selected from each line were sequenced to an average depth of 20x. Two popular software, CNVnator and Pindel, were used to call genomic CNVs separately. The results were combined to obtain a union set of genomic CNVs in the two chicken lines. Results: A total of 5,680 CNV regions (CNVRs) were identified after merging the two datasets, of which 1,546 and 1,866 were specific to the MD resistant or susceptible line, respectively. Over half of the line-specific CNVRs were shared by 2 or more chickens, reflecting the reduced diversity in both inbred lines. The CNVRs fixed in the susceptible lines were significantly enriched in genes involved in MAPK signaling pathway. We also found 67 CNVRs overlapping with 62 genes previously shown to be strong candidates of the underlying genes responsible for the susceptibility to MD. Conclusions: Our findings provide new insights into the genetic architecture of the two chicken lines and additional evidence that MAPK signaling pathway may play an important role in host response to MD virus infection. The rich source of line-specific CNVs is valuable for future disease-related association studies in the two chicken lines.