Abstract
BackgroundCopy 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.MethodsThree chickens randomly selected from each line were sequenced to an average depth of 20×. 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. ResultsA 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2080-5) contains supplementary material, which is available to authorized users.
Highlights
Copy number variation (CNV) is a major source of genome polymorphism that directly contributes to phenotypic variation such as resistance to infectious diseases
After combing the two datasets together, a collective set consisting of 5,680 Copy number variation region (CNVR) were obtained, which are distributed over all chromosomes and two linkage groups (LGE22C19W28_E50C23 and LGE64) (Additional file 1: Table S1)
The CNVRs belonging to loss, gain, or both account for 90.4 %, 7.6 % and 2.0 %, respectively
Summary
Copy number variation (CNV) is a major source of genome polymorphism that directly contributes to phenotypic variation such as resistance to infectious diseases. Improving genetic resistance to MD of chickens is a desirable and sustainable long-term MD control measure. To achieve this objective, studies have been carried out to uncover the genetic variants underlying resistance to MD. Genome-wide QTL scans have identified a number of genomic regions associated with the resistance to MD [4,5,6,7]. The resolution limits of these strategies make it difficult to identify the underlying causative genes, and the variants only explain a small proportion of total genetic variation [9], leaving a large part of variation unexplained [10]. Cheng et al [11] found that SNPs in allele-specific expression (ASE) genes captures
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