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Background  Marek’s disease (MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. However, the mechanisms of genetic resistance for MD are complex and not fully understood. MD-resistant line 6 3  and MD-susceptible line 7 2  are two highly inbred progenitor lines of White Leghorn. Recombinant Congenic Strains (RCS) were developed from these two lines, which show varied susceptibility to MD.    Results  We investigated genetic structure and genomic signatures across the genome, including the line 6 3  and line 7 2 , six RCSs, and two reciprocally crossed flocks between the lines 6 3  and 7 2  (F1 6 3  × 7 2  and F1 7 2  × 6 3 ) using Affymetrix® Axiom® HD 600 K genotyping array. We observed 18 chickens from RCS lines were specifically clustered into resistance sub-groups distributed around line 6 3 . Additionally, homozygosity analysis was employed to explore potential genetic components related to MD resistance, while runs of homozygosity (ROH) are regions of the genome where the identical haplotypes are inherited from each parent. We found several genes including  SIK, SOX1, LIG4, SIK1  and  TNFSF13B  were contained in ROH region identified in resistant group (line 6 3  and RCS), and these genes have been reported that are contribute to immunology and survival. Based on  F  ST  based population differential analysis, we also identified important genes related to cell death and anti-apoptosis, including  AKT1 ,  API5 ,  CDH13 ,  CFDP  and  USP15 , which could be involved in divergent selection during inbreeding process.    Conclusions  Our findings offer valuable insights for understanding the genetic mechanism of resistance to MD and the identified genes could be considered as candidate biomarkers in further evaluation.    Electronic supplementary material  The online version of this article (10.1186/s40104-018-0281-x) contains supplementary material, which is available to authorized users.

Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marek’s disease