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Marek's disease virus(MDV),the causative agent of Marek's disease(MD)inchickens,isanalpha-herpesvirus.MDVinfection can cause significant economic losses to the poultry industry.To develop more effective intervention strategies to prevent and control MDV infection in poultry,it is essential to elucidate molecular mechanisms of host response to MDV infection in chickens.MicroRNAs(miRNAs)are small non-coding regulatory RNAs that play key roles in many biological processes such as immune response.The objective of this study was to identify miRNAsand target genes and also pathways associated with resistance to MDV infection in twohighly inbred B-haplotype leghorn chicken lines(B21 haplotype,relatively resistant to MDV infection,and B19 haplotype,susceptible to MDV infection).One-day-old chickens were inoculated with 800pfu/300ul of Md5,and the bursa of Fabriciustissues were harvested at 5,11,20daypost inoculation(dpi.).Twelvesmall RNA cDNA libraries(3libraries each for infected and noninfectedB21 haplotype,and infected and noninfectedB19)were prepared from the bursa of Fabricius samples and sequenced by HiSeq 2000,which yielded over 142 millionhigh-quality clean reads.80% small RNAsof each librarywere mapped to chicken genomeby SOAP program.A custom data analysis pipeline identified 210-262 known chicken miRNAs and 63-204novel candidate miRNAsfrom each samples,respectively.60,54 and 103 miRNAs were differentially exprcssed between the two noninfectedchickenlines,and 35,94 and 53 miRNAs were differentially expressed between the two infected chicken lines at 5,11,and 20 dpi,respectively.38,108,143and 36,65,128 miRNAs were differentially expressedbetween infected and noninfectedin B21 and B19haplotypechicken lines at 5,11,and 20 dpi,respectively.Furthermore,globalbioinformatics analysis,expression and function validation workwill follow.GO and KEGG pathway analyses of the predicted miRNA targets will further illustrate the likely roles for these differentially expressed miRNAs in disease resistance to MDV infection in chickens.Further investigation of the roles of these miRNAs(including gga-miR-2954,-155,21,146b,etc.)and target genes and pathways in the regulation of host-MDV interaction can lead new directions for the development of antiviral drugs or vaccines in poultry.