Chicks and single-nucleotide polymorphisms: an entrée into identifying genes conferring disease resistance in chicken
Hans H. Cheng A B E , Sean MacEachern C , Sugalesini Subramaniam B and William M. Muir D
+ Author Affiliations
- Author Affiliations
A USDA, ARS, Avian Disease and Oncology Laboratory, 3606 East Mount Hope Road, East Lansing, MI 48823, USA.
B Comparative Medicine and Integrative Biology Graduate Program, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA.
C Cobb-Vantress Inc., PO Box 1030, 4703 US Highway 412 East, Siloam Springs, AR 72761, USA.
D Department of Animal Sciences, 1151 Lilly Hall, Purdue University, West Lafayette, IN 47907, USA.
E Corresponding author. Email: hans.cheng@ars.usda.gov
Animal Production Science 52(3) 151-156 https://doi.org/10.1071/AN11099
Submitted: 3 June 2011 Accepted: 12 January 2012 Published: 13 February 2012
Journal Compilation © CSIRO Publishing 2012 Open Access CC BY-NC-ND
Abstract
Marek’s disease (MD) is one of the most serious chronic infectious disease threats to the poultry industry worldwide. Selecting for increased genetic resistance to MD is a control strategy that can augment current vaccinal control measures. Although our previous efforts integrating various genomic screens successfully identified three resistance genes, the main limitation was mapping precision, which hindered our ability to identify and further evaluate high-confidence candidate genes. Towards identifying the remaining genes of this complex trait, we incorporated three additional approaches made substantially more powerful through next-generation sequencing and that exploit the growing importance of expression variation. First, we screened for allele-specific expression (ASE) in response to Marek’s disease virus (MDV) infection, which, when allelic imbalance was identified, is sufficient to indicate a cis-acting element for a specific gene. Second, sequencing of genomic regions enriched by chromatin immunoprecipitation (ChIP) combined with transcript profiling identified motifs bound and genes directly regulated by MDV Meq, a bZIP transcription factor and the viral oncogene. Finally, analysis of genomic sequences from two experimental lines divergently selected for MD genetic resistance allowed inference about regions under selection as well as potential causative polymorphisms. These new combined approaches have resulted in a large number of high-confidence genes conferring MD resistance reflecting the multigenic basis of this trait, which expands our biological knowledge and provides corresponding single-nucleotide polymorhpisms (SNPs) that can be directly evaluated for their genetic contribution towards disease resistance.
Additional keywords: gene expression, genetic resistance, Marek’s disease, next-generation sequencing, poultry.
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