ARS | Publication request: Chicks and SNPs--an entree into identifying genes conferring disease resistance in chicken

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: May 2, 2011
Publication Date: May 2, 2011
Citation: Cheng, H.H., MacEachern, S., Subramaniam, S., Muir, W.M. 2011. Chicks and SNPs--an entree into identifying genes conferring disease resistance in chicken [abstract]. Applied Genomics for Sustainable Livestock Breeding Conference Handbook, May 2-5, 2011, Melbourne, Australia. p. 3.

Technical Abstract: With high-density chicken rearing, control of infectious diseases are critical for economic viability and maintaining public confidence in poultry products. Among poultry diseases, Marek’s disease (MD), a lymphoproliferative disease caused by the highly oncogenic herpesvirus Marek's disease virus (MDV), continues to be a major concern. The fear of MD is further enhanced by unpredictable vaccine breaks that result in devastating losses. The field of genomics offers one of the more exciting avenues for enhancing control of MD. By identifying genes that confer genetic resistance, it should become possible to select for birds with superior disease resistance. Genetic resistance to MD is a complex trait controlled by many genes. Most genome-wide efforts for complex traits rely on linkage between the causative gene and a genetic marker, which results in limited detection power and resolution of gene location. An alternate method is to screen for allele-specific expression (ASE), a simple yet powerful approach, where the expression of each gene allele is compared within an RNA sample. When the expression of the alleles is not equal, then one can unequivocally declare ASE and the presence of a polymorphic cis-acting (genetic) element for that gene as linkage disequilibrium (LD) is confined to the transcriptional unit. The only requirements for ASE to work are: (1) the assumption that variation in expression between alleles of a gene are responsible for part of the phenotypic variation, and (2) the existence of a cSNP to monitor the alleles. Response to MDV inflection in chickens was evaluated using next generation sequencing on a limited number of samples to query for ASE followed by Illumina GoldenGate assays to validate and expand the number of samples. Our results clearly demonstrate that ASE is an efficient method to identify potentially most or all of the genes for this complex trait. The identified cSNPs can be further evaluated in resource populations to determine their size of effect on genetic resistance to MD as well as be directly implemented in genomic selection programs.