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Allele-Specific Expression, a New Genomics Tool for Development of Value-Added SNP chips and to Fine Map QTL

Thursday, August 21, 2014: 10:30 AM
Bayshore Grand Ballroom D (The Westin Bayshore)
William M. Muir , Purdue University, West Lafayette, IN
Sudeep Perumbakkam , Michigan State University, East Lansing, MI
Alexis Black-Pyrkosz , USDA, ARS, ADOL, East Lansing, MI
John R. Dunn , USDA, ARS, ADOL, East Lansing, MI
Hans H Cheng , USDA, ARS, ADOL, East Lansing, MI
Abstract Text:

A new tool emerging to fine map QTL is allele-specific expression (ASE). We used ASE to find specific genes and genetic markers conferring Marek's disease (MD) resistance in poultry. This resulted in 4,528 ASE SNPs putatively associated with MD genetic resistance. To estimate QTL effects, a 1,000 F6 MD resource population was analyzed using a mixed model analysis with SNPs and/or pedigree effects treated as random. In the F7 generation, roosters were genotyped, BLUP EBVs calculated, and selected roosters progeny tested for MD resistance. Based on the correlation of EBVs with progeny test performance, our results demonstrate the accuracy of selection was 61% higher for selection based on ASE SNPs compared to pedigree. We conclude ASE SNPs are functionally linked to causative polymorphisms that alter transcriptional levels in genes that manifest the changes in disease incidence.

Keywords:

allele-specific expression

Fine Mapping

Genomic Selection

SNP Chip

See more of: Symposium: Poultry Genomic Architecture and Genomic Selection
See more of: Species Breeding: Poultry
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