Whole Transcriptome Sequencing in Reciprocal Crosses Suggests Parent-of-Origin Effects on Gene Expression in the Chicken Genome

de Koning, Dirk-Jan

316
Whole Transcriptome Sequencing in Reciprocal Crosses Suggests Parent-of-Origin Effects on Gene Expression in the Chicken Genome

Monday, August 18, 2014: 11:30 AM

Bayshore Grand Ballroom D (The Westin Bayshore)

Fernando Lopes Pinto , Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden

Anna-Maja Molin , Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden

Elizabeth R. Gilbert , Virginia Polytechnic Institute and State University, Blacksburg, VA

Christa Honaker , Virginia Polytechnic Institute and State University, Blacksburg, VA

Paul B. Siegel , Virginia Polytechnic Institute and State University, Blacksburg, VA

Göran Andersson , Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden

Leif Andersson , Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

Dirk-Jan de Koning , Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden

Recorded Presentation (flv)

Abstract Text: The Virginia Tech body weight lines have undergone more than 50 generations of divergent selection for 56-day body weight. In this experiment we test for the preferential expression of alleles from certain lines (cis-acting effects) or parents (parent-of-origin effects) in six F1 individuals from reciprocal crosses of generation 54 parents. Using RNA samples extracted from liver, hypothalamus and breast muscle (Pectoralis major), we generated circa 250 million RNA sequencing reads per F1 individual as well as a 25-fold coverage DNA sequence of each of the parents. We identified 11338 line-specific SNPs in the RNA across the three tissues. Allelic imbalance was biased for the SNP allele corresponding to the reference genome with ~65% of the SNPs showing a significant imbalance at P < 0.05. The number of SNPs with parent-of-origin effects without allelic imbalance was between 500 and 650 for each tissue.

Keywords:

Chicken

Transcriptome

Parent-of-origin effect

10th World Congress on Genetics Applied to Livestock Production

August 17 - 22, 2014

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316
Whole Transcriptome Sequencing in Reciprocal Crosses Suggests Parent-of-Origin Effects on Gene Expression in the Chicken Genome

316 Whole Transcriptome Sequencing in Reciprocal Crosses Suggests Parent-of-Origin Effects on Gene Expression in the Chicken Genome

316
Whole Transcriptome Sequencing in Reciprocal Crosses Suggests Parent-of-Origin Effects on Gene Expression in the Chicken Genome