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

Lopes Pinto, Fernando A; Molin, Anna-Maja; Gilbert, Elisabeth R.; Honaker, Christa F.; Siegel, Paul B.; Andersson, Göran; Andersson, Leif; De Koning, Dirk-Jan


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 (cisacting 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.

Published in

Title: Proceedings of the 10th World Congress of Genetics Applied to Livestock Production.
Publisher: WCGALP