Skip to main content
SLU publication database (SLUpub)

Other publication2014Peer reviewed

All Transcriptome Sequencing of Reciprocal Chicken Crosses to Explore Monoallelic Expression

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


The Virginia Tech high-growth and low-growth selection lines of White Plymouth Rock chickens have been developed by more than 50 generations of divergent selection for body weight at 56 days of age. These lines have been extensively used for QTL mapping in order to reveal the genetic basis for the huge selection response. In order to further clarify the mechanisms for how QTLs control phenotypic differences, we measured allelic RNA expression ratios to detect differential expression between alleles derived from the two lines. Using whole transcriptome sequencing, we set out to detect allelic imbalance in the RNA expression of 6 F1 progeny from reciprocal crosses between S54 parents from the high and low parental lines. The detection of allelic imbalance provides evidence for cis-acting regulatory QTLs. This experimental design also allows us to detect parent-of-origin specific differential expression. Using RNA samples extracted from liver, hypothalamus and pectoralis major, we generated circa 250 M (100 bp) RNA sequencing reads per F1 individual. The latter allows us to predict and test obligatory heterozygous loci in the F1 birds. The coverage exceeds the sequencing depth shown necessary to allow for the reliable measurement of mRNA expression across all genes in the chicken genome. The liver showed the strongest reciprocal difference in F1 birds with more than 700 differentially expressed genes. A dedicated bioinformatics pipeline was developed to identify allelic imbalance among F1 birds and the results from this analysis will be presented during the meeting.

Published in

Title: Plant and Animal Genome XXII Conference
Publisher: .