Allele-specific expression in reciprocal crosses of Virginia Tech high-growth and low-growth selection lines

Allele-specific expression in reciprocal crosses of Virginia Tech high-growth and low-growth selection lines

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 considerable selection response. 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.

By performing 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. Using RNA samples extracted from liver, hypothalamus and pectoralis major, we generated circa 250 M (100 bp) RNA sequencing reads per F1 individual. This experimental design also allows us to detect allele-specific expression.

Initially, the sequencing reads were filtered following the GATK Best Practices workflow for RNAseq. The downstream pipeline included applying a Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes, followed by a generalized linear model for decomposing cis-regulatory, parent-of-origin, and maternal effects on allele-specific gene expression.