Battle of the Sexes: Examining Gender Differences on the Trachea, Lung, and Harderian Gland Transcriptomes in Young Chickens

The transcriptome of three tissues (trachea, lung, and Harderian gland) were examined for local immune response after oculo-nasal challenge with a lentogenic Newcastle Disease Virus (NDV) in two inbred chicken lines. The transcriptomes of 48 males and females were compared for each tissue using RNA-seq. Multi-dimensional scaling plots showed a clear effect of sex on the lung and Harderian gland transcriptome, but not on the trachea transcriptome, suggesting a tissue dependent effect of sex on gene expression. The trachea and lung had the highest numbers of differentially expressed genes (DEG) (FDR<0.05) between males and females at 463 and 453 respectively, while the Harderian gland had 296. The average male to female log fold change (LFC) of the DEG on the Z chromosome was approximately 0.67 in all tissues, suggesting partial dosage compensation. Across the three tissues, 247 DEG were shared, of which 190 were located on the Z chromosome, 2 on the W chromosome, 1 on chromosome 28, and 54 genes were unidentified by Ensembl. The LFC of shared DEG was compared in three pair-wise t-tests, which showed that the LFC of shared DEG was significantly different between the Harderian gland and lung and the Harderian gland and trachea (p<0.0001, both tests), but there was no statistical difference between trachea and lung. Further analysis is needed to determine the effect of sex on the tissue-specific immune response to NDV. Support: USAID Feed the Future Innovation Lab for Genomics to Improve Poultry and Hatch project #5357.