The inclusion of some agro-industrial by-products in animals’
diet is becoming attractive not only for being part of an ambitious
waste management and sustainability policies but also
due to its possible nutritive values. The aim of this study was
to evaluate the effect of grape pomace (GP) - the polyphenolrich
by-product of the wine industry – on the transcriptome
of dairy cows. Twelve lactating Holstein Friesian cows, homogeneous
for age and lactation period, were assigned to two
groups of six animals each - in a randomized pretest-posttest
control group design. The first group received a basal diet
and served as a control (CTR), while the other received a
10% GP-supplemented diet for 67 days. Whole blood was collected
from each group at 2 time-points [beginning (T0), and
after 67 days of the GP supplementation (Tf)], then
total RNA was isolated, quality-controlled, and then used for
library preparation. The sequencing of twenty-four samples (2
groups6 animals/group2 time-points) resulted in an
average of 17 million reads per sample. The 50bp single-end
reads were quality-controlled, mapped to the Bos taurus reference
genome (UMD 3.1 assembly), then tested for the presence
of differentially expressed genes (DEGs) in the same
group (CTR or GP) after (compared with before) 67-days-supplementation
period (Tf vs T0). On average, 95.6% of the
reads were mapped to the reference genome. Reads mapped
to exons were counted with HTSeq-count, then analysed by
the DESeq2 R package. The bioinformatics analysis evidenced
a significant (adjusted p<.1) change in expression of 14 and
88 genes in the CTR and GP groups, respectively. Four genes
were found to be overlapping between the two groups, thus
they were excluded from the GP group results as being
‘temporally’- and not experimentally-affected DEGs. Of the
remaining 84 GP-affected genes, 73 were down-regulated,
with most of them being ‘ribosomal protein’-coding genes.
The functional analysis evidenced the positive enrichment of
‘defence response to other organism’ (p¼.0002) biological
process and the ‘interleukin signalling’ pathway (p¼.0002),
as well a negative enrichment of the ‘ribosome’ pathway (35
genes, p¼5x1055). Overall, the transcriptomic signature of
GP-supplemented diet reflects an induced immune system
and a suppressed ‘ribosome biogenesis’, which can b