Skeletal muscle transcriptional profiling of Canadian crossbred beef cattle divergent for feed efficiency traits

In beef cattle, skeletal muscle tissue represents a large
energy sink within the animal, accounting for over 60%
of the animal’s systemic metabolism. Therefore, identifying
the differentially expressed (DE) genes between
the muscle tissues of beef cattle with divergent feed
intake and growth rate would enhance our understanding
of the molecular mechanisms that regulate feed
efficiency in beef cattle. Using RNAseq analyses we
investigated transcriptome expression differences of Gluteus medias muscle tissues between crossbred steers
with divergent residual feed intake (RFI), daily dry
matter intake (DMI), or average daily gain (ADG). For
each of these traits, RNAseq data of six (n=6) Kinsella
Composite (KC) steers with extreme high and six (n=6)
with extreme low phenotypes were analyzed to identify
DE genes. On average, we obtained 26.4 million
reads per sample with an average quality score of 36,
and 97.5% were of the desired length (90-101bp) with
92% of the reads uniquely mapped to the bovine reference
genome (UMD3.1). At a false discovery rate <
0.05 and fold change > 2, we identified 271, 383, and
22 DE genes between RFI, ADG, and DMI divergent
steers, respectively. Of the identified DE genes,
17 (TFRC, AFF4, NBEAL1, PHIP, NFAT5, HSPA6,
FRAS1, HSPA1A, UHMK1, KMT2A, HOOK3,
KLHL24, SMG1, ZBED6, RPL12, ROCK2 and
ENSBTAG00000017233) were common among the
three traits, of which 16 DE genes except for RPL12
were downregulated in steers of low phenotypic values
for all the traits. The DE genes between the steers divergent
in RFI were primarily involved in gene expression
regulation, cellular development, cellular growth and
proliferation, cellular function and maintenance and
carbohydrate metabolism. Results from this study provide
insight into the molecular control of skeletal muscle
tissue contributing to divergence in feed efficiency
potential in beef cattle.