GSE98736
TRANSCRIPTIONAL ANALYSIS OF MUSCLE FROM CATTLE WITH ALTERNATIVE NCAPG/LCORL GENOTYPES
The LCORL-NCAPG locus is a major quantitative trait locus (QTL) on bovine chromosome 6 (BTA6) that influences growth and carcass composition in cattle. To further understand the molecular mechanism responsible for the changes associated with this locus, twenty-four Charolais-sired calves were selected for muscle transcriptome analysis based on alternative homozygous LCORL-NCAPG haplotypes (i.e., 12 "QQ" and 12 "qq", where "Q" is a haplotype harboring variation associated with increased growth). At 300 days of age, a biopsy of the longissimus dorsi muscle was collected from each animal for RNA sequencing. Total RNA was isolated and used for NGS library construction and libraries were sequenced on a HiSeq2500 using single-end chemistry. Sequencing yielded 898 million reads (average of >37 million reads/sample) that were mapped to the bovine reference genome (ARS-UCD 2.0). Gene expression analysis identified 733 genes as differentially expressed between QQ and qq animals (q-value < 0.05). Notably, LCORL and genes known to be important regulators of growth such as IGF2 were upregulated in QQ individuals, while genes associated with adiposity such as FASN and LEP were downregulated, reflecting the increase in lean growth associated with this locus. Gene set enrichment analysis revealed an overall trend of downregulation of pathways associated with adipogenesis, and upregulation of ribosomal and mitochondrial-related transcripts in QQ individuals, molecular differences which imply increased muscle hypertrophy instead of accumulation of fat in animals with this haplotype. These findings suggest this haplotype could be linked to a difference in LCORL expression that potentially leads to the downstream transcriptional effects observed, though further research will be needed to confirm the molecular mechanisms underlying the associated changes in phenotype. Overall design: Use of RNA-Seq for the examination of differential gene expression profiles between muscle samples from cattle with alternative genotypes for the NCAPG/LCORL QTL. UPDATE: [08-30-2024] The processed data and data processing description were updated.