Transcriptional Analysis of Muscle from Cattle with Alternative NCAPG/LCORL QTL Genotypes

The NCAPG/LCORL locus is a major QTL on bovine chromosome 6 (BTA6) that influences growth and composition in cattle. Genetic variation at this locus is associated with alterations in the developmental program of individuals throughout life that may be detected through transcriptional and epigenetic variation. Here, we propose to characterize transcriptional and epigenetic differences between individuals with alternative NCAPG/LCORL haplotypes/genotypes. Charolais calves (n=804) were genotyped using the Illumina^® BovSNP50 BeadChip and their sires (n=38) were genotyped with the BovineHD BeadChip. Sire genotypes were used to impute the calf genotypes, resulting in approximately 638,230 markers per individual used for GWAS analyses. Twenty-four animals were selected based on alternative homozygous NCAPG/LCORL haplotypes/genotypes (i.e. 12 “QQ” and 12 “qq”, where “Q” is the QTL allele associated with increasing birth weight and “q” the alternative allele) and a muscle biopsy was taken from each animal at 300 days of age. 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 >30 million reads/sample) that were mapped to the bovine reference genome (Build UMD3.1). Future experiments include differential gene expression analyses, and, depending on the results, MethylCap-seq followed by bisulfite sequencing for the identification of differentially methylated regions. The characterization of molecular changes influencing phenotypic differences between individuals with alternative NCAPG/LCORL haplotypes/genotypes will allow us to better understand the regulation of growth and composition in cattle.