Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits.
BACKGROUND
Genome wide association studies (GWAS) on residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) were conducted in a population of 7573 animals from multiple beef cattle breeds based on 7,853,211 imputed whole genome sequence variants. The GWAS results were used to elucidate genetic architectures of the feed efficiency related traits in beef cattle.


RESULTS
The DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants followed a scaled inverse chi-squared distribution to a greater extent. With a threshold of P-value < 1.00E-05, 16, 72, 88, and 116 lead DNA variants on multiple chromosomes were significantly associated with RFI, DMI, ADG, and MWT, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on DMI, ADG, and MWT were found on chromosomes 6, 14 and 20. On average, missense, 3'UTR, 5'UTR, and other regulatory region variants exhibited larger allele substitution effects in comparison to other functional classes. Intergenic and intron variants captured smaller proportions of additive genetic variance per DNA variant. Instead 3'UTR and synonymous variants explained a greater amount of genetic variance per DNA variant for all the traits examined while missense, 5'UTR and other regulatory region variants accounted for relatively more additive genetic variance per sequence variant for RFI and ADG, respectively. In total, 25 to 27 enriched cellular and molecular functions were identified with lipid metabolism and carbohydrate metabolism being the most significant for the feed efficiency traits.


CONCLUSIONS
RFI is controlled by many DNA variants with relatively small effects whereas DMI, ADG, and MWT are influenced by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory region and synonymous functional classes play a more important role per sequence variant in determining variation of the feed efficiency traits. The genetic architecture as revealed by the GWAS of the imputed 7,853,211 DNA variants will improve our understanding on the genetic control of feed efficiency traits in beef cattle.
['Zhang|Feng|F|', 'Wang|Yining|Y|', 'Mukiibi|Robert|R|', 'Chen|Liuhong|L|', 'Vinsky|Michael|M|', 'Plastow|Graham|G|', 'Basarab|John|J|', 'Stothard|Paul|P|', 'Li|Changxi|C|http://orcid.org/0000-0002-0092-7047']
D000818:Animals D002417:Cattle D004435:Eating D056726:Genetic Association Studies D014644:Genetic Variation D040481:Genome Components D055106:Genome-Wide Association Study D023281:Genomics D020641:Polymorphism, Single Nucleotide D040641:Quantitative Trait Loci D019655:Quantitative Trait, Heritable D000073336:Whole Genome Sequencing
Genetic architecture Beef cattle Genome wide association studies Imputed whole genome sequence variants Feed efficiency