title: Systems biology analysis merging phenotype, metabolomic and genomic data identifies Non-SMC Condensin I Complex, Subunit G (NCAPG) and cellular maintenance processes as major contributors to genetic variability in bovine feed efficiency.
abstract: Feed efficiency is a paramount factor for livestock economy. Previous studies had indicated a substantial heritability of several feed efficiency traits. In our study, we investigated the genetic background of residual feed intake, a commonly used parameter of feed efficiency, in a cattle resource population generated from crossing dairy and beef cattle. Starting from a whole genome association analysis, we subsequently performed combined phenotype-metabolome-genome analysis taking a systems biology approach by inferring gene networks based on partial correlation and information theory approaches. Our data about biological processes enriched with genes from the feed efficiency network suggest that genetic variation in feed efficiency is driven by genetic modulation of basic processes relevant to general cellular functions. When looking at the predicted upstream regulators from the feed efficiency network, the Tumor Protein P53 (TP53) and Transforming Growth Factor beta 1 (TGFB1) genes stood out regarding significance of overlap and number of target molecules in the data set. These results further support the hypothesis that TP53 is a major upstream regulator for genetic variation of feed efficiency. Furthermore, our data revealed a significant effect of both, the Non-SMC Condensin I Complex, Subunit G (NCAPG) I442M (rs109570900) and the Growth /differentiation factor 8 (GDF8) Q204X (rs110344317) loci, on residual feed intake and feed conversion. For both loci, the growth promoting allele at the onset of puberty was associated with a negative, but favorable effect on residual feed intake. The elevated energy demand for increased growth triggered by the NCAPG 442M allele is obviously not fully compensated for by an increased efficiency in converting feed into body tissue. As a consequence, the individuals carrying the NCAPG 442M allele had an additional demand for energy uptake that is reflected by the association of the allele with increased daily energy intake as observed in our study.
authors: Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Genome Physiology Unit, Dummerstorf, Germany.
authors: Philipp
authors: P
authors: Widmann
authors: CSIRO Agriculture Flagship, Brisbane, Australia.
authors: Antonio
authors: A
authors: Reverter
authors: Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Genome Physiology Unit, Dummerstorf, Germany.
authors: Rosemarie
authors: R
authors: Weikard
authors: Weill Cornell Medical College in Qatar, Doha, State of Qatar; Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
authors: Karsten
authors: K
authors: Suhre
authors: Leibniz Institute for Farm Animal Biology, Institute for Nutritional Physiology "Oskar Kellner", Dummerstorf, Germany.
authors: Harald M
authors: HM
authors: Hammon
authors: Leibniz Institute for Farm Animal Biology, Institute for Muscle Biology and Growth, Dummerstorf, Germany.
authors: Elke
authors: E
authors: Albrecht
authors: Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Genome Physiology Unit, Dummerstorf, Germany; Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany.
authors: Christa
authors: C
authors: Kuehn
mesh_terms: D000483:Alleles; D000821:Animal Feed; D000818:Animals; D001835:Body Weight / Q000235:genetics; D002417:Cattle; D018797:Cell Cycle Proteins / Q000235:genetics*; D003433:Crosses, Genetic; D004435:Eating / Q000235:genetics*; D005247:Feeding Behavior / Q000502:physiology; D015870:Gene Expression; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D056426:Genetic Loci; D014644:Genetic Variation; D016678:Genome; D055106:Genome-Wide Association Study; D005838:Genotype; D055435:Myostatin / Q000235:genetics; D010641:Phenotype; D019655:Quantitative Trait, Heritable; D053773:Transforming Growth Factor beta1 / Q000235:genetics; D016159:Tumor Suppressor Protein p53 / Q000235:genetics
chemical_list: D018797:Cell Cycle Proteins; D055435:Myostatin; D053773:Transforming Growth Factor beta1; D016159:Tumor Suppressor Protein p53