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Application of mixed linear models for the estimation of functional effects on bovine stature based on SNP summary statistics from a whole-genome association study
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In: Genetics Selection Evolution, Vol. 54, 80, 12.2022.
Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review
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TY - JOUR
T1 - Application of mixed linear models for the estimation of functional effects on bovine stature based on SNP summary statistics from a whole-genome association study
AU - Kotlarz, Krzysztof
AU - Kosinska-Selbi, Barbara
AU - Cai, Zexi
AU - Sahana, Goutam
AU - Szyda, Joanna
N1 - © 2022. The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - Genome-wide association studies (GWAS) help identify polymorphic sites or genes linked to phenotypic variance, but a few identified genes and/or single nucleotide polymorphisms (SNPs) are unlikely to explain a large part of the phenotypic variability of complex traits. In this study, the focus was moved from single loci to functional units, expressed by the metabolic pathways as defined in the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database. Consequently, the aim of this study was to estimate KEGG effects on stature in three Nordic dairy cattle breeds using SNP effects from GWAS as the dependent variable. The SNPs were annotated to genes, then the genes to KEGG pathways. The effects of KEGG pathways were estimated separately for each breed using a mixed linear model incorporating the similarity between pathways expressed by common genes. The KEGG pathway D-amino acid metabolism (map00473) was estimated to be significant for stature in two of the analysed breeds and revealed a borderline significance in the third breed. Thus, we demonstrate that the approach to statistical modelling of higher order functional effects on complex traits is useful, and provides evidence of the importance of D-amino acids for growth in cattle.
AB - Genome-wide association studies (GWAS) help identify polymorphic sites or genes linked to phenotypic variance, but a few identified genes and/or single nucleotide polymorphisms (SNPs) are unlikely to explain a large part of the phenotypic variability of complex traits. In this study, the focus was moved from single loci to functional units, expressed by the metabolic pathways as defined in the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database. Consequently, the aim of this study was to estimate KEGG effects on stature in three Nordic dairy cattle breeds using SNP effects from GWAS as the dependent variable. The SNPs were annotated to genes, then the genes to KEGG pathways. The effects of KEGG pathways were estimated separately for each breed using a mixed linear model incorporating the similarity between pathways expressed by common genes. The KEGG pathway D-amino acid metabolism (map00473) was estimated to be significant for stature in two of the analysed breeds and revealed a borderline significance in the third breed. Thus, we demonstrate that the approach to statistical modelling of higher order functional effects on complex traits is useful, and provides evidence of the importance of D-amino acids for growth in cattle.
U2 - 10.1186/s12711-022-00771-1
DO - 10.1186/s12711-022-00771-1
M3 - Journal article
C2 - 36526979
VL - 54
JO - Genetics Selection Evolution
JF - Genetics Selection Evolution
SN - 0999-193X
M1 - 80
ER -