title: Pathway-Based Genome-Wide Association Studies for Two Meat Production Traits in Simmental Cattle.
abstract: Most single nucleotide polymorphisms (SNPs) detected by genome-wide association studies (GWAS), explain only a small fraction of phenotypic variation. Pathway-based GWAS were proposed to improve the proportion of genes for some human complex traits that could be explained by enriching a mass of SNPs within genetic groups. However, few attempts have been made to describe the quantitative traits in domestic animals. In this study, we used a dataset with approximately 7,700,000 SNPs from 807 Simmental cattle and analyzed live weight and longissimus muscle area using a modified pathway-based GWAS method to orthogonalise the highly linked SNPs within each gene using principal component analysis (PCA). As a result, of the 262 biological pathways of cattle collected from the KEGG database, the gamma aminobutyric acid (GABA)ergic synapse pathway and the non-alcoholic fatty liver disease (NAFLD) pathway were significantly associated with the two traits analyzed. The GABAergic synapse pathway was biologically applicable to the traits analyzed because of its roles in feed intake and weight gain. The proposed method had high statistical power and a low false discovery rate, compared to those of the smallest P-value and SNP set enrichment analysis methods.
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing 100193, China.
authors.forename: Huizhong
authors.initials: H
authors.lastname: Fan
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing 100193, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Department of Mathematics, Heilongjiang Bayi Agricultural University, 163319 Daqing, China.
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing 100193, China.
authors.forename: Jiangwei
authors.initials: J
authors.lastname: Xia
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing 100193, China.
authors.forename: Wengang
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing 100193, China.
authors.forename: Yuxin
authors.initials: Y
authors.lastname: Song
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing 100193, China.|College of Animal Science and Technology, Agricultural University of Hebei Province, Baoding, 071001, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Liu
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing 100193, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing 100193, China.
authors.forename: Lupei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing 100193, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Gao
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing 100193, China.
authors.forename: Huijiang
authors.initials: H
authors.lastname: Gao
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing 100193, China.
authors.forename: Junya
authors.initials: J
authors.lastname: Li
mesh_terms: D000465:Algorithms; D000818:Animals; D002417:Cattle; D002418:Cattle Diseases / Q000235:genetics; D004435:Eating / Q000235:genetics; D059330:GABAergic Neurons / Q000378:metabolism; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D008460:Meat; D008957:Models, Genetic; D018482:Muscle, Skeletal / Q000378:metabolism; D065626:Non-alcoholic Fatty Liver Disease / Q000235:genetics / Q000662:veterinary; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D040641:Quantitative Trait Loci / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics*; D013569:Synapses / Q000235:genetics; D015430:Weight Gain / Q000235:genetics