title: Epistatic effects on abdominal fat content in chickens: results from a genome-wide SNP-SNP interaction analysis.
abstract: We performed a pairwise epistatic interaction test using the chicken 60 K single nucleotide polymorphism (SNP) chip for the 11(th) generation of the Northeast Agricultural University broiler lines divergently selected for abdominal fat content. A linear mixed model was used to test two dimensions of SNP interactions affecting abdominal fat weight. With a threshold of P<1.2×10(-11) by a Bonferroni 5% correction, 52 pairs of SNPs were detected, comprising 45 pairs showing an Additive×Additive and seven pairs showing an Additive×Dominance epistatic effect. The contribution rates of significant epistatic interactive SNPs ranged from 0.62% to 1.54%, with 47 pairs contributing more than 1%. The SNP-SNP network affecting abdominal fat weight constructed using the significant SNP pairs was analyzed, estimated and annotated. On the basis of the network's features, SNPs Gga_rs14303341 and Gga_rs14988623 at the center of the subnet should be important nodes, and an interaction between GGAZ and GGA8 was suggested. Twenty-two quantitative trait loci, 97 genes (including nine non-coding genes), and 50 pathways were annotated on the epistatic interactive SNP-SNP network. The results of the present study provide insights into the genetic architecture underlying broiler chicken abdominal fat weight.
authors: Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, People's Republic of China ; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, People's Republic of China ; College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China.
authors: Fangge
authors: F
authors: Li
authors: Guo
authors: G
authors: Hu
authors: Hui
authors: H
authors: Zhang
authors: Shouzhi
authors: S
authors: Wang
authors: Zhipeng
authors: Z
authors: Wang
authors: Hui
authors: H
authors: Li
mesh_terms: D050153:Abdominal Fat / Q000378:metabolism*; D000818:Animals; D002645:Chickens / Q000235:genetics* / Q000378:metabolism*; D004843:Epistasis, Genetic; D053263:Gene Regulatory Networks; D005819:Genetic Markers / Q000235:genetics; D023281:Genomics; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
chemical_list: D005819:Genetic Markers