Epistatic Effects on Abdominal Fat Content in Chickens: Results from a Genome-Wide SNP-SNP Interaction AnalysisReport as inadecuate




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We performed a pairwise epistatic interaction test using the chicken 60 K single nucleotide polymorphism SNP chip for the 11th 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.



Author: Fangge Li, Guo Hu, Hui Zhang, Shouzhi Wang, Zhipeng Wang , Hui Li

Source: http://plos.srce.hr/



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