摘要
研究旨在分析北京鸭龙骨长(Keel bone length,KBL)性状在全基因组水平上多态位点间的相互作用,包括542只北京鸭和60238个SNP位点。REML方法估计龙骨长遗传力为0.56,为中等遗传力性状。全基因组关联分析(Genome-wide association study,GWAS)共检测到基因组水平上显著的28个SNP位点(P<8.30×10^(-7)),其中11个位于CLEC16A、GPATCH1和CLCA2基因上,8个位于LOC101792208、DCLK3和ADRA1B基因上下游20 kb区间内。全基因组互作进一步分析,共检测到具有显著互作效应的1644对SNP位点(P<5.51×10^(-13)),分别为36对加性×加性、57对显性×加性和1551对显性×显性上位效应。最显著的上位效应为1号(Chr1.49519635_A.G)和9号染色体(Chr9.7036234_A.G)上SNP间显性互作(P=2.05×10^(-18))。通过构建影响龙骨长性状的成对SNP互作网络,发现其中有15个SNP节点的度大于15,网络中心节点Chr27.1210834_C.T、Chr2.86757383_C.G和Chr3.23516978_A.G的度分别为211、145和102。对网络中SNP节点邻近基因进行功能富集注释,共得到16条显著信号通路,其中包括可能同龙骨长性状相关的Wnt、Notch、MAPK和钙信号通路(P<0.05)。研究利用GWAS和全基因组互作分析,有助于深入理解北京鸭龙骨长性状复杂遗传机制,为北京鸭龙骨长性状遗传基础和分子机制研究提供新思路,为北京鸭育种选择和改良提供重要参考依据。
The study aimed to analyze the interactions among polymorphic loci affecting the traits of keel bone length(KBL)in Pekin ducks,including 542 Pekin ducks and 60238 SNPs.Heritability of KBL was 0.56 using the REML method and KBL had moderate heritability.Genome-wide association analysis(GWAS)identified 28 significant SNPs(P<8.30×10^(-7)),of which 11 were located on CLEC16A,GPATCH1 and CLCA2 genes,and eight were located 20 kb upstream and downstream of LOC101792208,DCLK3 and ADRA1B genes within the range.After further genome-wide interaction effect analysis,a total of 1644 pairs of interactions with significant effects(P<5.51×10^(-13))were detected,including 36 pairs of additive×additive,57 pairs of dominant×additive and 1551 pairs of dominant×dominant epistasis.The most significant epistatic effect was the dominant interaction between SNPs on chromosome 1(Chr1.49519635_A.G)and chromosome 9(Chr9.7036234_A.G)(P=2.05×10^(-18)).By constructing a paired SNP interaction network that affected keel bone length traits,it was found that there were 15 SNP nodes with degrees greater than 15,and the degrees of the network central nodes Chr27.1210834_C.T,Chr2.86757383_C.G and Chr3.23516978_A.G were respectively 211,145 and 102.According to functional enrichment analysis of genes in the network,a total of 16 significant signaling pathways were obtained,including Wnt,Notch,MAPK and calcium signaling pathways,potentially related to keel bone length(P<0.05).In summary,the results obtained after GWAS and genome-wide epistasis analysis help to understand the complex genetic basis of KBL,provide a novel insight for studying the genetic basis and molecular mechanism of KBL,and important reference on genetic improvement of Pekin ducks.
作者
张镕
高炳熙
张昱
厐彦芹
王立
侯卓成
杨彩侠
杜志强
ZHANG Rong;GAO Bingxi;ZHANG Yu;PANG Yanqin;WANG Li;HOU Zhuocheng;YANG Caixia;DU Zhiqiang(School of Animal Science,Yangtze University,Jingzhou Hubei 434025,China;School of Animal Science and Technology,China Agricultural University,Beijing 100193,China)
出处
《东北农业大学学报》
CAS
CSCD
北大核心
2023年第8期38-45,87,共9页
Journal of Northeast Agricultural University
基金
国家自然科学基金面上项目(31972525)。
作者简介
张镕(1996-),男,硕士研究生,研究方向为动物遗传育种与繁殖。E-mail:202071757@yangtzeu.edu.cn;通讯作者:杜志强,教授,博士生导师,研究方向为动物遗传育种与繁殖。E-mail:zhqdu@yangtzeu.edu.cn。
