基于全基因组Fst和nSL分析鉴别苏淮猪中性洗涤纤维表观消化率相关候选基因位点

Identification of Candidate Gene Loci Related to Apparent NDF Digestibility of Suhuai Pigs Based on Genome-wide Fst and nSL Analyses

旨在鉴定苏淮猪(含25%淮猪和75%大白猪血统的国家级新品种)在培育过程中受选择的与纤维表观消化率性状相关的基因片段,为解析苏淮猪耐粗饲遗传机制奠定基础。本研究首先检测分析了331头160日龄苏淮猪个体的中性洗涤纤维(neutral detergent fiber,NDF)表观消化率,计算群体NDF表观消化率估计育种值(estimated breeding value,EBV),选择其中EBV极高和极低各10%的个体(N=66)进行猪80K芯片基因分型。借助群体分化指数(fixation index,Fst)和按长度划分隔离点数(number of segregating sites by length,nSL)法分析苏淮猪群体内的选择信号分布情况,寻找选择信号区域内与纤维消化相关的重要基因。最后,选择两种分析中受选择的共有SNPs位点在苏淮猪全群分型,开展与NDF表观消化率的关联性分析,进一步确定影响苏淮猪NDF表观消化率的SNPs位点。结果显示,通过对高、低NDF表观消化率苏淮猪群体芯片分型数据质控,共有51367个有效SNPs位点用于后续分析。通过Fst和nSL选择信号分析,共鉴定到146个受选择信号区域和361个受选择的基因,其中多个基因被报道与肠道健康和肠道发育等功能相关,包括MTHFD1L、PHLPP1、TRPM6、MCC、NEDD9、UVRAG和KLF5等基因。选择两种分析中受选择且共有的8个SNPs位点,通过SNP与苏淮猪全群NDF表观消化率的关联性分析,发现rs81363074、rs327393763和rs81404927位点与苏淮猪群体NDF表观消化率存在显著关联(P<0.05),rs81347101和rs318870857位点与苏淮猪群体NDF表观消化率存在极显著关联(P<0.01)。其中,rs81363074位点位于MCC基因第二内含子上。通过高、低NDF表观消化率苏淮猪群体Fst和nSL选择信号分析,筛选到146个受选择信号区域,鉴定到影响苏淮猪NDF表观消化率的受选择候选基因MTHFD1L、PHLPP1、TRPM6、MCC、NEDD9、UVRAG和KLF5,筛选到了5个与NDF表观消化率显著关联的SNPs位点。本研究结果为解析苏淮猪耐粗饲性状的遗传机制奠定了重要基础。

This study aimed to identify the selected gene regions related to the apparent NDF digestibility during the breeding process of Suhuai pigs(a national new breed containing 25%Huai pig lineage and 75%Large White pig lineage)and provide an important foundation for analyzing the genetic mechanism of crude fiber tolerance in Suhuai pigs.Firstly,the apparent digestibility of neutral detergent fiber(NDF)of 331160-day-old Suhuai pigs were measured.The estimated breeding value(EBV)of apparent NDF digestibility in Suhuai pigs were calculated.Suhuai pigs with extremely high 10%(n=33)and extremely low 10%(n=33)of EBVNDF were selected to perform 80K chip genotyping.The fixation index(Fst)and the number of segregating sites by length(nSL)methods were adopted to analyze the selection signals distribution in Suhuai pig populations,and to detect the candidate genes related to fiber digestion located in selected signal regions.Finally,the common SNPs of selected sites in the Fst and nSL analyses were selected to genotype in the whole group of Suhuai pigs,and then the association analysis between SNPs and apparent NDF digestibility was carried out to further determine the candidate SNPs related to the apparent NDF digestibility in Suhuai pigs.A total of 51367 effective SNPs sites were used for the further analysis through the quality control of chip data of Suhuai pig populations with high and low apparent NDF digestibility.Furthermore,146 selected signals regions and 361 selected genes were identified via Fst and nSL selection signals analysis.Among them,many genes had been reported to be related to intestinal health and intestinal development,including MTHFD1L,PHLPP1,TRPM6,MCC,NEDD9,UVRAG and KLF5.Only 8 common SNPs sites were identified in the two analyses.Association analysis results of SNPs with apparent NDF digestibility showed that rs81363074,rs327393763,and rs81404927 were significantly associated with apparent NDF digestibility(P<0.05),and the rs81347101 and rs318870857 were extremely significantly associated with the apparent NDF digestibility in Suhuai pig populations(P<0.01).Among them,the rs81363074 was located on the second intron of the MCC gene.One hundred and forty-six selected signals regions were identified based on the methods of Fst and nSL selection signals in Suhuai pigs with high and low apparent NDF digestibility.The selected candidate genes MTHFD1L,PHLPP1,TRPM6,MCC,NEDD9,UVRAG and KLF5 were identified to affect the apparent NDF digestibility in Suhuai pigs.Besides,5 SNPs sites were significantly related to the apparent NDF digestibility.This results of this study provided an important foundation for analyzing the genetic mechanism of fiber tolerance trait in Suhuai pigs.