Genome-wide association study of growth traits in Channa argus
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摘要:目的
乌鳢(Channa argus)是中国重要的淡水经济鱼类,近年来受环境和养殖方式等影响,其种质资源逐渐退化。本文利用全基因组关联分析(GWAS)方法研究乌鳢生长性状的遗传基础,以期为其种质资源保护和良种选育提供依据。
方法利用Illumina Nova(PE150)平台和SuperGBS技术对405尾乌鳢进行简化基因组测序;利用EMMAX软件的高效混合模型进行GWAS分析,寻找与乌鳢生长性状显著关联的单核苷酸多态性(SNP)位点;扫描显著性位点上下游50 kb的序列,查找潜在候选基因,根据NCBI数据库和文献检索结果,注释候选基因的生物学功能,筛选与目标性状相关的候选功能基因。
结果测序数据过滤后,共获得
47536 个SNP位点,GWAS分析筛选到3个与体质量性状显著关联的SNP位点,即2831060、2830864、2830886。扫描显著性位点上下游50 kb序列,注释到7个与体质量相关联的候选功能基因;此外,还筛选到6个全长性状潜在关联的SNP位点,注释到17个与全长性状相关联的潜在候选功能基因。在这些功能基因中,有7个基因与全长和体质量性状均存在关联,分别是irak3、tuba1a、hspa14、prl、rint1、helb和net1,其主要参与乌鳢的生长代谢、发育调控、细胞增殖和免疫调控等生物学过程。结论本研究挖掘的SNP及功能基因与乌鳢的体质量和全长性状存在显著关联,可为乌鳢生长性状的机制解析、良种选育和资源保护提供重要参考。
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关键词:
- 乌鳢 /
- 全基因组关联分析(GWAS) /
- 生长性状 /
- 简化基因组测序
Abstract:ObjectiveChanna argus is an important freshwater economic fish in China. In recent years, due to environmental impacts and breeding methods, the genetic resources of C. argus have gradually deteriorated. This study aims to investigate the genetic basis of growth traits in C. argus using genome-wide association studies (GWAS) to provide a basis for the conservation of genetic resources and the selection of superior breeds in C. argus.
MethodsA total of 405 individuals of C. argus were subjected to reduced-representation genome sequencing using the Illumina Nova (PE150) platform and SuperGBS technology. The GWAS analysis was performed using the efficient mixed model of the EMMAX software to identify SNPs significantly associated with growth traits. Sequences within 50 kb upstream and downstream of the significant loci were scanned to identify potential candidate genes. The biological functions of the candidate genes were annotated based on the NCBI database and literature search results, and candidate functional genes related to the target traits were screened.
ResultsAfter filtering the sequencing data, a total of 47 536 SNP loci were obtained. GWAS analysis identified three SNPs significantly associated with body mass traits: 2831060, 2830864, and 2830886. By scanning sequences within 50 kb upstream and downstream of the significant loci, seven candidate functional genes related to body mass in C. argus were annotated. In addition, six potential SNPs associated with total length traits were identified, and 17 potential candidate functional genes related to total length traits were annotated. Among these functional genes, seven were associated with both total length and body mass traits, namely irak3, tuba1a, hspa14, prl, rint1, helb and net1. These functional genes are mainly involved in biological processes such as growth metabolism, developmental regulation, cell proliferation, and immune regulation in C. argus.
ConclusionThe identified SNPs and functional genes are significantly associated with body mass and total length traits in C. argus, providing important references for the mechanism analysis of growth traits, superior breed selection, and resource conservation in C. argus.
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Keywords:
- Channa argus /
- genome-wide association study (GWAS) /
- growth traits /
- SuperGBS
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全基因组关联分析(Genome-wide association study,GWAS)是针对随机群体设计的关联分析方法,最初被用于人类疾病相关基因位点的分析,如今已被广泛应用于育种研究,成为推动水产养殖业可持续发展的重要技术手段[1]。何骞等[2]使用GWAS方法在大黄鱼(Larimichthys crocea)5条染色体上定位到6个与肌纤维性状显著相关的单核苷酸多态性(Single nucleotide polymorphism,SNP)位点;崔爱君等[3]利用GWAS方法在黄条鰤(Larimichthys crocea)中找到17个体质量性状和12个全长性状相关的SNP位点和候选基因;方家璐等[4]通过GWAS定位到与黄河鲤(Cyprinus carpio)体质量性状相关的5个SNP和候选基因。通过GWAS筛选出与优良生长性状相关的分子标记,可以在早期快速筛选出具有优良性状的个体,加速育种进程,为水产动物经济性状的全基因组选择和品种培育提供重要依据。
乌鳢(Channa argus)属鲈形目(Perciformes)、鳢科(Channidae)、鳢属(Channa),是中国重要的淡水经济鱼类。乌鳢生长速度快、环境适应性强,肉质细腻、营养丰富、无肌间刺,是预制水产品的主要来源之一,市场前景广阔[5-6]。然而,随着养殖规模的扩大和养殖密度的增加,以及养殖企业长期自养自繁等原因,乌鳢种质资源逐渐退化,出现生长变缓、病害频发、成活率低等现象,严重影响了其商品价值和养殖效益。因此,开展乌鳢种质资源保护和新品种培育已成为产业可持续发展的重要需求。目前,乌鳢的良种培育主要以杂交鳢为主[7],尚未有采用GWAS方法开展乌鳢经济性状选育的报道。为深入分析乌鳢生长性状的遗传基础,定位相关候选基因,本研究选择体质量和体长2个生长性状为目标性状,采用GWAS方法寻找目标性状关联的SNP位点和候选功能基因,以期为乌鳢的种质资源保护、良种创制和持续利用提供基础资料。
1. 材料与方法
1.1 实验材料
实验材料选择微山乌鳢省级原种场同批次繁育的乌鳢,均一化养殖至12月龄,共选取13个家系405尾乌鳢用于分析。分别使用卡尺和电子天平测量乌鳢的全长(精确到0.01 cm)和体质量(精确到0.01 g)。剪取乌鳢胸鳍,置于无水乙醇中,24 h后换液,在−20 ℃冰箱中保存。山东省淡水渔业研究院批准动物实验,批准编号为LLSC2025001。
1.2 文库构建与测序
样品使用TIANGEN动物基因组抽提试剂盒进行基因组DNA提取,再使用分光光度计检测DNA纯度(OD260/OD280比值),并通过琼脂糖凝胶电泳分析DNA纯度和完整性。DNA抽提质检合格后,利用SuperGBS技术[8]构建测序文库,采用PstI-HF/MspI酶切DNA,酶切后的片段两端通过T4连接酶加接头和barcode,使用磁珠回收系统回收300~700 bp的片段,对回收片段使用高保真酶进行聚合酶链式反应(Polymerase chain reaction,PCR)扩增,使用Qubit测定PCR产物浓度(浓度需大于5 ng/μL),而后使用Illumina Nova(PE150)平台,将各样本按照一定浓度进行混库上机测序。
1.3 数据分析
1.3.1 表型数据分析
使用Excel和SPSS软件对测得的体质量和全长性状进行描述性统计分析,计算各性状的最大值、最小值、中位数、平均值和标准差等,并进行独立样本t检验和相关性分析。
1.3.2 测序数据分析
经Illumina Nova高通量测序的原始图像数据序列用碱基识别后转化为原始测序序列(Raw Reads),其结果以FASTQ(简称为fq)文件格式存储。使用预处理软件fastp对Raw Reads进行质量过滤,去除接头序列、N碱基≥5和平均碱基质量值<20的Reads,获取Clean Reads。利用BWA[9]软件将Clean Reads比对到参考基因组上,根据比对结果统计样品深度信息并计算测序数据对乌鳢参考基因组(Accession:PRJNA721844)的覆盖度。使用Qualimap[10]统计各样本的插入片段长度分布。
1.3.3 SNP注释
基于样本与参考基因组的比对结果,使用GATK4[11]软件的Haplotypecaller模块进行SNP检测。QD是突变质量值(Quality)除以覆盖深度(Depth)得到的比值,以QD≥2.0进行过滤,降低SNP和InDel检测的错误率,只保留同时满足该条件的突变位点。使用VCFtools[12]进一步过滤,保留Reads支持深度不小于4的位点,去除最小等位基因频率(Minor allele frequency,MAF)小于0.01的位点,保留80%的个体能够分型的位点。对于有注释文件(gff文件)的基因组,使用SnpEff[13]软件对得到的SNP进行注释,以确定SNP在基因元件的位置、对氨基酸的变化影响等。
1.4 全基因组关联分析
使用EMMAX软件的高效混合模型进行SNP标记和GWAS分析,以基因型为主要自变量、表型值为因变量,同时考虑并控制群体结构、亲缘关系等其他因素可能造成的假阳性。GWAS的主要结果是每个SNP位点(或其他类型的标记)与表型的相关性程度,一般用P值表示,每个SNP能得到1个相对应的统计概率P值。零假设为该SNP位点与表型无关,备择假设为该SNP位点与表型有关,当在零假设下得到的P值很小时,表示该SNP位点与表型无关的可能性很小,也就是说该SNP位点很可能与表型相关,这类SNP位点优先进行下一步的实验验证。研究使用2种阈值筛选强显著性位点,第一种控制错误发现率(False discovery rate,FDR)法是由Benjamini和Hochberg提出的通过控制错误发现的概率对P值进行调整的方法[14];第二种Bonferroni校正法是多重比较中控制假阳性最为严格和保守的一种方法[15],将单次检验的显著性P值0.05除以多重比较的次数(在GWAS中为SNP位点的个数)作为校正后的阈值,将各位点的P值与之进行比较,如果某位点的P值小于校正阈值,则可判别该位点与性状之间存在显著性关联。根据GWAS分析结果绘制Quantile-Quantile(QQ)plot和曼哈顿图。
1.5 候选基因鉴定及功能分析
筛选表型P值小于0.05的位点,利用已发表的乌鳢基因注释信息,扫描显著性位点上下游50 kb的序列,查找潜在候选基因。根据NCBI数据库和文献检索结果,注释候选基因的生物学功能,筛选与目标性状相关的候选功能基因。
2. 结果
2.1 表型性状描述性统计
本研究所用乌鳢样品的体质量和全长性状的描述性统计结果参见表1,所用乌鳢全长为16.61~27.22 cm,平均值为20.92 cm,变异系数为7.28;体质量为22.66~180.66 g,平均值为77.13 g,变异系数为24.29。统计分析显示,乌鳢的体质量和全长性状数据呈近正态分布。
表 1 乌鳢表型性状Table 1. Descriptive statistics of C. argus性状
Traits最大值
Max最小值
Min中位数
Median平均值
Mean标准差
SD变异系数/%
CV全长 Total length 27.22 16.61 20.91 20.92 1.52 7.28 体质量 Body mass 180.66 22.66 75.55 77.13 18.73 24.29 2.2 SNP分型
对SuperGBS技术简化基因组测序的数据进行进一步过滤,保留Reads支持深度不小于4的位点,去除MAF< 0.01的位点,保留80%的个体能够分型的位点。过滤后得到
47536 个SNP位点,用于乌鳢表型性状的GWAS分析。2.3 全基因组关联分析
根据EMMAX软件运行结果,得到每个SNP位点与各性状关联的P值,绘制乌鳢全长和体质量的QQ plot,比较各SNP的P值观测值(纵轴)与期望值(横轴)的一致性(图1和图2)。如图所示,散点分布与阈值实线在前段基本一致,表明得到的SNP假阳性率低,GWAS分析结果较为准确。根据EMMAX软件结果和Bonferroni校正P值,得到乌鳢全长和体质量曼哈顿图(图3和图4)。全长和体质量性状未找到Bonferroni校正后的阈值线以上显著关联的SNP位点,但经FDR校正后,找到了3个与体质量性状显著关联的SNP位点。
2.4 候选基因及功能注释
对获得的体质量显著位点上下游50 kb区域进行扫描,比对NCBI和Ensemble数据库,3个体质量性状显著关联SNP位点共找到7个潜在关联基因;对潜在关联基因进行功能注释,共注释到7个与乌鳢体质量相关联的候选功能基因(表2)。
表 2 乌鳢体质量性状GWAS分析结果及候选基因Table 2. GWAS analysis results and candidate genes for body mass trait of C. argus染色体
ChromosomeSNP位置
SNP locationP值
P value基因ID
Gene ID候选基因
Candidate genes编码蛋白
Coding protein21 2831060 2.30E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 21 2830864 3.37E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 21 2830886 3.37E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 全长性状未找到显著关联SNP位点;对全长性状SNP位点P值从小到大排序,得到6个P值小于1×10−4的SNP位点,对这6个位点上下游50 kb区域进行扫描,寻找潜在候选关联基因并对其进行功能注释,共注释到17个与乌鳢体全长性状相关的潜在功能基因(表3)。
图 3 乌鳢全长性状曼哈顿图注:红线是对GWAS给出的P值划定的显著性水平线(已经进行−log10转换),红线经Bonferroni矫正后的P=0.05。Figure 3. Manhatton plot of total length trait of C. argusNotes: The red line represents the significance level line for the P values given by GWAS (which have already been transformed by −log10). The red line indicates the P value of 0.05 after Bonferroni correction.表 3 乌鳢全长性状GWAS分析结果及候选基因Table 3. GWAS analysis results and candidate genes for total length trait of C. argus染色体
ChromosomeSNP位置
SNP locationP值
P value基因ID
Gene ID候选基因
Candidate genes编码蛋白
Coding protein16 3305852 3.01E-05 EXN66_Car016480 foxi1c Forkhead box protein I1c EXN66_Car016481 cfd Complement factor D EXN66_Car016482 dnaaf9 Dynein axonemal assembly factor 9 EXN66_Car016479 plaat4 Phospholipase A and acyltransferase 4 21 2831060 2.30E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 21 2830864 3.37E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 21 2830886 3.37E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 19 4093798 7.13E-05 EXN66_Car019069 pfkp ATP-dependent 6-phosphofructokinase, platelet type EXN66_Car019070 klf6 Krueppel-like factor 6 22 8803643 9.22E-05 EXN66_Car021470 trim3 Tripartite motif-containing protein 3 EXN66_Car021471 fhdc1 FH2 domain-containing protein 1 EXN66_Car021472 arfip2 Arfaptin-2 EXN66_Car021468 frem2 FRAS1-related extracellular matrix protein 2 图 4 乌鳢体质量性状曼哈顿图注:红线和蓝线是对GWAS给出的P值划定2条显著性水平线(已经进行−log10转换),蓝线是FDR=0.05,红线是Bonferroni矫正后的P=0.05。Figure 4. Manhatton plot of body mass trait of C. argusNotes: The red and blue lines represent two significance level lines for the P values given by GWAS (which have already been transformed by −log10). The blue line corresponds to a false discovery rate (FDR) of 0.05, while the red line indicates the P value of 0.05 after Bonferroni correction.3. 讨论
乌鳢的性状关联基因研究已取得一定的进展,主要集中在体色、生长、性别等性状方面。黄苏静等[16]比较分析了乌鳢3种性腺组织的转录组,筛选出大量乌鳢性别分化和精巢、卵巢发育调控相关的候选基因和信号通路;徐成豪[17]基于构建的乌鳢遗传图谱定位到3个全长性状显著相关SNP位点,2个体重性状、2个体色性状和1个性别数量性状位点(Quantitative trait locus,QTL)区间;Luo等[18]研究发现amh基因在乌鳢性腺性别分化中起重要作用;Sun等[19]证实slc45a2基因的无义突变(c.383G>A)是乌鳢体色性状突变的原因;Fan等[20]研究发现肝脏和脾脏中的pcdhf 4、nlrc3 和card 15-like基因可能与白色乌鳢的发育和免疫相关。
研究中定位到7个与体质量和全长性状均相关的候选基因。其中,重组DNA修复蛋白(rint1)基因是染色体结构维护(SMC)蛋白家族成员,参与多种细胞过程,包括DNA双链断裂修复、细胞周期检查点激活、端粒维护和减数分裂,在细胞增殖中起重要作用[21]。DNA解旋酶B(helb)是一种在高等真核生物中保守的解旋酶,主要在G期核内参与DNA复制的起始过程,在DNA损伤和复制应激反应中也有重要作用[22]。神经上皮细胞转化基因1(net1)在细胞内信号传导中起关键作用,主要通过调节Rho家族小G蛋白的活性来影响包括肌动蛋白细胞骨架的组织、细胞周期进展等多种功能[23-24]。X-微管蛋白(tuba1a)属于微管蛋白家族,是一种重要的细胞骨架蛋白,在细胞分裂、物质运输和细胞形态维持等过程中发挥关键作用[25]。白介素1受体关联激酶3(irak3)是受体相关激酶蛋白家族成员,是Toll/IL-R 免疫信号转导通路的重要组成部分,主要在单核细胞和巨噬细胞中表达,在副溶血弧菌感染的斑马鱼(Danio rerio)幼鱼中参与天然免疫应答 [26-27]。热休克蛋白14(hspa14)是广泛存在的一类小分子热休克蛋白基因,在进化过程中的高度保守,可提高细胞的应激能力,研究发现在中华鲟(Aclpenser sinensis)、达氏鲟(Acipenser dabryanus)和青海湖裸鲤(Gymnocypris przewalskii)中均参与机体应激外源性胁迫的生物过程[28]。催乳素(prl)是由动物脑垂体合成与分泌的一种单链多肽类激素,是硬骨鱼类调节渗透压和离子平衡的主要激素,研究发现prl在草鱼(Ctenopharyngodon idella)、罗非鱼(Oreochromis niloticus)等鱼类中与生长性状显著相关。研究中筛选出的这些候选基因在生长代谢、发育调控、细胞增殖、免疫调控、生理调控等生物学功能中起重要作用[29-30],与乌鳢的生长性状可能存在密切的关联,是乌鳢体质量和全长性状的重要候选功能基因,但在乌鳢生长发育过程中的作用有待进一步的验证。
徐成豪[17]在采用2b-RAD(2b-restriction site-associated DNA)测序技术对130尾1月龄杂交乌鳢(野生型乌鳢♀×突变型乌鳢♂)全长性状QTL定位研究中,发现了3个显著相关的编码蛋白基因znf208、znf91、mxa,且均位于17号连锁群上。本研究定位到的7个生长性状候选基因均位于乌鳢21号染色体上,在鲤、红罗非鱼(Oreochromis spp.)和大黄鱼的GWAS分析中也有类似现象[31-33],即目标性状SNP和关联基因表现出成簇分布的特点,说明某些特定性状的关联位点往往集中于部分染色体,甚至集中于染色体的某个特定区域。
本研究发现,体质量性状显著关联的SNP位点及7个关联基因均出现在全长性状潜在关联的SNP位点及候选基因中,且P值仅高于位点SNP 3305852,表现出与全长性状较高的关联性。目前,大多数GWAS分析是根据单性状进行目标性状和遗传位点之间的关联分析,但当对多个表型性状同时进行分析时,会存在1个位点或基因同时影响多个性状的情况,即一因多效性[34]。鱼类多性状的GWAS研究处于起步阶段,蒋仪等[35]使用表型正交化混合模型对大菱鲆(Scophthalmus maximus)体质量、体长和尾柄长性状进行了多性状的GWAS关联分析,提高了检索效率并检测到更多数量性状核苷酸(Quantitative trait nucleotides,QTNs)。Porter等[36]认为多性状GWAS分析与单性状GWAS分析相比,具有更高的遗传变异检测效率。本研究中有7个潜在关联基因同时与乌鳢体质量和全长性状表现出较高的关联性,说明在乌鳢的生长性状中也存在一因多效现象。后续研究可以考虑引入多性状联合分析方法,进一步提高检测效率和定位的准确性。
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图 3 乌鳢全长性状曼哈顿图
注:红线是对GWAS给出的P值划定的显著性水平线(已经进行−log10转换),红线经Bonferroni矫正后的P=0.05。
Figure 3. Manhatton plot of total length trait of C. argus
Notes: The red line represents the significance level line for the P values given by GWAS (which have already been transformed by −log10). The red line indicates the P value of 0.05 after Bonferroni correction.
图 4 乌鳢体质量性状曼哈顿图
注:红线和蓝线是对GWAS给出的P值划定2条显著性水平线(已经进行−log10转换),蓝线是FDR=0.05,红线是Bonferroni矫正后的P=0.05。
Figure 4. Manhatton plot of body mass trait of C. argus
Notes: The red and blue lines represent two significance level lines for the P values given by GWAS (which have already been transformed by −log10). The blue line corresponds to a false discovery rate (FDR) of 0.05, while the red line indicates the P value of 0.05 after Bonferroni correction.
表 1 乌鳢表型性状
Table 1 Descriptive statistics of C. argus
性状
Traits最大值
Max最小值
Min中位数
Median平均值
Mean标准差
SD变异系数/%
CV全长 Total length 27.22 16.61 20.91 20.92 1.52 7.28 体质量 Body mass 180.66 22.66 75.55 77.13 18.73 24.29 表 2 乌鳢体质量性状GWAS分析结果及候选基因
Table 2 GWAS analysis results and candidate genes for body mass trait of C. argus
染色体
ChromosomeSNP位置
SNP locationP值
P value基因ID
Gene ID候选基因
Candidate genes编码蛋白
Coding protein21 2831060 2.30E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 21 2830864 3.37E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 21 2830886 3.37E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 表 3 乌鳢全长性状GWAS分析结果及候选基因
Table 3 GWAS analysis results and candidate genes for total length trait of C. argus
染色体
ChromosomeSNP位置
SNP locationP值
P value基因ID
Gene ID候选基因
Candidate genes编码蛋白
Coding protein16 3305852 3.01E-05 EXN66_Car016480 foxi1c Forkhead box protein I1c EXN66_Car016481 cfd Complement factor D EXN66_Car016482 dnaaf9 Dynein axonemal assembly factor 9 EXN66_Car016479 plaat4 Phospholipase A and acyltransferase 4 21 2831060 2.30E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 21 2830864 3.37E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 21 2830886 3.37E-06 EXN66_Car020554 irak3 Interleukin-1 receptor-associated kinase 3 EXN66_Car020555
EXN66_Car020556
EXN66_Car020557
EXN66_Car020558
EXN66_Car020559tuba1a Tubulin alpha-1A chain EXN66_Car020561 hspa14 Heat shock 70 kDa protein 14 EXN66_Car020562 prl Prolactin EXN66_Car020563 rint1 RAD50-interacting protein 1 EXN66_Car020560 helb DNA helicase B EXN66_Car020564 net1 Neuroepithelial cell-transforming gene 1 protein 19 4093798 7.13E-05 EXN66_Car019069 pfkp ATP-dependent 6-phosphofructokinase, platelet type EXN66_Car019070 klf6 Krueppel-like factor 6 22 8803643 9.22E-05 EXN66_Car021470 trim3 Tripartite motif-containing protein 3 EXN66_Car021471 fhdc1 FH2 domain-containing protein 1 EXN66_Car021472 arfip2 Arfaptin-2 EXN66_Car021468 frem2 FRAS1-related extracellular matrix protein 2 -
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