杜长大猪、二花脸猪和莱芜猪3个群体25种血液性状的全基因组关联分析

发布时间：2018-10-30 14:45

【摘要】：【目的】利用全基因组关联分析定位影响杜长大猪(DLY)、二花脸猪(EHL)和莱芜猪(LW)3个群体25种血液性状的染色体位点,为最后鉴定影响这些性状的因果基因提供前期基础,同时为猪抗病育种和生产提供参考。【方法】将610头杜长大三元杂猪在(180±5)日龄,336头二花脸猪和333头莱芜猪在(300±5)日龄进行统一屠宰。收集2 m L血液于抗凝管中,利用全自动生化分析仪进行25种血液性状的血常规检测。采集猪耳组织提取DNA并测浓度和质量。将质检合格的DNA样品利用Illumina 60K SNP芯片进行基因型判定。运用PLINK软件对判型结果进行质量控制,将合格的SNP标记用于后续的关联分析。使用R语言Gen ABEL软件包中的广义混合线性模型进行全基因组关联分析,定位影响3个群体25种血常规性状的显著性染色体位点。据全基因组关联分析结果,在Ensembl或NCBI网站上搜寻潜在的位置候选基因。【结果】杜长大猪、二花脸猪和莱芜猪三个群体通过质控的有效表型数据个体数分别为552头、325头和281头。60K SNPs经过质量控制过后,杜长大猪剩余56 216SNPs,莱芜猪剩余49 343 SNPs,二花脸猪剩余35 974 SNPs,用于Meta分析的SNPs共有32 967。运用全基因组关联分析和Meta分析共定位到610个显著影响3个群体25种血液性状的SNPs,其中135个SNPs达基因组显著水平,475个SNPs达建议水平;分布在所有染色体上。在杜长大猪中共鉴别到32个基因组显著水平SNPs以及85个建议水平SNPs,且8种性状有基因组显著水平的SNPs,分别是淋巴细胞数目(LYM)、淋巴细胞比率(LYMR)、嗜碱性粒细胞数目(BAS)、嗜碱性粒细胞比率(BASR)、平均红细胞体积(MCV)、红细胞分布宽度变异系数(RDW_CV)、平均红细胞血红蛋白含量(MCH)和血小板分布宽度(PDW)。在二花脸猪中共鉴别到33个基因组显著水平SNPs以及139个建议水平SNPs,且9种性状有基因组显著水平的SNPs,分别是LYM、MCH、平均红细胞血红蛋白浓度(MCHC)、单核细胞数目(MON)、单核细胞比率(MONR)、平均血小板体积(MPV)、中性粒细胞比率(NEUR)、大血小板细胞(P_LCC)以及血小板压积(PCT)。在莱芜猪中共鉴别到54个基因组显著水平SNPs以及169个建议水平SNPs,且6种性状有基因组显著水平的SNPs,分别是BASR、红细胞压积(HCT)、MCH、MCHC、MCV和红细胞数目(RBC)。在Meta分析结果中,共鉴别到16个基因组显著水平SNPs以及82个建议水平SNPs,且6种性状有基因组显著水平SNPs,分别是RBC、HCT、MCH、MCHC、MCV以及MON。通过在Ensembl或NCBI网站上搜寻最强相关SNP区域内的候选基因,初步将F13A1、SPTA1、DBNL、SLC25A28、CTSC基因分别确定为影响BASR、HCT、LYM、MCHC、NEUR的重要候选基因。【结论】通过全基因组关联分析和Meta分析共得到610个显著影响杜长大猪、二花脸猪和莱芜猪3个群体25种血液性状的SNP位点,初步确定F13A1、SPTA1、DBNL、SLC25A28和CTSC基因分别是BASR、HCT、LYM、MCHC和NEUR的重要位置候选基因,为解析商业猪和纯种地方猪的血液性状或免疫性疾病提供重要参考。
[Abstract]:[objective] to localize the chromosomal loci of 25 blood traits in three populations of (DLY), Erhualian pig (EHL) and Laiwu pig (LW) by using the whole genome association analysis. For the final identification of causal genes affecting these traits, it provides a preliminary basis for the breeding and production of swine disease resistance. [methods] 610 Dudu Sanyuan crossbred pigs were grown at the age of (180 卤5) days. 336 Erhualian pigs and 333 Laiwu pigs were slaughtered at (300 卤5) days old. 2 mL blood was collected in the anticoagulant tube, and the blood routine examination of 25 kinds of blood traits was carried out by using automatic biochemical analyzer. DNA was extracted from porcine ear tissue and its concentration and quality were measured. The qualified DNA samples were determined by Illumina 60 K SNP chip. PLINK software was used to control the quality of the judging results, and the qualified SNP markers were used in the subsequent correlation analysis. Using the generalized mixed linear model in R language Gen ABEL software package, the whole genome association analysis was carried out, and the significant chromosomal loci affecting 25 blood routine traits in three populations were located. According to the results of genome-wide association analysis, potential locational candidate genes were searched on Ensembl or NCBI websites. [results] the effective phenotypic data of three populations, including Du-grown pig, Erhualian pig and Laiwu pig, were 552, respectively. After the quality control of 325 and 281K SNPs, the SNPs of the remaining 56,216SNPs in du long pig and 35,974 SNPs, in Laiwu pig 49,343 SNPs, Erhuface pig were used for Meta analysis. Genomic association analysis and Meta analysis were used to localize 610 SNPs, with significant effect on 25 blood traits in 3 populations. 135 SNPs reached the genomic significant level and 475 SNPs reached the recommended level, which were distributed on all chromosomes. A total of 32 genomic significant levels of SNPs and 85 suggested levels of SNPs, were identified in du long pigs, and SNPs, with genomic significance in 8 traits were identified as lymphocyte number (LYM), lymphocyte ratio (LYMR), respectively. Number of basophil (BAS), basophil ratio (BASR), mean RBC Volume (MCV), RBC Distribution width variation coefficient (RDW_CV), Mean erythrocyte hemoglobin content (MCH) and platelet distribution width (PDW). In Erhualian pigs, 33 genome-wide significant levels of SNPs and 139 suggested levels of SNPs, were identified as LYM,MCH, mean erythrocyte hemoglobin concentration (MCHC), respectively, and 9 traits with genomic significant levels were identified. Number of monocytes (MON), monocyte ratio (MONR), mean platelet volume (MPV), neutrophil ratio (NEUR), large platelet cell (P_LCC) and platelet compression (PCT). In Laiwu pig, 54 genome-wide significant levels of SNPs and 169 suggested levels of SNPs, were identified as BASR, hematocrit (HCT), MCH,MCHC,MCV and erythrocyte number (RBC). With 6 traits with genomic significant level, respectively. In Meta analysis, 16 genome-wide significant levels of SNPs and 82 recommended levels of SNPs, were identified, and six traits with genomic significant level SNPs, were identified as RBC,HCT,MCH,MCHC,MCV and MON., respectively. By searching for candidate genes in the strongest relevant SNP region on the Ensembl or NCBI website, we preliminarily identified the F13A1 gene SPTA1, DBNL, SLC25A28 and CTSC genes as influencing BASR,HCT,LYM,MCHC, respectively. [conclusion] A total of 610 SNP loci were obtained by genomic association analysis and Meta analysis to significantly affect 25 blood traits in three populations of Duroc pig, Erhualian pig and Laiwu pig. SLC25A28 and CTSC genes are important candidate genes for BASR,HCT,LYM,MCHC and NEUR respectively, which provide important reference for the analysis of blood traits or immunological diseases in commercial pigs and purebred local pigs.
【作者单位】：江西农业大学省部共建猪遗传改良与养殖技术国家重点实验室;
【基金】：国家“973”项目(2012CB722502) 甘肃省生物技术专项(31200926) 江西省科技支撑计划(2009BNA06900)
【分类号】：S828

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