【摘要】：【目的】利用全基因組關(guān)聯(lián)分析定位影響杜長大豬(DLY)、二花臉豬(EHL)和萊蕪豬(LW)3個(gè)群體25種血液性狀的染色體位點(diǎn),為最后鑒定影響這些性狀的因果基因提供前期基礎(chǔ),同時(shí)為豬抗病育種和生產(chǎn)提供參考。【方法】將610頭杜長大三元雜豬在(180±5)日齡,336頭二花臉豬和333頭萊蕪豬在(300±5)日齡進(jìn)行統(tǒng)一屠宰。收集2 m L血液于抗凝管中,利用全自動(dòng)生化分析儀進(jìn)行25種血液性狀的血常規(guī)檢測(cè)。采集豬耳組織提取DNA并測(cè)濃度和質(zhì)量。將質(zhì)檢合格的DNA樣品利用Illumina 60K SNP芯片進(jìn)行基因型判定。運(yùn)用PLINK軟件對(duì)判型結(jié)果進(jìn)行質(zhì)量控制,將合格的SNP標(biāo)記用于后續(xù)的關(guān)聯(lián)分析。使用R語言Gen ABEL軟件包中的廣義混合線性模型進(jìn)行全基因組關(guān)聯(lián)分析,定位影響3個(gè)群體25種血常規(guī)性狀的顯著性染色體位點(diǎn)。據(jù)全基因組關(guān)聯(lián)分析結(jié)果,在Ensembl或NCBI網(wǎng)站上搜尋潛在的位置候選基因。【結(jié)果】杜長大豬、二花臉豬和萊蕪豬三個(gè)群體通過質(zhì)控的有效表型數(shù)據(jù)個(gè)體數(shù)分別為552頭、325頭和281頭。60K SNPs經(jīng)過質(zhì)量控制過后,杜長大豬剩余56 216SNPs,萊蕪豬剩余49 343 SNPs,二花臉豬剩余35 974 SNPs,用于Meta分析的SNPs共有32 967。運(yùn)用全基因組關(guān)聯(lián)分析和Meta分析共定位到610個(gè)顯著影響3個(gè)群體25種血液性狀的SNPs,其中135個(gè)SNPs達(dá)基因組顯著水平,475個(gè)SNPs達(dá)建議水平;分布在所有染色體上。在杜長大豬中共鑒別到32個(gè)基因組顯著水平SNPs以及85個(gè)建議水平SNPs,且8種性狀有基因組顯著水平的SNPs,分別是淋巴細(xì)胞數(shù)目(LYM)、淋巴細(xì)胞比率(LYMR)、嗜堿性粒細(xì)胞數(shù)目(BAS)、嗜堿性粒細(xì)胞比率(BASR)、平均紅細(xì)胞體積(MCV)、紅細(xì)胞分布寬度變異系數(shù)(RDW_CV)、平均紅細(xì)胞血紅蛋白含量(MCH)和血小板分布寬度(PDW)。在二花臉豬中共鑒別到33個(gè)基因組顯著水平SNPs以及139個(gè)建議水平SNPs,且9種性狀有基因組顯著水平的SNPs,分別是LYM、MCH、平均紅細(xì)胞血紅蛋白濃度(MCHC)、單核細(xì)胞數(shù)目(MON)、單核細(xì)胞比率(MONR)、平均血小板體積(MPV)、中性粒細(xì)胞比率(NEUR)、大血小板細(xì)胞(P_LCC)以及血小板壓積(PCT)。在萊蕪豬中共鑒別到54個(gè)基因組顯著水平SNPs以及169個(gè)建議水平SNPs,且6種性狀有基因組顯著水平的SNPs,分別是BASR、紅細(xì)胞壓積(HCT)、MCH、MCHC、MCV和紅細(xì)胞數(shù)目(RBC)。在Meta分析結(jié)果中,共鑒別到16個(gè)基因組顯著水平SNPs以及82個(gè)建議水平SNPs,且6種性狀有基因組顯著水平SNPs,分別是RBC、HCT、MCH、MCHC、MCV以及MON。通過在Ensembl或NCBI網(wǎng)站上搜尋最強(qiáng)相關(guān)SNP區(qū)域內(nèi)的候選基因,初步將F13A1、SPTA1、DBNL、SLC25A28、CTSC基因分別確定為影響B(tài)ASR、HCT、LYM、MCHC、NEUR的重要候選基因。【結(jié)論】通過全基因組關(guān)聯(lián)分析和Meta分析共得到610個(gè)顯著影響杜長大豬、二花臉豬和萊蕪豬3個(gè)群體25種血液性狀的SNP位點(diǎn),初步確定F13A1、SPTA1、DBNL、SLC25A28和CTSC基因分別是BASR、HCT、LYM、MCHC和NEUR的重要位置候選基因,為解析商業(yè)豬和純種地方豬的血液性狀或免疫性疾病提供重要參考。
[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 鹵5) days. 336 Erhualian pigs and 333 Laiwu pigs were slaughtered at (300 鹵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.
【作者單位】： 江西農(nóng)業(yè)大學(xué)省部共建豬遺傳改良與養(yǎng)殖技術(shù)國家重點(diǎn)實(shí)驗(yàn)室;
【基金】：國家“973”項(xiàng)目(2012CB722502) 甘肅省生物技術(shù)專項(xiàng)(31200926) 江西省科技支撐計(jì)劃(2009BNA06900)
【分類號(hào)】：S828

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