【摘要】：營養(yǎng)管理與遺傳改良的不匹配導致現代肉雞品種的遺傳潛力得不到充分發(fā)揮,限制了肉雞生產性能的提高,而營養(yǎng)表觀遺傳學為挖掘肉雞品種的遺傳潛力提供了思路。胚胎發(fā)育早期是表觀基因組重編程的關鍵時期,容易受外界環(huán)境的影響,也因此成為表觀遺傳學研究的焦點時期。由于部分營養(yǎng)物質(如維生素C)無法在蛋中積累,加上不同于哺乳動物的胚胎發(fā)育過程,使家禽胚期營養(yǎng)物質干預變得困難,而雞胚給養(yǎng)技術為以胚胎發(fā)育期為切入點的家禽營養(yǎng)表觀遺傳學研究提供了手段。本研究以維生素C為營養(yǎng)素,以雞胚給養(yǎng)為手段,在獲取雞胚DNA甲基化模式的基礎上,選擇不同的處理時間,初步探究了胚期補充維生素C調控肉雞生長和免疫的機理,同時借助二代測序技術研究了雞胚給養(yǎng)對肉雞脾臟發(fā)育的影響。試驗一雞胚發(fā)育過程中基因組DNA甲基化水平變化規(guī)律本試驗旨在優(yōu)化用于基因組DNA甲基化水平檢測的高效液相色譜法(HPLC),并探索雞胚發(fā)育過程中DNA甲基化模式。試驗首先從DNA提取、酶解體系和檢測條件三個方面對HPLC法進行了改進,然后以AA肉雞胚胎為材料,檢測了雞胚發(fā)育過程中基因組DNA甲基化水平變化規(guī)律。試驗結果顯示,雞胚發(fā)育過程中心臟、肝臟和肌肉的DNA甲基化水平均隨胚齡逐漸升高,且可劃分為三個明顯的階段:胚胎發(fā)育第2天(E2)~4,E5~13,E14~19;胚胎發(fā)育后期肝臟的DNA甲基化水平顯著高于心臟和肌肉(P0.05)。本試驗結果顯示,優(yōu)化后的HPLC法可快速、準確地測定各種組織基因組DNA甲基化水平。另外,雞胚發(fā)育過程中基因組DNA甲基化水平階段性逐漸升高。試驗二雞胚發(fā)育過程中特異基因甲基化模式本試驗旨在研究雞胚發(fā)育過程中特異基因的DNA甲基化模式。研究采用重亞硫酸鹽修飾后測序法測定了TNF-α和IGF2啟動子和基因體的DNA甲基化水平,并檢測了DNA甲基轉移酶(DNMTs)、TNF-α和IGF2在mRNA和蛋白水平的表達量。試驗結果表明:(1)肌肉和肝臟組織中,TNF-α啟動子區(qū)域的甲基化水平呈先升高后降低的變化規(guī)律,且TNF-α基因體的甲基化水平以E17顯著高于E8、E11和E14(P0.05);(2)IGF2啟動子區(qū)域甲基化水平隨胚齡逐漸降低,而基因體甲基化水平持續(xù)升高;(3)肝臟和肌肉中,TNF-α在E17的表達量均高于其它三個胚齡(P0.05),而在E8、E11和E14的表達量無差異(P0.05);(4)肝臟和肌肉中,IGF2的表達量均隨胚齡逐漸升高;(5)dnmts均隨胚齡增加呈現逐漸升高的規(guī)律。本研究結果提示,不同組織基因組dna甲基化水平與其整體的基因表達活性相關,且基因表達可能同時受到啟動子區(qū)域低甲基化與基因體高甲基化的調節(jié)。試驗三胚期第11天注射維生素c對肉雞生長性能及免疫功能的影響本試驗旨在探索胚期第11天注射維生素c對肉雞生長性能、抗氧化性能和免疫功能的影響。240枚aa肉雞種蛋隨機分為2個處理,于胚期第11天分別注射0和3mg維生素c,各處理挑選健康的出殼雛雞,隨機分為6個重復,每重復10只雞。結果表明:(1)與生理鹽水注射組相比,胚期第11天注射3mg維生素c提高了種蛋的孵化率(χ2=14.895,p0.001),肉雞21-42d和1-42d的adfi(p0.05),1-21d的adg和fcr(p0.05);(2)提高了肉雞1d血漿維生素c含量(p0.05),且有提高21d肉雞血漿維生素c含量的趨勢(p=0.060);(3)提高了35d肉雞t淋巴細胞增殖活性(p0.05),1d血漿iga和igm含量(p0.05),21d血漿溶菌酶活性(p0.05)和igm含量(p0.05);(4)提高了42d肉雞血漿的總抗氧化能力(p0.05);(5)提高了21d肉雞十二指腸的隱窩深度和絨毛高度/隱窩深度(p0.05),及42d肉雞回腸的絨毛高度/隱窩深度(p0.05);(6)提高了21d肉雞脾臟il-4、gcn5、dnmt1和dnmt3a的mrna表達量(p0.05),同時降低了il-1β、tet2、tet3和gadd45β的mrna表達量(p0.05);(7)提高了42d肉雞脾臟il-4、gcn5、tip60、dnmt3a和gadd45α的mrna表達量(p0.05),降低了ifn-γ、tet3、mbd4和tdg的mrna表達量(p0.05),同時有降低svct1和svct2mrna表達量的趨勢(p=0.065,p=0.095)。本研究結果提示,胚期第11天注射3mg維生素c提高了種蛋的孵化率,在一定程度上改善了肉雞的生產性能,抗氧化能力,免疫功能和腸道形態(tài),且免疫功能的提高可能與dna甲基化和組蛋白乙�；降奶岣哂嘘P。試驗四胚期第15天注射維生素c對肉雞生長性能及免疫功能的影響本試驗旨在探索胚期第15天注射維生素c對肉雞生長性能、抗氧化性能和免疫功能的影響。240枚aa肉雞種蛋隨機分為2個處理,于胚期第15天分別注射0和3mg維生素c,各處理挑選健康的出殼雛雞,隨機分為6個重復,每重復10只雞。結果表明:(1)與生理鹽水注射組相比,胚期第15天注射3mg維生素c提高了種蛋的孵化率(χ2=4.219,p=0.040);(2)提高了1和42d肉雞的胸腺指數(p0.05);(3)提高1d肉雞血漿igm含量(p0.05),21d血漿溶菌酶活性(p0.05),及igg和igm含量(p0.05);(4)提高了42d肉雞血漿的總抗氧化能力(p0.05);(5)提高了21d肉雞十二指腸的隱窩深度(p0.05),降低了回腸的絨毛高度/隱窩深度(p0.05),提高了42d肉雞十二指腸的絨毛高度和絨毛高度/隱窩深度(p0.05);(6)提高了21d肉雞脾臟dnmt1的mrna表達量(p0.05),同時降低了il-6、ifn-γ、tet1和tdg的mrna表達量(p0.05);(7)提高了42d肉雞脾臟gcn5、dnmt1、dnmt3b和gadd45β的mrna表達量(p0.05),同時降低了il-6、tnf-α和mbd4的mrna表達量(p0.05)。本研究結果提示,胚期第15天注射3mg維生素c提高了種蛋的孵化率,在一定程度上改善了肉雞的抗氧化能力,免疫功能和腸道形態(tài),且免疫性能的提高可能與dna甲基化和組蛋白乙酰水平的提高有關。試驗五胚期注射維生素c調控肉雞脾臟發(fā)育的轉錄組分析本試驗旨在借助轉錄組測序(rna-seq)揭示胚期注射維生素c調控雞胚脾臟發(fā)育的差異表達基因及相關調控通路。120枚aa肉雞種蛋隨機分為2個處理,于胚期第11天分別注射0和3mg維生素c。胚期第19天,每處理選取發(fā)育良好的種蛋15枚,完整取脾臟,混合后提取rna進行轉錄組測序。測序結果顯示,處理組與對照組共得到12gb有效且高質量的數據,與參考基因組的比對效率分別達到90.76%和91.41%。差異表達分析共發(fā)現184個差異表達基因,其中117個表達上調,67個表達下調。go和kegg等生物信息學分析表明,差異表達基因涉及免疫調節(jié)、胚胎發(fā)育、組蛋白修飾和繁殖等生物過程。本研究結果提示,以雞胚給養(yǎng)為手段施加胚期維生素c干預可影響胚胎發(fā)育、免疫調節(jié)和表觀遺傳學修飾等生物過程。試驗六胚期注射維生素c調控肉雞脾臟發(fā)育的全基因組甲基化分析本試驗旨在借助全基因組甲基化測序(wgbs)揭示胚期注射維生素c調控雞胚脾臟發(fā)育的差異甲基化基因及相關調控通路。120枚aa肉雞種蛋隨機分為2個處理,于胚期第11天分別注射0和3mg維生素c。胚期第19天,每處理選取發(fā)育良好的種蛋15枚,完整取脾臟,混合后提取dna進行全基因組甲基化測序。測序結果顯示,對照組與處理組共得到98gb有效且高質量的數據,平均測序深度32x。甲基化分析發(fā)現,胚期注射維生素c改變了脾臟組織的甲基化模式,且其去甲基化作用主要體現在chg和chh位點及基因的蛋白質編碼區(qū)。生物信息學分析共得到5514個差異甲基化基因,涉及免疫調節(jié)、胚胎發(fā)育、表觀遺傳學修飾、繁殖和氧化還原等生物過程。本研究結果提示,胚期補充維生素c改變了參與胚胎發(fā)育、免疫調節(jié)和表觀遺傳學修飾等生物過程相關基因的甲基化狀態(tài)。另外,研究揭示了雞胚脾臟全基因組甲基化圖譜,為后續(xù)相關研究奠定了基礎。試驗七胚期注射維生素c調控肉雞脾臟發(fā)育的rna-seq與wgbs組合分析本試驗旨在將rna-seq數據與wgbs數據進行組合分析,找出共有差異基因,并進行相關功能分析。組合分析共發(fā)現59個差異甲基化且差異表達基因,其中處理組相比對照組的去甲基化率為98.3%,涉及胚胎發(fā)育、免疫功能和表觀遺傳學修飾,表明胚期注射維生素c通過廣泛的去甲基化作用參與調控胚胎發(fā)育、免疫功能和表觀遺傳學修飾等生物過程。本研究結果揭示了胚期維生素c干預下dna甲基化與基因表達的關系,為維生素C參與調控的DNA甲基化模式研究提供了參考。另外,研究發(fā)現維生素C在動物(肉雞)體內同樣可發(fā)揮廣泛的去甲基化作用,并調控基因表達,且基因體的去甲基化既可調控基因表達上調,也可調控基因表達下調。本研究表明,雞胚給養(yǎng)維生素C可通過廣泛的去甲基化作用調控脾臟發(fā)育,且可提高飼養(yǎng)階段肉雞的生產性能和免疫功能。
[Abstract]:The mismatch between nutritional management and genetic improvement results in the inadequate utilization of genetic potential of modern broiler breeds, which limits the improvement of broiler performance. Nutritional epigenetics provides a way to tap the genetic potential of broiler breeds. Because some nutrients (such as vitamin C) can not be accumulated in eggs and the embryonic development process is different from that of mammals, it is difficult to interfere with nutrients in the embryonic stage of poultry. Vitamin C was used as nutrient and chicken embryo as feeding medium. On the basis of acquiring DNA methylation pattern of chicken embryo and choosing different treatment time, the mechanism of vitamin C supplementation in embryo regulating growth and immunity of broiler chickens was preliminarily explored. At the same time, the effect of chicken embryo feeding on spleen hair of broiler chickens was studied by second-generation sequencing technique. The purpose of this experiment is to optimize the high performance liquid chromatography (HPLC) for the detection of genomic DNA methylation level and to explore the DNA methylation pattern during chicken embryo development. The results showed that the DNA methylation levels in heart, liver and muscle of AA broiler embryos increased gradually with the embryonic age and could be divided into three distinct stages: the second day (E2) ~ 4, E5 ~ 13, E14 ~ 19 of embryonic development. The results showed that the optimized HPLC method could rapidly and accurately determine the DNA methylation level of various tissues. In addition, the DNA methylation level of chicken embryos increased gradually during the development of chicken embryos. The aim of this study was to investigate the DNA methylation patterns of specific genes during chicken embryo development. The DNA methylation levels of TNF-a and IGF2 promoters and gene bodies were determined by bisulfite Modified Sequencing method, and the expression levels of DNA methyltransferase (DNMTs), TNF-a and IGF2 at mRNA and protein levels were detected. The results showed that: (1) the methylation level of TNF-a promoter region increased first and then decreased in muscle and liver tissues, and the methylation level of TNF-a gene was significantly higher in E17 than in E8, E1 1 and E14 (P 0.05); (2) the methylation level of IGF2 promoter region decreased gradually with embryonic age, while the methylation level of gene body continued to increase; (3) liver In the viscera and muscle, the expression of TNF-alpha in E17 was higher than that in the other three embryonic ages (P 0.05), but there was no difference in the expression of E8, E11 and E1 4 (P 0.05); (4) The expression of IGF2 in liver and muscle increased gradually with the embryonic age; (5) The expression of DNMTs increased gradually with the embryonic age. The effect of vitamin C injection on growth performance and immune function of broilers at the 11th day of triembryonic stage was studied in order to explore the effect of vitamin C injection on growth performance and anti-hypermethylation of broilers at the 11th day of embryonic stage. 240 AA broiler eggs were randomly divided into two treatments. On the 11th day of embryo, 0 and 3 mg vitamin C were injected. Healthy chickens were randomly divided into 6 replicates, 10 chickens per replicate. Eggs hatching rate (_2 = 14.895, p0.001), broiler 21-42 days and 1-42 days ADFI (p0.05), 1-21 days ADG and FCR (p0.05); (2) increased the 1-day plasma vitamin C content (p0.05), and increased the 21-day plasma vitamin C content of broiler (p = 0.060); (3) increased the 35-day broiler T lymphocyte proliferation activity (p0.05), 1-day plasma IgA and IgM content (p0.05), 21-day blood plasma vitamin C content (p0.05), 21-day blood vitamin C content (p0.05). Plasma lysozyme activity (p0.05) and IgM content (p0.05); (4) increased plasma total antioxidant capacity (p0.05); (5) increased the duodenal recess depth and villus height / recess depth (p0.05), and villus height / recess depth of ileum (p0.05); (6) increased spleen il-4, gcn5, DNMT1 and Dnmt3a mRNA in 21 d broilers (p0.05). The expression of IL-1 beta, tet-2, tet-3 and gadd-45 beta was decreased (p 0.05); (7) the expression of il-4, gcn-5, tip-60, dnmt-3a and gadd-45a in spleen was increased (p 0.05), and the expression of ifn-gamma, tet-3, mbd-4 and TDG was decreased (p 0.05), and the expression of svct 1 and SVCT2 mRNA was decreased (p = 0.065, P = 0.095). The results suggested that 3 mg vitamin C Injection on the 11th day of embryo increased hatchability of broiler eggs, improved production performance, antioxidant capacity, immune function and intestinal morphology to a certain extent, and the improvement of immune function might be related to the increase of DNA methylation and histone acetylation level. Effects of vitamin C Injection on growth performance, antioxidant capacity and immune function of broilers were studied. 240 AA broiler eggs were randomly divided into two treatments. On the 15th day of embryo, 0 and 3 mg vitamin C were injected into broilers. Healthy shelled chickens were selected and randomly divided into 6 treatments. The results showed that: (1) compared with saline injection group, 3 mg vitamin C Injection on the 15th day of embryonic stage increased hatching rate of eggs (_2 = 4.219, P = 0.040); (2) increased thymus index (p0.05); (3) increased plasma IgM content (p0.05), plasma lysozyme activity (p0.05) and IgG and IgM content (p0.05); (2) increased thymus index (p0.05) increased 1 and 42 days of Broilers (p0.05). 4) increased the total antioxidant capacity of plasma (p0.05); (5) increased the depth of duodenal recess (p0.05), decreased the villus height / recess depth of ileum (p0.05), increased the villus height and villus height / recess depth of duodenum (p0.05); (6) increased the expression of DNMT1 mRNA in spleen (p0.05) of 21-day broilers. At the same time, the expression of il-6, ifn-gamma, tet-1 and TDG mRNA was decreased (p0.05); (7) the expression of gcn-5, dnmt-1, dnmt-3b and gadd-45 beta in spleen of 42-day broilers was increased (p0.05), and the expression of il-6, TNF-a and mbd-4 mRNA was decreased (p0.05). The results showed that the antioxidant capacity, immune function and intestinal morphology of broilers were improved, and the improvement of immune function might be related to the increase of DNA methylation and histone acetyl level. 120 AA broiler eggs were randomly divided into two treatments. On the 11th day of embryonic stage, 0 and 3 mg vitamin C were injected into the eggs. On the 19th day of embryonic stage, 15 well-developed eggs were selected for each treatment. The whole spleen was harvested and the RNA was extracted after mixing and sequenced. A total of 184 differentially expressed genes were found, of which 117 were up-regulated and 67 were down-regulated. Bioinformatics analysis such as go and KEGG showed that the differentially expressed genes involved in immune regulation, embryonic development, and egg formation. The results of this study suggest that embryonic vitamin C intervention may affect embryonic development, immune regulation and epigenetic modification by feeding chicken embryos. The whole genome methylation analysis of spleen development regulated by vitamin C injection at six embryonic stages was carried out. Group methylation sequencing (wgbs) revealed differential methylation genes and related regulatory pathways in spleen development of embryonic chicken embryos regulated by vitamin C injection. 120 AA broiler eggs were randomly divided into two treatments, 0 and 3 mg vitamin C were injected on the 11th day of embryonic development and 15 eggs were selected from each treatment on the 19th day of embryonic development. DNA was taken for whole genome methylation and sequencing. The results showed that 98 GB effective and high quality data were obtained in the control group and the treatment group. The average sequencing depth was 32 X. Methylation analysis showed that vitamin C injection during embryonic period changed the methylation pattern of spleen tissue, and its demethylation effect was mainly reflected in the CHG and CHH sites and gene protein. 5 514 differentially methylated genes were identified by bioinformatics analysis, involving biological processes such as immune regulation, embryonic development, epigenetic modification, reproduction and redox. In addition, the whole genome methylation map of chicken embryo spleen was revealed, which laid the foundation for the follow-up study. In the experiment, the combination analysis of RNA-seq and wgbs by vitamin C injection during the seven embryonic stages was carried out. The purpose of this experiment was to combine the RNA-seq data with wgbs data, find out the common differentially expressed genes and carry out the analysis. A total of 59 differentially methylated and differentially expressed genes were identified by combinatorial analysis. The demethylation rate of the treated group was 98.3% compared with the control group, which involved embryonic development, immune function and epigenetic modification. The results showed that vitamin C injection during embryonic stage participated in embryonic development, immune function and table regulation through extensive demethylation. This study revealed the relationship between DNA methylation and gene expression under the intervention of vitamin C during embryonic stage, and provided a reference for the study of DNA methylation patterns regulated by vitamin C. In addition, it was found that vitamin C could also play an extensive demethylation role in animals (broilers) and regulate genes. The results showed that vitamin C from chicken embryo could regulate the spleen development through extensive demethylation and improve the production performance and immune function of broilers in feeding stage.
【學位授予單位】：西北農林科技大學
【學位級別】：博士
【學位授予年份】：2017
【分類號】：S831

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