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西藏小型猪遗传背景分析以及分子遗传标记的研究

发布时间:2018-09-05 20:44
【摘要】: 研究背景 藏猪(Tibet hog,Sus scrofa)是世界上体型较小的小型猪之一,原产于青藏高原、海拔2500~4300m的农区和半农半牧区,分布于中国的西藏自治区、云南省、四川省和甘肃省等地。藏猪保存了较为纯正的品种资源,是唯一能够适应高海拔气候和以放牧为主的猪种。由于长期的地理隔离和环境的差异,不同地区的藏猪出现了一定程度的分化,如四川藏猪与云南藏猪相比,四川藏猪偏离Hardy-Weiberg定律的基因座数多于云南藏猪;四川藏猪体型较小,而云南减猪体型较大。目前虽然对四川藏猪或云南藏猪开展了一些研究,但对于来自西藏自治区的藏猪研究报导较少。2004年南方医科大学从西藏自治区工布江达县将50头藏猪(雌、雄各半)引种到广州,首次开展对藏猪进行实验动物化的培育,并将其命名为西藏小型猪(Tibet mini-pig)。2006底获得广东省实验用西藏小型猪生产质量合格证,目前存栏数已达600余头。 目的 测定西藏小型猪的mtDNA控制区序列和Cyt b基因序列,研究西藏小型猪mtDNA控制区和Cyt b基因序列的遗传分化,及其对血液生理生化指标的影响,并和其他猪的序列比对分析,研究其亲缘关系;探讨西藏小型猪氟烷基因座位的群体结构特征,检测氟烷基因型隐性纯合子个体,寻找西藏小型猪独特的分子遗传标记,从理论上指导西藏小型猪实验动物化的培育。 方法 1随机抽取120头西藏小型猪血液,利用试剂盒提取血液基因组DNA;设计引物扩增西藏小型猪以及7头巴马小型猪、23头贵州香猪和17头五指山猪的mtDNA控制区,测序并结合Clustalw软件和MEGA3.0软件进行所测序列多重比对,确定变异位点、单倍型,并建立西藏小型猪和国内其他猪的亲缘关系树。对其中58头8月龄的西藏小型猪分别测定血液生理生化指标。血液生理指标14项:白细胞、红细胞、血红蛋白、血小板、淋巴细胞、单核细胞、粒细胞、嗜酸性粒细胞、嗜碱性粒细胞、血细胞比容、平均红细胞体积、平均红细胞血红蛋白含量、平均红细胞血红蛋白浓度、红细胞分布宽度。血液生化指标11项:谷丙转氨酶、谷草转氨酶、谷丙转氨酶与谷草转氨酶比值、总蛋白、碱性磷酸酶、葡萄糖、尿素氮、肌酐、总胆固醇、甘油三酯、白蛋白。分类后进行指标的比较。统计学分析采用SPSS13.0版统计学软件进行两个样本的t检验,所有数据以均数±标准差((?)±SD)表示。 2以代表mtDNA控制区5′端序列单倍型的西藏小型猪和部分巴马小型猪、贵州香猪、五指山猪的全基因组DNA为研究对象,设计引物扩增四种小型猪的Cyt b基因序列,测序后利用MEGA3.0软件进行碱基序列和氨基酸序列比对,建立亲缘关系树,分析西藏小型猪的进化地位。 3应用PCR-RFLP技术,研究西藏小型猪的氟烷基因多态性。以杜洛克猪和长白猪基因组样本为对照,用特异性引物扩增3个猪种的氟烷基因片段,然后进行限制性内切酶(HhaⅠ)酶切以及酶切结果的鉴定,通过基因型辨读,获得群体的基因型频率特征数据,确定隐性纯合子基因型个体。对酶切电泳结果进行辨读时,HAL~NHAL~N基因型表现出493bp和166bp两条电泳条带,HAL~NHAL~n基因型表现出659bp、493bp和166bp三条电泳条带,HAL~nHAL~n基因型只出现659bp一条电泳条带。 结果 1前人的研究表明,猪的mtDNA控制区的串联重复区存在长度异质性(15—29个重复片段),重复片段全部是:GTACACGTGC,称之为完全重复。但是本研究显示,西藏小型猪不仅有完全重复(A型),而且有不完全的重复(B型),即一部分西藏小型猪10bp的重复片段不仅有GTACACGTGC,而且还有GTACACATGC和GTACACGTAC这两个片段及其交替排列现象。系谱分析显示,这种排列类型同样按母系遗传方式由母本传给后代,与父本没有关系。 西藏小型猪mtDNA控制区3′端侧翼区为340bp,变异位点少,与国内其他家猪的序列一样比较保守;5′端侧翼区704bp,有20个变异位点,由此归纳出26个单倍型。西藏小型猪5′端侧翼区三个转换位点(305,500,691)的变化几乎与串联重复序列所分的A、B两组类型相对应:B型中三个变异位点的碱基分别为t,a,a(100%);A型中三个变异位点的碱基分别是c,g,g的占87%,其他13%。 与西藏小型猪相比,巴马小型猪、贵州香猪和五指山猪mtDNA控制区5′端变异位点较少,分别只有4、4、3种单倍型,串联重复区也只有一种类型,A型。对西藏小型猪A型和B型群体与血液生理生化特性的进行相关分析,结果表明A型和B型群体血液红细胞数量有显著性差异(A型<B型,P<0.05)。 2利用控制区5′端侧翼区序列归纳出的单倍型建立亲缘关系树的分析表明,西藏小型猪与中国地方家猪有较近的亲缘关系,特别与中国西南地区几种家猪的亲缘关系最近。 3西藏小型猪与国内家猪的Cyt b基因序列几乎相同;与欧洲猪相比差异较大,共有16个主要变异位点,其中有两个特殊转换位点:420位点T—C转换和883位点的G—A转换,几乎各占一半。利用Mege3.0软件将碱基序列转换为氨基酸序列后的分析表明,西藏小型猪与国内其他猪有一个氨基酸位点(295位点)、与欧洲猪有三个氨基酸位点(89,295,314位点)存在着差异。在295位点,大部分A型西藏小型猪与欧洲猪同为缬氨酸(Ⅴ),而B型和少部分A型为异亮氨酸(Ⅰ)。巴马小型猪、五指山猪和贵州香猪的氨基酸序列在295位点也为异亮氨酸(Ⅰ)。结果进一步证实,西藏小型猪群体内存在分化,mtDNA控制区的序列变异与功能基因的结构变化存在一定相关性。 4 120头西藏小型猪个体氟烷基因型全部为HAL~NHAL~N,没有发现应激敏感基因,氟烷基因显性纯合子基因型:HAL~NHAL~N的频率为100%;HAL~NHAL~n型和HAL~nHAL~n型均为0。而在杜洛克猪样本中检测到4份杂合子样本,长白猪样本中检出1份杂合子个体,但都没有发现隐性纯合子个体。西藏小型猪群体内未发现应激敏感性的隐性基因,整个群体抗应激能力强。 结论 1根据西藏小型猪mtDNA控制区串联重复区的长度和重复片段存在异质性,可将西藏小型猪群体分为A型和B型。A、B类型和5′端的三个碱基转换位点:305,500,691,可以联合组建西藏小型猪的遗传标记。建议通过人工选择,A型B型分为两个群体,淘汰A型中少量变异个体(13%),强化西藏小型猪的标记,培育成两个封闭群体:B型三个转换位点分别为t,a,a;A型封闭群的三个转换位点纯化为c,g,g。 2由于西藏小型猪串联重复区的排列类型A型或B型都可以由母本传给后代,而目前所报导的国内家猪全部为A型,没有B型的报导,因此提出A型西藏小型猪和其他中国家猪有共同起源,B型可能是基因突变或者是两种母系起源的结果。 3西藏小型猪Cyt b基因的全序列有两个转换位点,与A型和B型西藏小型猪有一定对应关系。利用Mege3.0软件将碱基序列转换为氨基酸序列后的分析表明,西藏小型猪Cyt b第295位氨基酸大部分为缬氨酸(Ⅴ),而少部分为异亮氨酸(Ⅰ)。其他国内家猪的氨基酸序列全部为异亮氨酸(Ⅰ)。结果进一步证实,在西藏小型猪群体内存在分化。 4西藏小型猪群体氟烷基因,未发现应激敏感性的隐性基因,说明西藏小型猪的应激敏感性比较低,适合于开展外科手术或器官移植等实验研究。
[Abstract]:Research background
Tibet hog (Sus scrofa) is one of the * * smaller pigs in the world. It is located in the Qinghai Tibet Plateau, with an elevation of 2500 to 4300m in the agricultural area and semi agricultural and semi pastoral areas. It is distributed in Tibet autonomous region of China, Yunnan, Sichuan and Gansu provinces. * Tibetan pigs preserve relatively pure variety resources and are the only ones that can adapt to the high altitude climate. * due to long-term geographical isolation and environmental differences, Tibetan pigs in different areas have been differentiated to some extent. * * compared with Sichuan Tibetan pigs, the number of locus of Tibetan pigs deviating from Hardy-Weiberg's law is higher than that of Yunnan Tibetan pigs, while that of Sichuan Tibetan pigs is smaller than that of Yunnan Tibetan pigs. Tibetan Pig * * or Yunnan Tibetan Pig carried out some researches, but less research reports on Tibetan pigs from Tibet autonomous region *.2004 introduced 50 Tibetan pigs (female, male and half) from Tibet autonomous region to Tibet for the first time. It was the first time to carry out laboratory animal cultivation of Tibetan pigs and named it "Tibet miniature pig" (Tibet min). I-pig) at the bottom of the.2006 *, we have obtained the quality certificate for the production of Tibet miniature pigs in Guangdong province. At present, the number of livestock has reached 600.
objective
The sequence of mtDNA control region and Cyt B gene sequence of Tibet miniature pig were determined. The genetic differentiation of mtDNA control region and Cyt B gene sequence of Tibet minipigs and their effects on blood physiological and biochemical indexes were studied. The genetic relationship between them was compared with other pig sequences, and the genetic structure of halothane gene loci in Tibet miniature pigs was studied. To detect halothane genotype recessive homozygous individuals, search for unique molecular genetic markers of Tibet miniature pigs, and guide the cultivation of Tibet miniature pigs experimentally.
Method
1 randomly selected 120 Tibet miniature pig blood, extracted genomic DNA from blood by kit, designed primers to amplify the mtDNA control area of Tibet miniature pig and 7 Bama miniature pigs, 23 Guizhou Xiang Pigs and 17 Five Fingers Group pigs, sequenced and compared multiple sequences of the tested sequences with Clustalw software and MEGA3.0 software to determine the mutation sites and haplotypes. * * and establish the phylogenetic tree of Tibet miniature pig and other domestic pigs. 58 * 8 month old Tibet miniature pigs were used to measure blood physiological and biochemical indexes. Blood physiological indexes were 14 items: white blood cells, red blood cells, hemoglobin, platelets, lymphocytes, monocytes, granulocytes, eosinophils, basophils, hematocrit, and flat. BLOOD BIOCHEMICAL INDEXES 11 items: ALT, ALT, ALT/AST, ALT/AST ratio, total protein, alkaline phosphatase, glucose, urea nitrogen, creatinine, total cholesterol, triglyceride, albumin. Statistical analysis was performed with SPSS13.0 statistical software for t-test of two samples. All data were expressed as mean (?) + standard deviation ((?) + SD).
2 the genomic DNA of Tibet miniature pigs and haplotype pigs representing Guizhou * * Xiang Pigs and Five Fingers Group pigs, which represent haplotypes of the 5 * end sequence of mtDNA control area, were designed. Primers were used to amplify the Cyt B gene sequences of four miniature pigs. After sequencing, the nucleotide sequences and amino acid sequences were compared with MEGA3.0 software to establish the phylogenetic tree. * the evolution status of Tibet miniature pigs.
3 using PCR-RFLP technology, we studied the polymorphism of halothane gene in Tibet miniature pig * * *, using the genome samples of Duroc and Landrace pigs as controls, we amplified the halothane gene fragments of 3 pig breeds with specific primers, then performed restriction enzyme (Hha I) digestion and enzyme digestion results, and obtained genotype frequencies by genotype analysis. The HAL~NHAL~N genotype showed two electrophoretic bands of 493 BP and 166 bp, the HAL~NHAL~n genotype showed three electrophoretic bands of 659 bp, 493 BP and 166 bp, and the HAL~nHAL~n genotype showed only one electrophoretic band of 659 bp.
Result
1 previous studies have shown that there are length heterogeneity (15 * 29 repeats) in the tandem repeat region of mtDNA control area in pigs. All repeat fragments are GTACACGTGC, which is called complete duplication. However, this study shows that * Tibet miniature pigs not only have complete duplication (type A) but also have incomplete duplication (B *), that is, the weight of part of Tibet miniature pig 10bp. The complex fragments not only contain GTACACGTGC, but also GTACACATGC and GTACACGTAC fragments and their alternate arrangement. The pedigree analysis showed that this arrangement type was also passed from mother to offspring according to maternal inheritance, and had no relationship with father.
The 3 * end flanking area of mtDNA control area in Tibet miniature pig is 340bp, with less variation sites, and * conservative compared with other domestic pig sequences. There are 20 mutation sites in the 5 'flanking region 704bp, and 26 haplotypes are induced. * the change of three transformation sites (305500691) in 5' flanking region of Tibet miniature pigs is almost identical to that of tandem repeats. The bases of three mutation sites in type B were t, a, a (100%) and the bases of three mutation sites in type A were c, g, g (87%) and the others (13%).
Compared with Tibet * * * pigs, Bama miniature pigs, Guizhou Xiang Pigs and Five Fingers Group pigs mtDNA control area had 5 fewer variants, only 4,4,3 haplotypes. There was only one type of tandem repeat type, A type. Correlation analysis between A and B groups and blood physiological and biochemical characteristics of Tibet miniature pigs showed that A and B group blood There was a significant difference in the number of red blood cells (type A < B, P < 0.05).
2 the analysis of the phylogenetic tree based on haplotypes derived from the 5 * flank region of the control area showed that the Tibet miniature pig had a close relationship with the local pig in China, especially with the * * relationship of several pigs in Southwest China.
3 * Tibet miniature pig and domestic pig * * Cyt B gene sequence is almost the same. Compared with the European pig, there are 16 major mutation sites, including two special transformation sites: 420 locus T - C transformation and 883 - site G - A transformation, almost half. There is an amino acid locus (295 loci) in Tibet miniature pig and other pigs in China. There are three amino acid loci (89295314 loci) in European pig breeds. At the 295 locus, most A Tibet miniature pigs are valine (V) compared with European pigs, while B and A are isoleucine (I.) Bama miniature pigs, Five Fingers Group pigs and Guizhou. The amino acid sequence of Xiang pig is also isoleucine at the 295 locus. (1) it is further confirmed that there is differentiation in the Tibet miniature pig population. The sequence variation in the mtDNA control region is related to the structural change of the functional gene.
The individual halothane genotype of 4120 Tibet miniature pigs was HAL~NHAL~N. No stress sensitive genes were found. The dominant homozygote genotype of halothane gene was HAL~NHAL~N: the frequency of HAL~NHAL~N was 100%, HAL~NHAL~n and HAL~nHAL~n were 0., while 4 heterozygote samples were detected in Duroc pig samples, and 1 heterozygous individuals were detected in Landrace samples. No recessive homozygous individuals were found. * the stress sensitive recessive gene was not found in the Tibet miniature pig population, and the whole population had strong anti stress ability.
conclusion
1 * according to the heterogeneity of the tandem repeats and repetitive fragments in the mtDNA control area of Tibet mini pig, the * Tibet miniature pig population can be divided into A base and B type.A, B base type and 5 'end * three base conversion sites: 305500691, which can be combined to form the genetic markers of Tibet miniature pig. Through the artificial selection, the A type B can be divided into two groups. A small number of variant individuals in A * (13%) were strengthened, and the markers of Tibet miniature pigs were strengthened to form two closed populations. The three transformation sites of B type were t, a and a, and three transformation sites of A closed group were purified to C, G, g..
2 * the type of tandem repeats in Tibet minipigs can be passed from maternal to offspring. The reported domestic pigs are all A type. There is no report on B * *. Therefore, it is proposed that A Tibet miniature pig and other Chinese pigs have a common origin. B type may be the result of A mutation or the origin of two maternal origins.
3 * the complete sequence of Cyt B gene in Tibet miniature pig has two conversion sites, which is corresponding to A type and B * Tibet miniature pig. The analysis of the conversion of nucleotide sequence to amino acid sequence using Mege3.0 software shows that most of the 295th amino acids of Cyt * B in Tibet miniature pig are valine (V), while a few are isoleucine (I). * all the amino acid sequences of pigs were isoleucine (*). The results further confirmed that there were differentiation in the Tibet miniature pig population.
4 * the halothane gene in Tibet miniature pig population did not detect stress sensitive recessive genes. * it indicates that the sensitivity of Tibet miniature pigs is relatively low, and is suitable for experimental studies such as surgery or organ transplantation.
【学位授予单位】:南方医科大学
【学位级别】:博士
【学位授予年份】:2008
【分类号】:R-332

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