甘肃不同地区绵羊TLR9基因多态性分析

针对由于急、慢性呼吸道引起的生产性能降低甚至死亡,选择与该病相关的基因TLR9为研究对象,分析群体中该基因的遗传多态性及变异特征,为进一步揭示舍饲绵羊的遗传特性和生产利用提供基础数据。采用PCR-SSCP检测427只表型正常和58只患呼吸道疾病的舍饲绵羊TLR9基因的多态性,测序群体内变异的各等位基因数列,并构建系统发育树以明确舍饲绵羊TLR9基因等位基因之间的遗传关系。结果显示,甘肃地区绵羊在TLR9基因中发现了4个等位基因,共7个核苷酸多态位点,这些位点多是由点突变形成,其中转换4个(占57.14%),颠换3个(占42.86%)。甘肃地区绵羊TLR9基因具有较丰富的多态性;TLR9基因多态性与绵羊呼吸道疾病有一定的相关性。     

贵州黑山羊和黔北麻羊LEPR基因第7、8、10和18外显子的多态性分析

为探究LEPR基因的遗传多态性,丰富山羊LEPR基因的研究,本研究以贵州黑山羊和黔北麻羊为试验材料,运用DNA池结合直接测序方法进行LEPR基因SNPs位点的筛选,从而对突变的SNPs位点进行RNA二级结构以及所编码蛋白质的二级结构和三级结构进行生物信息学分析。在试羊LEPR基因中共发现4个SNPs,分别为Exon7-T81C(同义突变)、Exon8-C39T(同义突变)、Exon10-A70G(Asn-Ser)和Exon18-C94T(Ser-Leu)。分析表明,4个位点突变前后的等位基因频率、mRNA二级结构的最小自由能、LEPR蛋白质二级结构和三级结构均有改变。结果表明,LEPR基因拥有较为丰富的遗传多态性。     

新疆维吾尔族人群过氧化物酶体增殖物激活受体基因相关SNP位点的多态性

对过氧化物酶体增殖物激活受体基因(PPARG)的31个SNP位点进行群体遗传学分析,利用质谱检测技术检测PPARG基因的31个SNPs位点多态性,并根据质谱峰图判读样本目标位点基因型,统计分析31个SNP位点的基因型和等位基因的分布频率,利用x2检验确定筛选的SNP位点是否符合Hardy-Weinberg平衡定律。结果发现31个SNP位点中,23个位点的次等位基因分布频率MAF≥0.05,在新疆维吾尔族人群中具有多态性,其他8个SNP位点的MAF0.05,没显示多态性。基因型和等位基因频率在男女两组间均无统计学差异(P0.05),表明这些位点等位基因分布不存在性别差异。     

本土绵羊品种GH与IGF-1基因多态性分析

生长性状是绵羊育种中关注的重要性状.GH和IGF-1基因已被证明是影响动物生长发育的重要候选基因.因此,了解中国本土绵羊GH和IGF-1基因的遗传多样性,将为提高本土绵羊的生产效率、制定遗传育种和品种改良措施奠定基础.本研究以本土绵羊品种呼伦贝尔羊、藏羊、湖羊、阿勒泰羊、小尾寒羊和滩羊为主要研究对象,以澳白羊为参考,通过Sanger测序检测了340只绵羊GH和IGF-1外显子单核苷酸多态性.研究发现,GH和IGF-1基因外显子区分别检测到11个和3个SNPs,呈品种特异性分布,在群体中处于低度至中度多态.连锁不平衡分析发现,GH基因的SNP1、SNP3、SNP6、SNP7和SNP8呈强连锁不平衡,构建的7种单倍型中,CGACAG是优势单倍型(52.6％),而IGF-1基因的3个SNPs之间连锁关系很弱.生物信息学分析发现,检测到的14个SNPs中GH的SNP2、SNP4、SNP8和IGF-1的SNP1、SNP3为新发现的多态位点,其中SNP4和SNP9为错义突变,可能会导致编码蛋白质二级结构与三级结构发生改变.研究结果表明,与其他本土品种和澳白羊相比,湖羊的GH和IGF-1基因具有较为丰富的遗传变异.已有研究证实GH的SNP6和SNP9以及IGF-1的SNP2不同基因型与绵羊的生长和胴体性状相关联,且在本土品种中均有多态,推测GH基因的SNP6、SNP9和IGF-1基因的SNP2可作为本土绵羊生长性状分子标记辅助选择的候选SNPs.     

云南乌骨绵羊乌质性状与TYR基因多态性的相关分析

乌骨乌肉是乌骨绵羊的主要乌质性状。本文测定了乌骨绵羊、兰坪本地羊和罗姆尼羊血液TYR活性并分析了乌骨绵羊与乌骨鸡组织器官黑色素结构,结果表明：乌骨绵羊TYR活性显著高于兰坪本地绵羊和罗姆尼羊（P<0.05）;乌骨绵羊黑色素与乌骨鸡黑色素的IR光谱基本一致,黑色物质主要是真黑色素。首次克隆了绵羊TYR基因第一外显子长667 bp序列,并检测了乌骨绵羊和非乌骨绵羊TYR基因多态性。结果发现,检测的乌骨绵羊TYR基因第一外显子有两个变异位点,分别位于第64和154号编码氨基酸上,但都属于同义突变。通过对64号位置设计酶切位点检测TYR基因多态性,结果发现,该突变与乌质性状有关基因紧密连锁,TYR基因上可能存在乌质性状相关功能突变位点。另外,TYR基因多态性与毛色的表型相关极显著（P<0.01）,该基因可能也是毛色功能基因。     

小尾寒羊高繁殖力候选基因BMP15和GDF 9的研究

以控制Belclare和Cambridge绵羊高繁殖力的骨形态发生蛋白 15 (bonemorphogeneticprotein 15 ,BMP15 )基因和生长分化因子 9(growthdifferentiationfactor 9,GDF9)基因为候选基因 ,采用PCR RFLP技术检测BMP15基因和GDF9基因在高繁殖力绵羊品种 (小尾寒羊、湖羊 )以及低繁殖力绵羊品种 (多赛特羊、特克塞尔羊、德国肉用美利奴羊 )中的单核苷酸多态性 ,同时研究这两个基因对小尾寒羊高繁殖力的影响。结果表明 :在 5个绵羊品种中都没有检测到GDF9基因的G8突变 (C→T) ,也没有检测到BMP15基因的B4突变 (G→T)。高繁殖力的小尾寒羊在BMP15基因编码序列第 718位碱基处发生了与Belclare绵羊和Cambridge绵羊相同的B2突变 (C→T) ,而其余 4个绵羊品种则没有发生这种突变。对于BMP15基因的B2突变 ,在小尾寒羊中检测到AA、AB两种基因型 ,A等位基因频率为 0 734,B等位基因频率为 0 2 6 6。小尾寒羊与其余 4个绵羊品种间B2突变基因型分布差异极显著 (P <0 0 0 1)。突变杂合基因型 (AB)小尾寒羊平均产羔数比野生纯合基因型 (AA)多 0 6 2只 (P <0 0 1)。研究结果表明 ,BMP15B2突变对小尾寒羊高繁殖力影响作用十分明显 ,同时排除了GDF9G8突变和BMP15B4突变影响小尾寒羊高繁殖力的可能性     

绵羊GDF9基因PCR-SSCP分析

生长分化因子9（GDF9）是由卵母细胞分泌的一种生长因子,它对早期卵泡的生长和分化起重要的调节作用。采用PCR－SSCP技术分析了GDF9基因在小尾寒羊、湖羊、多赛特羊和萨福克羊4个绵羊品种的多态性。结果表明：GDF9基因在两对引物扩增片段中均存在PCR－SSCP多态性。对于引物1扩增片段,4个绵羊品种均检测到AA基因型,AB基因型只出现在湖羊、多赛特羊和萨福克羊中,仅在萨福克羊中检测到BB基因型;在4个绵羊品种中,A等位基因频率明显高于B等位基因频率。对于引物2扩增片段,4个绵羊品种均检测到AA基因型,AB基因型只出现在湖羊、多赛特羊和萨福克羊中,4个绵羊品种均没有检测到BB基因型;在4个绵羊品种中,AA基因型频率最高,A等位基因频率明显高于B等位基因频率。引物1的多态性片段测序分析表明：位于GDF9基因cDNA第152处发生了单碱基的改变（A→G）,并导致了氨基酸的改变（天冬酰胺→天冬氨酸）。     

贵州白山羊和贵州黑山羊DRB1基因第3外显子遗传变异分析

为研究贵州黑山羊、贵州白山羊MHC-DRB1基因遗传机制,试验运用混合DNA池结合PCR产物直接测序方法,对MHC-DRB1基因第三外显子区域进行多态性分析,利用生物信息学分析软件对PCR扩增所获序列进行m RNA二级结构及蛋白质的二级结构和抗原表位分析。经序列对比发现9个SNPs位点,其中A~(8858)G(ILe-Val)、G~(8969)A(Gly-Ser)、G~(8978)A(Glu-Lys)、T~(9094)G(Asp-Glu)4个单核苷酸突变,导致所编码氨基酸发生改变,其它5个位点均属于同义突变。进一步分析发现,A~(8858)G、C~(8974)T、T~(9094)G、C~(9100)T、G~(9124)A突变位点导致m RNA二级结构的变化,A~(8858)G以及T~(9094)G对蛋白质二级结构影响最大。     

优良的BMPR-IB基因型可提高绵羊冷冻胚胎的受胎效果

以控制BooroolaMerino羊高繁殖力的BMPR-IB基因为候选基因,以小尾寒羊及其杂交羊、东北半细毛羊、澳洲美利奴羊、德国肉用美利奴羊、萨福克羊、特克塞尔羊、夏洛莱羊为试验对象,采用PCR-限制性片段长度多态性(PCR-RFLP)方法进行基因单核苷酸多态性(SNP)检测和基因型分析,同时研究基因对高繁殖力的影响.研究结果表明:小尾寒羊及其杂交羊、东北半细毛羊和夏洛莱羊群体中发现了与BooroolaMerino羊相同的A746G碱基突变,而小尾寒羊及其杂交羊群体的B等位基因频率明显高于其他2个品种.另外4个品种中未发现此突变.携带B等位基因的群体较非携带B等位基因群体排出更多的卵子,排卵后黄体直径较小.移植入冷冻胚胎后, 、B 和BB3种基因型群体的妊娠率分别为38.78%、45.71%和66.67%.由此推断,BMPR-IB基因突变很有可能从增加卵巢排卵数和提高胚胎着床及妊娠建立效率两个方面同时影响绵羊高繁殖力性状.所得BB型群体冻胚移植妊娠率明显高于 和B 型群体,已接近鲜胚移植水平,通过PCR-RFLP方法进行基因型分析,选用合适基因型群体作为胚胎移植受体,有可能为提高绵羊胚胎移植受胎率提供新的方向.     

猪TLR4基因外显子1新等位基因的分离及遗传变异分析

文章采用PCR-SSCP方法对亚洲野猪、3个引进的商业化品种和10个中国地方猪品种共893个个体TLR4基因外显子1的遗传变异进行了检测,旨在系统分析国内外猪种TLR4基因的多态性,为探讨该基因在免疫和防御系统中发挥的作用提供依据。结果,在猪TLR4基因外显子1中分离到新的等位基因,共检测到3个等位基因,6种基因型。其中杜洛克检测到AA、BB、CC、AB、AC、BC基因型,有杜洛克血统的苏太猪中检测到BB、CC、BC基因型,长白猪、约克夏中检测到CC、BC基因型,野猪及所有10个中国地方猪品种TLR4基因外显子1高度保守,只检测到CC基因型,中国地方猪品种和引进品种TLR4基因外显子1多态性存在极显著的差异。3种基因型中CC型与GenBank中的序列一致,BB和AA基因型分别存在G93C同义突变位点和G194A无义突变位点,这2个变异位点与抗逆性和一般抗病力的关系值得进一步深入研究。     

Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken

Background

Toll like receptors (TLR) play the central role in the recognition of pathogen associated molecular patterns (PAMPs). Mutations in the TLR1, TLR2 and TLR4 genes may change the ability to recognize PAMPs and cause altered responsiveness to the bacterial pathogens.

Results

The study presents association between TLR gene mutations and increased susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP) infection. Novel mutations in TLR genes (TLR1- Ser150Gly and Val220Met; TLR2 – Phe670Leu) were statistically correlated with the hindrance in recognition of MAP legends. This correlation was confirmed subsequently by measuring the expression levels of cytokines (IL-4, IL-8, IL-10, IL-12 and IFN-γ) in the mutant and wild type moDCs (mocyte derived dendritic cells) after challenge with MAP cell lysate or LPS. Further in silico analysis of the TLR1 and TLR4 ectodomains (ECD) revealed the polymorphic nature of the central ECD and irregularities in the central LRR (leucine rich repeat) motifs.

Conclusion

The most critical positions that may alter the pathogen recognition ability of TLR were: the 9^th amino acid position in LRR motif (TLR1–LRR10) and 4^th residue downstream to LRR domain (exta-LRR region of TLR4). The study describes novel mutations in the TLRs and presents their association with the MAP infection.     

The maintenance of extreme amino acid diversity at the disease resistance gene, RPP13, in Arabidopsis thaliana

We have used the naturally occurring plant-parasite system of Arabidopsis thaliana and its common parasite Peronospora parasitica (downy mildew) to study the evolution of resistance specificity in the host population. DNA sequence of the resistance gene, RPP13, from 24 accessions, including 20 from the United Kingdom, revealed amino acid sequence diversity higher than that of any protein coding gene reported so far in A. thaliana. A significant excess of amino acid polymorphism segregating within this species is localized within the leucine-rich repeat (LRR) domain of RPP13. These results indicate that single alleles of the gene have not swept through the population, but instead, a diverse collection of alleles have been maintained. Transgenic complementation experiments demonstrate functional differences among alleles in their resistance to various pathogen isolates, suggesting that the extreme amino acid polymorphism in RPP13 is maintained through continual reciprocal selection between host and pathogen.     

TLR4 and TLR8 variability in Amazonian and West Indian manatee species from Brazil

Amazonian (Trichechus inunguis) and West Indian (Trichechus manatus) manatees are aquatic mammals vulnerable to extinction found in the Amazon basin and the coastal western Atlantic. Toll-like receptors (TLR) play a key role in recognizing pathogen-associated molecular patterns using leucine-rich repeats (LRRs). We described the diversity of TLR4 and TLR8 genes in these two species of manatee. Amazonian manatee showed seven SNPs in TLR4 and the eight in TLR8, while West Indian manatee shared four and six of those SNPs, respectively. In our analysis, TLR4 showed one non-conservative amino acid replacement substitution in LRR7 and LRR8, on the other hand, TLR8 was less variable and showed only conserved amino acid substitutions. Selection analysis showed that only one TLR4 site was subjected to positive selection and none in TLR8. TLR4 in manatees did not show any evidence of convergent evolution compared to species of the cetacean lineage. Differences in TLR4 and TLR8 polymorphism may be related to distinct selection by pathogens, population reduction of West Indian manatees, or an expected consequence of population expansion in Amazonian manatees. Future studies combining pathogen association and TLR polymorphism may clarify possible roles of these genes and be used for conservation purposes of manatee species.     

Positive selection signatures in the TLR7 family

While adaptive immunity genes evolve rapidly under the influence of positive selection, innate immune system genes are known to evolve slowly due to strong purifying selection. Among the sensors of the innate immune system, Toll-like receptors (TLRs) are particularly important due to their ability to recognize and respond to pathogen-associated molecular patterns (PAMP), such as lipopolysaccharides, peptidoglycans, and nucleic acids from bacteria or viruses. In the present study, we examine the evolutionary process that has operated on the TLR7 family genes TLR7, TLR8, and TLR9. The results demonstrate that the average Ka/Ks (the ratio between nonsynonymous and synonymous substitution rates) of each TLR family gene is far lower than one regardless of estimating methods, supporting previous observations of strong purifying selection in this gene family. Interestingly, however, analysis of Ka/Ks ratios along the coding regions of TLR7 family genes by sliding-window analysis reveals a few narrow high peaks (Ka/Ks > 1). The most prominent peak corresponds to a specific region in the ectodomain, which exists only in the TLR7 family, suggesting that this unique structure of the TLR7 family might have been a target of positive selection in a variety of lineages. Furthermore, maximum likelihood model tests suggest that positive selection is the best explanation for a certain fraction of the amino acid substitutions in the TLR9.     

Molecular analysis of mutations in a patient with purine nucleoside phosphorylase deficiency.

Purine nucleoside phosphorylase (PNP) deficiency is an inherited autosomal recessive disorder resulting in severe combined immunodeficiency. The purpose of this study was to determine the molecular defects responsible for PNP deficiency in one such patient. The patient's PNP cDNA was amplified by PCR and sequenced. Point mutations leading to amino acid substitutions were found in both alleles. One point mutation led to a Ser-to-Gly substitution at amino acid 51 and was common to both alleles. In addition, an Asp-to-Gly substitution at amino acid 128 and an Arg-to-Pro substitution at amino acid 234 were found in the maternal and paternal alleles, respectively. In order to prove that these mutations were responsible for the disease state, each of the three mutations was constructed separately by site-directed mutagenesis of the normal PNP cDNA, and each was transiently expressed in COS cells. Lysates from cells transfected with the allele carrying the substitution at amino acid 51 retained both function and immunoreactivity. Lysates from cells transfected with PNP alleles carrying a substitution at either amino acid 128 or amino acid 234 contained immunoreactive material but had no detectable human PNP activity. In summary, molecular analysis of this patient identified point mutations within the PNP gene which are responsible for the enzyme deficiency.     

Molecular evolution of vertebrate Toll-like receptors: evolutionary rate difference between their leucine-rich repeats and their TIR domains

Toll-like receptors (TLRs) that initiate an innate immune response contain an extracellular leucine rich repeat (LRR) domain and an intracellular Toll IL-receptor (TIR) domain. There are fifteen different TLRs in vertebrates. The LRR domains, which adopt a solenoid structure, usually have higher rates of evolution than do the TIR globular domains. It is important to understand the molecular evolution and functional roles of TLRs from this standpoint. Both pairwise genetic distances and Ka/Ks's (the ratios between non synonymous and synonymous substitution rates) were compared between the LRR domain and the TIR domain of 366 vertebrate TLRs from 96 species (from fish to primates). In fourteen members (TLRs 1, 2, 3, 4, 5, 6, 7, 8, 9, 11/12, 13, 14, 21, and 22/23) the LRR domains evolved significantly more rapidly than did the corresponding TIR domains. The evolutionary rates of the LRR domains are significantly different among these members; LRR domains from TLR3 and TLR7 from primates to fishes have the lowest rate of evolution. In contrast, the fifteenth member, TLR10, shows no significant differences; its TIR domain is not highly conserved. The present results suggest that TLR10 may have a different function in signaling from those other members and that a higher conservation of TLR3 and TLR7 may reflect a more ancient mechanism and/or structure in the innate immune response system. Gene conversions are suggested to have occurred in platypus TLR6 and TLR10. This study provides new insight about structural and functional diversification of vertebrate TLRs.     

高山美利奴羊INHA基因多态性生物信息学分析及与产羔数关联分析

本研究旨在研究高山美利奴羊INHA基因外显子多态性及其与产羔数的相关性。本实验通过比对高山美利奴羊全基因组测序结果中不同个体INHA外显子,分析高山美利奴羊INHA基因的单核苷酸多态性,应用生物信息学软件分析高山美利奴羊INHA基因突变前后不同等位基因的m RNA二级结构、蛋白质的二级结构及三级结构。通过上述分析,将引起高山美利奴羊INHA编码氨基酸变化的位点作为该基因的特异性候选位点,通过直接测序法分析高山美利奴羊特异性候选位点INHA基因多态性,并分析其与产羔数的相关性。结果发现,高山美利奴羊INHA基因外显子区域存在3个SNPs,分别为T206A (Met→Lys)、T387A(Thr→Thr)、G900A (Pro→Pro);INHA基因3个SNPS都改变了RNA的最小自由能以及二级结构,错义突变T206A (Met→Lys)引起蛋白质二级结构和三级结构的改变;高山美利奴羊INHA基因T206A突变表现出3种基因型分别命名为TT、TA、AA,基因型与产羔数关联分析发现TT、TA基因型个体的产羔数极显著高于TT基因型个体(p<0.01)。本研究初步表明INHA基因是影响高山美利奴羊产羔数的一个主效基因。     

陕北白绒山羊DRB1基因外显子2遗传变异分析

本研究通过对123只陕北白绒山羊DRB1基因外显子2的遗传变异分析,旨在获得陕北白绒山羊DRB1基因的多态性及变异信息,为山羊抗病基因的挖掘研究提供基础资料。本研究共获得6条陕北白绒山羊DRB1基因外显子2序列,其中4条为首次发现。生物信息学分析表明DRB1位点具有较高的多态性,6条等位基因可能起源于2个祖先基因。在长期的进化过程中,DRB1位点受到了明显的选择压力作用,这种选择作用有助于陕北白绒山羊对当地气候的适应。蛋白质结构的预测证实了DRB1*1与其它等位基因间的差异性,说明核苷酸变异可能会引起蛋白质结构的改变,最终可能影响宿主对病原体的免疫应答。本次对陕北白绒山羊DRB1基因多态性的调查与分析有助于筛选疾病抗性和易感性MHC (Major histocompatibility complex)候选基因,进而可加速绒山羊抗病品系的改良与培育进程。     

RPP13 is a simple locus in Arabidopsis thaliana for alleles that specify downy mildew resistance to different avirulence determinants in Peronospora parasitica

Disease resistance (R) genes are found in plants as either simple (single allelic series) loci, or more frequently as complex loci of tandemly repeated genes. These different loci are likely to be under similar evolutionary forces from pathogens, but the contrast between them suggests important differences in mechanisms associated with DNA structure and recombination that generate and maintain R gene diversity. The RPP13 locus in Arabidopsis represents an important paradigm for studying the evolution of an R gene at a simple locus. The RPP13 allele from the accession Nd-1, designated RPP13-Nd, confers resistance to five different isolates of the biotrophic oomycete, Peronospora parasitica (causal agent of downy mildew), and encodes an NBS-LRR type R protein with a putative amino-terminal leucine zipper. The RPP13-Rld allele, cloned from the accession Rld-2, encodes a different specificity. Comparison of three RPP13 alleles revealed a high rate of amino acid divergence within the LRR domain, less than 80% identity overall, compared to the remainder of the protein (> 95% identity). We also found evidence for positive selection in the LRR domain for amino acid diversification outside the core conserved beta-strand/beta-turn motif, suggesting that more of the LRR structure is available for interaction with target molecules than has previously been reported for other R gene products. Furthermore, an amino acid sequence (LLRVLDL) identical in an LRR among RPP13 alleles is conserved in other LZ NBS-LRR type R proteins, suggesting functional significance.     

Evolutionary Analysis for Functional Divergence of the Toll-Like Receptor Gene Family and Altered Functional Constraints

The Toll-like receptor (TLR) gene family consists of type 1 transmembrane receptors, which play essential roles in both innate immunity and adaptive immune response by ligand recognition and signal transduction. Using all available vertebrate TLR protein sequences, we inferred the phylogenetic tree and then characterized critical amino acid residues for functional divergence by detecting altered functional constraints after gene duplications. We found that the extracellular domain of TLR genes showed higher functional divergence than that of the cytoplasmic domain, particularly in the region between leucine-rich repeat (LRR) 10 and LRR 15 of TLR 4. Our finding supports the concept that sequence evolution in the extracellular domain may be responsible for the broad diversity of TLR ligand-binding affinity, providing a testable hypothesis for potential targets that could be verified by further experimentation.