Characterisation of <Emphasis Type="Italic">Phoma tracheiphila</Emphasis> by RAPD-PCR,microsatellite-primed PCR and ITS rDNA sequencing and development of specific primers for <Emphasis Type="Italic">in planta</Emphasis> PCR detection

Thirty six isolates of Phoma tracheiphila from Italy, the causal agent of the mal secco disease on Citrus species, were characterised by different molecular tools in comparison with representative isolates of other phytopathogenic Phoma species. These included analysis of the distribution of RAPD and microsatellite markers and sequencing of the internal transcribed spacer (ITS) region of the nuclear rRNA genes. The results obtained with 12 RAPD primers (92 markers) and 7 microsatellite primers (56 markers) suggest that Italian isolates of P. tracheiphila are genetically homogeneous, leading to identical patterns upon amplification with all the tested primers. Accordingly, ITSI-5.8S-ITS2 sequences were highly conserved (98–100% identity along a 544-characters alignment) among all the isolates of P. tracheiphila. A neighbor-joining analysis of ITS sequences of P. tracheiphila in comparison with those of other Phoma species, as well as with alignable sequences from anamorphic and teleomorphic taxa retrieved in BLAST searches, revealed a close relationship between P. tracheiphila and Leptosphaeria congesta. A pair of P. tracheiphila-specific primers was designed on the consensus sequence (555 residues) obtained from the alignment of the newly generated P. tracheiphila ITS sequences. A PCR-based specific assay coupled to electrophoretic separation of amplicons made it possible to detect P. tracheiphila in naturally infected Citrus wood tissue collected from both symptomatic and symptomless plants. The limit of detection was 10 pg of genomic DNA and 5 fg of the ITS target sequence.     

云南半细毛羊精子冷冻前后转录组表达差异分析

【目的】 本研究旨在对云南半细毛羊精子冷冻前后差异表达的基因与精子冷冻损伤的关系进行研究。【方法】 采用电刺激法采集3只云南半细毛羊精液,各分成2份,一份直接用于提取精子RNA,另一份经过冷冻保存7 d后再进行精子RNA提取。利用获得的精子RNA,采用单细胞转录组测序技术分别检测新鲜精子和冻融精子的mRNA转录组,构建mRNA转录组文库,用Hiseq2500测序仪进行测序,对测序结果做进一步过滤处理,然后对差异表达基因进行GO功能注释和KEGG通路分析。【结果】 6份精液样本共产生623 399 754条原始测序序列,过滤处理后得到514 313 802条（82.50%）高质量的Clean reads。生物信息学分析结果表明,冷冻前后差异表达显著的基因共1 213个。其中,解冻后表达量下调的有1 208个,上调的有5个。通过GO功能注释和KEGG通路富集分析,差异表达基因分别归类于56个GO分类,参与40个信号通路。其中与精子功能密切相关的主要包括精子细胞过程、代谢过程、应激反应、生殖、质膜和氧化还原反应;精子冷冻前后差异表达基因参与的信号通路主要有炎症、细胞因子-细胞因子受体相互作用和细胞凋亡等通路。【结论】 云南半细毛羊精子的冷冻损伤可能与获得的差异表达基因参与的生物过程有关。此外,获得的差异表达基因也可作为分子标记物应用于绵羊冻精品质的评价。     

解淀粉芽孢杆菌DGL1促燕麦生长分子机制及代谢通路探究

分离自青海大格勒干旱沙地的解淀粉芽孢杆菌DGL1(Bacillus.amyloliquefaciens)被证实能够促进青海本地燕麦(Avena sativa)品种‘青燕1号’的生长。为了揭示DGL1促进燕麦生长的分子机制,本研究通过Illumina高通量转录组测序技术分析燕麦根部与菌株DGL1菌悬液分别互作2h,4h,8h,12h的处理组与对照组(CK)间的转录组差异表达基因,并通过GO富集、KEGG Pathway富集分析燕麦地上部分差异表达基因的相关代谢通路及关键基因。结果表明：燕麦根部与DGL1菌悬液互作2h,4h,8h和12h,燕麦叶部分别有1894,6130,8033和12215个差异表达基因,显著富集在氨基酸代谢、植物光合作用、次级产物代谢通路和与燕麦生长发育调控等相关代谢途径;通过KEGG富集分析发现IAA合成的色氨酸代谢途径中生长素早期响应蛋白编码基因AUXI、茉莉酸信号途径中核心受体编码基因COI1,铵转运蛋白编码基因AMT等基因显著上调,推测菌株DGL1对燕麦的促生机制是通过促进燕麦光合作用、激素代谢、次生代谢物合成、氨基酸代谢等多个途径相互协调的结果。     

鸡内参基因β-actin和GAPDH实时定量PCR重组质粒标准品的构建

本研究从SPF鸡皮肤中提取总RNA,并反转录为cDNA;以该cDNA为模板,通过聚合酶链式反应(PCR)分别扩增出看家基因β-actin和GAPDH,将PCR产物连入pGEM-T easy载体,转化DH5α菌,经蓝白斑筛选和质粒酶切鉴定和DNA含量测定,得到定量的β-actin和GAPDH基因融合的重组质粒(pGEM T-actin和pGEM T-GAPDH),即实时定量PCR内参标准品.构建成功的标准品经10倍梯度稀释,作为模板,获得扩增效率良好及可信度高的标准曲线.构建成功的标准品可大量制备,可用于鸡的靶基因定量PCR所需的内参标准品.     

云南省不同宿主H9N2感染调查和NA分子进化分析

2006年6月-2007年10月,从云南省16个地州随机采集的各种家禽、家猪的喉气管和口腔棉拭子样品7 901份,应用RT-PCR结合血凝、血凝抑制试验和抗原捕捉ELISA,检测H9N2亚型禽流感感染情况,选择具有代表性的阳性样品,克隆NA全基因并进行基因序列分和推导氨基酸的糖基化位点分析。结果表明,云南省2006-2007年H9N2亚型禽流感病毒在全省14个地州均有流行,感染宿主包括鸡、鸭、鹅和猪;分离的19个毒株中的13个鸡源和1个鹅源毒珠的NA全基因长1 407bp,编码469个氨基酸,同源性为96.1%～99.6%,是目前云南省流行的优势亚群;3个鸭源毒株、1个鹅源和1个猪源毒株NA基因长1 398bp,编码466个氨基酸,5个非鸡源毒株的NA基因的同源性为99%,构成云南目前流行的另一分支,推导氨基酸第61～63位3个氨基酸的缺失是与优势分支的特征性区别;2个分支间NA基因同源性为90%,与国内外其他毒株比较神经氨酸酶基因序列具有多态性。     

鹅产蛋性状全基因组选择信号分析

【目的】利用选择信号分析方法在伊犁鹅和霍尔多巴吉鹅中筛选与产蛋性状相关的候选基因。【方法】选取健康状况良好、饲养管理水平一致的2岁伊犁鹅母鹅和霍尔多巴吉鹅母鹅各24只,采集血液样本,提取基因组DNA,利用全基因组重测序技术进行选择信号检测分析,筛选出受到选择的候选区域,针对注释基因进行GO功能和KEGG通路富集分析,进一步筛选出与鹅产蛋性状相关的候选基因。【结果】全基因组重测序的平均测序深度为15.28×,与参考基因组比对率在97.31%以上。通过群体分化指数(Fst)对伊犁鹅和霍尔多巴吉鹅2个群体进行分析,共筛选到1 231个候选区域。与核苷酸多样性(Pi)进行联合分析后,伊犁鹅群体共筛选出10个候选区域,得到5个注释基因;霍尔多巴吉鹅群体中共筛选出353个候选区域,得到263个注释基因。GO功能和KEGG通路富集分析发现,初步筛选出6个可能与鹅产蛋性状相关的候选基因(BMP2、BMP6、MIS、ENO1、LIF、EP300),还发现了IL-18基因可能与禽类的免疫有关。【结论】本研究筛选出6个可能与鹅产蛋性状相关的候选基因,为揭示鹅产蛋性状的分子调控机制提供了参考。     

猪SGK家族基因的生物信息学分析及其在猪脂肪组织和细胞中的表达

【目的】 扩增猪血清和糖皮质激素诱导型激酶（SGK）家族基因并进行生物信息学分析,探索其在猪脂肪组织和细胞中的表达模式。【方法】 以藏猪脂肪细胞cDNA为模板PCR扩增SGK家族基因,通过在线工具预测其编码蛋白的理化性质及亚细胞定位;用Mega X软件构建系统进化树;采集30日龄巴马猪心脏、肝脏、脾脏、肾脏、肺脏、背肌、腿肌、颈部脂肪、背部脂肪、腹股沟脂肪、肾周脂肪等组织及7日龄和4月龄猪腹股沟脂肪组织,通过实时荧光定量PCR检测SGK家族基因在猪不同部位组织中的表达;采集30日龄巴马猪腹股沟脂肪组织并分离基质血管成分（SVF）细胞,诱导SVF细胞向白色脂肪细胞分化,通过实时荧光定量PCR检测SGK家族基因及脂肪分化标记基因CCAAT增强子结合蛋白α（C/EBPα）、过氧化物酶体增殖物激活受体（PPARγ）在脂肪细胞中的表达。【结果】 SGK1、SGK2和SGK3基因CDS区序列长度分别为1 296、1 104和1 473 bp,分别编码431、367和490个氨基酸;SGK1和SGK2定位于细胞质,SGK3定位于细胞核,三者均为亲水性蛋白,3个蛋白均含有相同基序,保守性高;系统进化树结果表明,猪与牛的亲缘关系最近;SGK1和SGK3基因在心脏、肝脏、脾脏、肺脏、肾脏、多种肌肉及脂肪组织广泛表达,SGK2基因在颈部、背部、腹股沟、肾周脂肪组织中均有较高表达;SGK1和SGK2基因在7日龄猪脂肪组织中表达量极显著高于4月龄猪脂肪组织（P<0.01）,SGK3基因在4月龄和7日龄的猪脂肪组织中表达量无显著差异（P>0.05）,且SGK3基因的表达量低于SGK1和SGK2基因;与未分化脂肪细胞相比,在分化后的脂肪细胞中SGK1和SGK2基因的表达量极显著上调（P<0.01）,且SGK1基因的表达量远高于SGK2基因,而SGK3基因的表达量无显著变化（P>0.05）。【结论】 SGK家族蛋白具有保守结构域,可能发挥着相似的功能,SGK1和SGK2可能参与调控猪脂肪细胞的分化过程,结果可为探究猪脂肪沉积的分子机制提供一定的理论基础。     

Disease severity and pathotype dynamics of Puccinia striiformis f.sp. tritici in Denmark

Disease severity of wheat yellow rust, Puccinia striiformis f.sp. tritici , was analysed in Denmark from 1985 to 1999 in relation to the effects of weather on winter survival, distribution of host cultivars and pathotype dynamics. Below-average temperatures in January and February (midwinter) reduced yellow rust on the susceptible cv. Anja, and in three of four growth seasons following cold winters no yellow rust was observed on any cultivar under natural conditions. The agronomic consequences of dispersal of yellow rust urediniospores from external sources to Denmark, in a period during which large areas were planted with relatively few wheat cultivars, were demonstrated in several cases, most evidently when the Yr9 and Yr17 resistance genes became ineffective. Yr9 was overcome by the pathogen in a period with severe yellow rust epidemics on commercial cultivars, while virulence for Yr17 was first observed in a year with almost no yellow rust. In contrast, the resistance in cv. Kraka ( Yr1, CV ) was increasingly effective in controlling yellow rust, because pathotypes with the matching combination of virulence declined in the pathogen population. Pathotype frequency dynamics were thus influenced by selection forces within the country, and by selection forces in areas where spores were spread to Denmark from outside. The importance of a sufficient level of partial resistance in the wheat germplasm to prevent too much damage by yellow rust epidemics, in the event that the resistance genes are overcome by the pathogen population, is emphasized.     

Erwinia carotovora Infection Enhances the Expression of Two Novel Abiotic Stress-inducible Genes in Potato

In this study, cDNAs of two Erwinia carotovora-induced potato genes, designated Solanum tuberosum–Erwinia-induced-1 and 2 (Stei1 and Stei2) were isolated by differential display technique. Stei1 and Stei2 were detected in low copy number in the potato genome and found to encode putative proteins with no significant homology to any genes with known function. Treatment of the leaves with salicylic acid, methyl jasmonate and ethylene elevated neither Stei1 nor Stei2 mRNA levels. However, Stei1 and Stei2 expression were induced not only by E. carotovora but also by infiltration of water in leaves, albeit to a lesser extent. In addition, Stei2 was up-regulated by NaCl, wounding, dehydration and abscisic acid. Thus Stei1 and Stei2 define novel genes belonging to the family of those pathogenesis-related genes whose expression can be induced both by biotic and abiotic stresses.