植物EST-SSR标记开发及其应用

随着生物科技的进步,大量的植物表达序列标签(expressed sequence tags,ESTs)已经成为开发SSR标记的重要资源。EST-SSR作为一种新型分子标记,其多态性可能与基因功能直接相关,而且在相近植物间具有良好通用性,使得EST-SSR标记在实际应用中更具价值。采用计算机方法大规模发掘EST-SSR多态性位点极大地提高了SSR标记开发效率。尤其随着新一代测序技术的成熟以及测序成本的急剧下降,利用新一代测序技术产生大量的转录组数据进行EST-SSR多态性标记的计算机大规模发掘将对SSR标记的开发带来深远影响。本文简要介绍了植物EST-SSR分布特点,并对EST-SSR标记开发现状以及相关应用作了综合评述,此外,还对EST-SSR标记的计算机开发新策略进行了展望。     

菠菜性别相关的ISSR标记

菠菜为雌雄异株植物,用CTAB法提取其雌、雄株成株幼嫩叶片DNA,分别构建雌、雄株DNA池,以之为模板,用已优化的ISSR体系扩增,在74条ISSR引物中,I62扩增出一条约1 200 bp雌性连锁标记,回收纯化该特异扩增片段,将其连接于pUCm-T载体,转化进大肠杆菌JM109菌株,并检测及测序。回收克隆和测序后发现该片段全长1 176 bp,富含AT,AT占57.0%。根据测序结果设计1对25 bp的特异引物将这个雌性连锁的ISSR标记转化为稳定性和特异性更好的SCAR标记。该特异引物对随机选取的雌雄菠菜单株进行PCR扩增,在雌株中均有1 176 bp的特异条带,而雄株中均无。此特异条带的获得为菠菜性别相关基因的克隆奠定基础。     

华仁杏EST-SSR标记引物设计与开发

随着生物科技的进步,ESTs（表达序列标签）已经成为开发SSR（简单重复序列）标记的重要资源。本文利用NCBI公共数据库下载蔷薇科EST序列22 458条,使用SSRHunter1.3软件进行了SSR搜索,从中获得22 527条SSR,应用Primer5.0软件设计并经由Oligo7.0软件检测,共得到61对EST-SSR引物。利用这些引物对8个华仁杏品种进行了PCR扩增及检测,得到10对能产生清晰多态性条带的EST-SSR标记,标明了10对引物的序列,为进一步开展华仁杏SSR分子标记辅助育种研究奠定了基础。     

菠菜性别相关SRAP分子标记的筛选及分析

菠菜(2n=2x=12)是研究雌雄异株植物性别分化的一种理想材料。本研究利用SRAP (sequence re-lated amplified polymorphism)分子标记方法,采用256对引物组合对菠菜雌、雄基因池进行筛选,后利用聚丙烯酰胺凝胶电泳和琼脂糖凝胶电泳进行检测。结果表明,经过对256对引物组合进行筛选,其中20对引物组合扩增效果较好,共获得47个雌性特异片段和29个雄性特异片段,其多态性达到19.9%;在这20对引物组合中,引物对em11+me14、em10+me10经琼脂糖凝胶电泳验证扩增效果最好,可以扩增出菠菜雄、雌稳定的分子标记。本研究获得的性别特异标记可以用于菠菜幼苗期性别鉴定,同时为菠菜性别相关基因的克隆奠定了基础。     

EST-SSR标记在水曲柳雌雄鉴定中的应用

选用黑龙江省青山林木种子园成年水曲柳200棵树为实验材料,在来自NCBI中的5 423条白蜡属EST序列和该实验室测得的水曲柳转录组的179 502条序列中查找SSR位点并设计引物,通过PCR扩增筛选有效扩增和有差异片段的引物,用于水曲柳雌雄的鉴别。结果显示:(1)白蜡属EST和水曲柳转录组中的5 423条和179 502条序列中,分别查找到9 488个和3 557个SSR位点,SSR出现的频率分别是174.96%和1.98%,SSR的类型都是以二核苷酸为主。(2)232对引物中有208对引物获得有效扩增,74对引物在雌雄DNA中有差异,27对扩增片段符合预定大小片段。(3)经过3轮筛选,选出19号和56号引物用于200棵水曲柳中,雌雄差异率分别是64.5%和89.5%。研究表明,利用EST-SSR分子标记对水曲柳性别进行鉴定是一种有效可行的方法。     

白菜EST-SSR标记的通用性

EST-SSR是从表达序列标签(expressedsequencetag,EST)中开发的新型简单序列重复(simplesequencerepeat,SSR)标记。根据白菜EST设计了15对SSR引物,对白菜、油菜、玉米、高粱、水稻和茶树等进行了PCR,研究了白菜的EST-SSR标记在不同物种间的通用性。所设计的引物对不同白菜品种、近缘种油菜和远缘种玉米、高粱、水稻和茶树的扩增成功率分别为100%、93.3%、80%、93.3%、93.3%和86.7%。在15对引物中,有11对在远缘种中都有扩增产物,而且一些引物可显示多态性,多态性引物分别占了可扩增引物的33.3%、28.6%、28.6%和61.5%。这些结果表明,白菜EST-SSR引物具有较高的通用性,这对于比较基因组学研究有重要意义。     

花生微卫星标记的研究进展

近年来花生微卫星标记的开发取得了一定的进展,初步揭示了花生在DNA水平上的遗传多样性。花生微卫星标记的开发途径主要包括通过构建小片段基因组文库开发基因组SSR标记,根据花生EST序列开发EST-SSR标记,根据豆科植物序列信息和SSR标记开发花生SSR标记,将SSR标记与其它分子标记结合开发新的DNA标记,以及基于SSR核心序列开发ISSR标记。花生微卫星标记主要应用于遗传多样性研究、遗传图谱与品种指纹图谱构建以及分子标记辅助育种等领域。本文综述了花生SSR标记开发研究的进展及应用。     

花生微卫星标记的研究进展

近年来花生微卫星标记的开发取得了一定的进展, 初步揭示了花生在DNA水平上的遗传多样性。花生微卫星标记的开发途径主要包括通过构建小片段基因组文库开发基因组SSR标记, 根据花生EST序列开发EST-SSR标记, 根据豆科植物序 列信息和SSR标记开发花生SSR标记, 将SSR标记与其它分子标记结合开发新的DNA标记, 以及基于SSR核心序列开发ISSR标记。花生微卫星标记主要应用于遗传多样性研究、遗传图谱与品种指纹图谱构建以及分子标记辅助育种等领域。本文综述了花生SSR标记开发研究的进展及应用。     

中国重要农业害虫韭菜迟眼蕈蚊多态性EST-SSR标记的开发

【背景】韭菜迟眼蕈蚊是我国重要的农业害虫,然而它的遗传资源有限。本研究旨在开发韭菜迟眼蕈蚊EST-SSR标记,为研究不同地区的韭菜迟眼蕈蚊种群结构和遗传多样性奠定基础。【方法】从韭菜迟眼蕈蚊的表达序列标签(EST序列)中设计16对简单重复序列(SSR)引物,进一步筛选出9对具有多态性的SSR引物。【结果】从42095条unigene中确定了3383个SSR位点。利用查找到的SSR位点共设计出16对引物,进一步检测筛选发现9对引物具有多态性,引物的每个位点平均有3.33个等位基因。利用9对引物对30头韭菜迟眼蕈蚊进行检测,共获得30个等位基因,观测杂合度和期望杂合度的范围分别为0.0000~0.6875和0.0370~0.6877;其中,9个位点中有5个位点显著偏离Hardy-Weinberg平衡。【结论与意义】本研究成功从迟眼蕈蚊EST序列中筛选出9个具有多态性的微卫星位点,这为进一步分析该害虫种群的遗传结构和遗传多样性奠定了基础。     

亚历山大藻属微卫星标记的筛选

采用生物信息学方法,从塔玛亚历山大藻的ESTs数据库中筛选微卫星(Simple Sequence Repeat, SSR)位点,设计SSR引物,利用毛细管电泳对4株塔玛亚历山大藻(Alexandrium tamarense)、2株相关亚历山大藻(Alexandrium affine)和1株链状亚历山大藻(Alexandrium catenella)进行种内、种间遗传多样性分析,获得以下主要结果:(1)从6830条非冗余的ESTs中共查找到222个SSR,平均每18.5kb就有一个SSR,三核苷酸重复在所有的重复类型中所占比例最大,达到48.2%,重复单元CTG/CAG出现频率最高.进一步筛选出12条SSR引物,用于遗传多样性分析.(2)种内遗传多样性水平整体偏低,多态性引物比率仅为41 67%,Nei's基因多样性平均为0.2130.种间遗传多样性水平较高,多态性引物比率为75%,Nei's基因多样性平均水平为0 4643;另外,种间遗传分化系数较高,平均水平为0.7051.(3)对7个样品的聚类图分析发现,A. tamarense CCMP116 与A. affine CCMP112遗传距离极为接近;A. tamarense ATHK9301、CCMP1598和ATDH01相互聚在一起;A. catenella ACDH01与A. tamarense分属两枝.以上结果表明,SSR标记在亚历山大藻种内遗传多样性分析方面是一种非常有用的工具.     

Isolation and Characterization of a Virus Inhibitor from Spinach (Spinacia oleracea L.)

A virus inhibiting protein (VI) was isolated from spinach (Spinacia oleracea L.). The VI inhibited infections of test plants with plus- and minus-strand RNA viruses. Inoculation of both local lesion and systemic hosts with TMV in the presence of varying amounts of the VI resulted in typical dose response curves for the number of local lesions or the amount of virus respectively. The lowest concentration of VI leading to a significant reduction in the number of local lesions was 0.06 μg/ml. The VI was found to inhibit local lesion formation only when applied within 2–3 h p.i. but still reduced the number of local lesions when applied up to 9 h prior to virus inoculation. The antiviral activity could be attributed to a protein of molecular weight 29,000 dalton with an isoelectric point of 10.3. Its activity was destroyed by heating for 30 min to 70°C. These characteristics resemble those of other virus inhibiting proteins described for members of the order Caryophyllales such as the Phytolacca inhibitor against which a serological relationship was obtained.     

The Diurnal Pattern of Nitrate Uptake and Reduction by Spinach (Spinacia oleracea L.)

Spinach plants were grown in bowls of aerated nutrient solutionin a controlled environment chamber for 24 h, and harvestedevery 3·5-5 h to record their growth, nitrate and wateruptake, and plant nitrate concentration. Twelve such experimentsare described, either with a 14/10 h dark/light regime, or continuouslight or darkness. The irradiance was either 110, 320, or 510µmol m^-2 s^-1 (PPFD). All these regimes began at the endof the light period of a 14/10 h dark/light regime (510 µmolm^-2 s^-1) lasting approximately 2 weeks. Nitrate uptake rate per g of dry weight of plant continued almostunabated at about 17 µmol h^-1 through the initial 14-hdark period, and then fell away sharply if the light was notrestored, but increased slightly when it was. With continuouslight at 510 µmol m^-2 s^-1, uptake rate rose steadily forthe first 24 h of light, and then fell sharply for about 6 h.Shoot nitrate concentration increased about three-fold in thedark phase, and declined in the light at a rate which was positivelyrelated to the irradiance. Root nitrate concentration was severaltimes higher than that of the shoot: its diurnal change wassmaller (relative to the mean) than that of the shoot. Nitratereduction occurred to a small extent in the dark, and increasedrapidly as soon as the lights came on, to remain at a roughlyconstant rate (related to the irradiance) throughout the lightphase. Dry matter increase in the light was related to irradiance,but with little increase above 320 µmol m^-2 s^-1. Respiratoryweight loss in the dark was not detectable. Rate of fresh weightincrease was approximately constant throughout light and darkperiods. The results compare quite well with the predictions of a simplesimulation model, based on the pump/leak principle.Copyright1994, 1999 Academic Press Spinacia oleracea, nitrate, uptake, reduction, influx, efflux, diurnal, regulation, model, simulation     

Role of Ascorbate in Detoxifying Ozone in the Apoplast of Spinach (Spinacia oleracea L.) Leaves

Both reduced and oxidized ascorbate (AA and DHA) are present in the aqueous phase of the extracellular space, the apoplast, of spinach (Spinacia oleracea L.) leaves. Fumigation with 0.3 [mu]L L-1 of ozone resulted in ozone uptake by the leaves close to 0.9 pmol cm-2 of leaf surface area s-1. Apoplastic AA was slowly oxidized by ozone. The initial decrease of apoplastic AA was <0.1 pmol cm-2 s-1. The apoplastic ratio of AA to (AA + DHA) decreased within 6 h of fumigation from 0.9 to 0.1. Initially, the concentration of (AA + DHA) did not change in the apoplast, but when fumigation was continued, DHA increased and AA remained at a very low constant level. After fumigation was discontinued, DHA decreased very slowly in the apoplast, reaching control level after 70 h. The data show that insufficient AA reached the apoplast from the cytosol to detoxify ozone in the apoplast when the ozone flux into the leaves was 0.9 pmol cm-2 s-1. The transport of DHA back into the cytosol was slower than AA transport into the apoplast. No dehydroascorbate reductase activity could be detected in the apoplast of spinach leaves. In contrast to its extracellular redox state, the intracellular redox state of AA did not change appreciably during a 24-h fumigation period. However, intracellular glutathi-one became slowly oxidized. At the beginning of fumigation, 90% of the total glutathione was reduced. Only 10% was reduced after 24-h exposure of the leaves to 0.3 [mu]L L-1 of ozone. Necrotic leaf damage started to become visible when fumigation was extended beyond a 24-h period. A close correlation between the extent of damage, on the one hand, and the AA content and the ascorbate redox state of whole leaves, on the other, was observed after 48 h of fumigation. Only the youngest leaves that contained high ascorbate concentrations did not exhibit necrotic leaf damage after 48 h.     

Cd2+ Effect on Photosynthetic Apparatus in Synechococcus elongatus and Spinach (Spinacia oleracea L.)

Thylakoid membranes (TM) of the cyanobacterium Synechococcus elongatus were exposed for 30 min to the influence of 0, 10, 100, and 1 000 mM CdCl₂ (= Cd₀, Cd₁₀, Cd₁₀₀, and Cd₁₀₀₀). Cd₁₀ and Cd₁₀₀ caused some increase in activity of photosystem 2, PS2 (H₂O DCPIP), while distinct inhibition was observed with Cd₁₀₀₀. We also observed a similar effect when measuring oxygen evolution (H₂O PBQ + FeCy). Chloroplasts of spinach (Spinacia oleracea L.) were incubated for 30 min with 0, 15, 30, and 60 mM CdCl₂ (= Cd₀, Cd₁₅, Cd₃₀, and Cd₆₀). All concentrations studied inhibited the PS2 activity, the effect being stronger with increasing concentration of Cd²⁺. The photosynthetic oxygen evolution activity was also influenced most distinctly by the highest concentration employed, i.e. Cd₆₀. Electrophoretic analysis of the protein composition of cyanobacterium TM showed chief changes in the molecular mass regions of M_r 29 000 and 116 000, while with spinach chloroplasts the most distinct differences were observed in the regions of M_r 15 000 and 50 000. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO) activity in cyanobacterial spheroplasts still remained on the 40 % level in the case of Cd₁₀₀₀, but it decreased down to approx. 2.5 % in the Cd₆₀ sample of spinach chloroplasts.     

Chalcone synthases from spinach (Spinacia oleracea L.)

The two chalcone-synthase forms from leaves ofSpinacia oleracea L. were purified to apparent homogeneity. Antibodies were raised against both proteins in rabbits. The specificity of the antibodies was tested using immunotitration, immunoblotting, and immunoelectrophoresis techniques. The antibodies exhibited exclusive specificity for chalcone synthase and did not discriminate between the two antigens. The homodimeric chalcone synthases had the same subunit molecular weight but differed in their apparent native molecular weights. The peptide maps indicated extensive homology between the proteins. Chalcone-synthase activity was not detected in isolated spinach chloroplasts. Both enzyme forms were present in spinach cell-suspension cultures in which they were induced by light.Abbreviations DEAE diethylaminoethyl - DTE 1,4-dithioerythritol - EDTA ethylenediaminetetraacetic acid - HPLC high-performance liquid chromatography - IgG immunoglobulin G - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis Parts of the results were presented at the 14^th International Botanical Congress at Berlin in July 1987     

亚麻EST-SSR信息分析与标记开发

与基因组SSR相比,以EST为基础的EST-SSR分子标记具有自身的优点。本研究从11240条亚麻（Linum sitatissmum L.）EST序列中检索出877条含有SSR的序列,其出现频率为7.8%。其中以三核苷酸重复出现的频率最高,占总SSR序列的60.1%;其次是二核苷酸重复,占21.9%;四、五和六核苷酸重复占18%。根据这些含SSR的EST序列共设计了73对SSR引物,在8份亚麻材料间通过PCR扩增检测,有63对引物扩增出清晰条带,引物可用率86.3%;有17对引物在8份亚麻材料间显现出多态性,占可扩增引物的26.3%。     

Polar Lipids of Spinach (Spinacia oleracea) Roots

The polar lipid components in the roots of spinach (Spinacia oleracea) plant were identified as phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, monogalactosyl-diglycerides, digalactosyldiglycerides, polygalactosyldiglycerides, sulpholipids and three unknown glycosides. Phospholipids constituted only 10% of the polar lipid fraction and 90% was of nonphosphatidic nature. This latter fraction was highly unsaturated and contained linoleic acid as the major fatty acid component.     

Purification and Characterization of Leu-Proteinase, the Leucine Specific Serine Proteinase from Spinach (Spinacia oleracea L.) Leaves

The leucine specific serine proteinase present in the soluble fraction of leaves from Spinacia oleracea L. (called Leu-proteinase) has been purified by acetone precipitation and a combination of gel-filtration, ion exchange, and adsorption chromatography. This enzyme shows a molecular weight of 60,000 ± 3,000 daltons, an isoelectric point of 4.8 ± 0.1, and a relative electrophoretic mobility of 0.58 ± 0.03. The Leu-proteinase catalyzed hydrolysis of p-nitroanilides of N-α-substituted(-l-)amino acids as well as of chromogenic macromolecular substrates has been investigated between pH 5 and 10 at 23 ± 0.5°C and I = 0.1 molar. The enzyme activity is characterized by a bell-shaped profile with an optimum pH value around 7.5, reflecting the acid-base equilibrium of groups with pK_a values of 6.8 ± 0.1 and 8.2 ± 0.1 (possibly the histidyl residue present at the active site of the enzyme and the N-terminus group). Among the substrates considered, N-α-benzoyl-l-leucine p-nitroanilide shows the most favorable catalytic parameters and allows to determine an enzyme concentration as low as 1 × 10⁻⁹ molar. In agreement with the enzyme specificity, only N-α-tosyl-l-leucine chloromethyl ketone, di-isopropyl fluorophosphate and phenylmethylsulfonyl fluoride, among compounds considered specific for serine enzymes, strongly inhibit the Leu-proteinase. Accordingly, the enzyme activity is insensitive to cations, chelating agents, sulfydryl group reagents, and activators.     

cDNA Cloning and Expression of the Plastidic Copper/Zinc-Superoxide Dismutase from Spinach (Spinacia oleracea L.) Leaves

A cDNA clone for copper/zinc-superoxide dismutase (Cu/Zn-SOD)was isolated from spinach (Spinacia oleracea L.) leaves. Itsnucleotide sequence showed that it codes for a precursor polypeptideof 222 amino acids, including the NH₂-terminal 68-residue extensionwhich corresponds to a plastidic transit peptide. Northern hybridization,using plastidic and cytosolic Cu/Zn-SOD cDNAs as the probes,revealed that these two genes are differentially expressed inthe roots and leaves of spinach. ¹Present address: Department of Biochemistry and Microbiology,Cook College, Rutgers University New Brunswick, NJ 08903-0231,U.S.A.