Purification and Characterization of Catalase from Loblolly Pine (Pinus taeda L.) Megagametophytes

Catalase (EC 1.11.1.6) was purified to near homogeneity from isolated megagametophytes of germinated loblolly pine (Pinus taeda L.) seeds, and monospecific antibodies were elicited in rabbits. Following a procedure that involved acetone extraction, (NH4)2SO4 fractionation, and four chromatographic steps (i.e. DE-52 cellulose, Superdex-200, hydroxylapatite, and phenyl-Sepharose CL-4B), catalase was purified about 140-fold to a final specific activity of 2215 mmol min-1 mg-1 of protein. Cotton isocitrate lyase antibodies were used, and protein immunoblots revealed that the resolution on hydroxylapatite and phenyl-Sepharose allowed for the complete separation of catalase from contaminating isocitrate lyase. The molecular masses of the native enzyme and its subunit are 235 and 59 kD, respectively, indicating that the pine holoenzyme is a homotetramer. Loblolly pine catalase exists as multiple isoforms. When megagametophytes taken 7 d after imbibition at 30[deg]C were extracted, subjected to nondenaturing isoelectric focusing, and stained for catalase activity, at least four catalase isoforms were observed, including one dominant form with an isoelectric point of 6.87. Purified pine catalase is not a glycoprotein and has a ratio of absorbance at 208 nm to absorbance at 405 nm of 1.5. When probed with loblolly pine catalase antibodies, protein blots of cell-free extracts from megagametophytes of mature, stratified, and germinated loblolly pine seeds, the megagametophyte glyoxysomal fraction, and purified loblolly pine catalase all revealed one immunoreactive 59-kD polypeptide. This indicates that no detectable change in the enzyme's monomeric molecular mass occurs during seed stratification and germination, early seedling growth, and purification.     

火炬松组织培养研究和应用进展

从离体再生途径、影响因素、遗传转化、存在问题等方面对火炬松组织培养研究和应用进展作了介绍和讨论,以期对同类树种相关研究的开展提供参考。     

Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

The largest genus in the conifer family Pinaceae is Pinus, with over 100 species. The size and complexity of their genomes (∼20–40 Gb, 2n = 24) have delayed the arrival of a well-annotated reference sequence. In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine (Pinus taeda L.), which comprises 20.1 Gb of sequence. The MAKER-P annotation pipeline combined evidence-based alignments and ab initio predictions to generate 50,172 gene models, of which 15,653 are classified as high confidence. Clustering these gene models with 13 other plant species resulted in 20,646 gene families, of which 1554 are predicted to be unique to conifers. Among the conifer gene families, 159 are composed exclusively of loblolly pine members. The gene models for loblolly pine have the highest median and mean intron lengths of 24 fully sequenced plant genomes. Conifer genomes are full of repetitive DNA, with the most significant contributions from long-terminal-repeat retrotransposons. In depth analysis of the tandem and interspersed repetitive content yielded a combined estimate of 82%.     

Modelling Inter- and Intra-specific Competition in Loblolly Pine (Pinus taeda L.) Plantations on Cutover, Site-prepared Lands

The presence of volunteer hardwood species in loblolly pineplantations demands studies on both intra- and inter-specificcompetition in order to build growth and yield models and toguide vegetation management for these stands. This paper, basedon analyses of data collected from a thinning study, reportsan investigation of responses of loblolly pine and hardwoodspecies towards intra- and inter-specific competition. Underhigh levels of overall competition, hardwood species were morecompetitive, both intra- and inter-specifically. Intra-specificcompetition was more effective in reducing hardwood basal areagrowth than inter-specific competition under high levels ofoverall competition. However, under low levels of overall competition,intra- and inter-specific competition were quantitatively similartoward loblolly pine basal area growth. The basal area growthof hardwoods was significantly related to levels of inter-specificcompetition, but not with intra-specific effects under low levelsof overall competition. More than half of the variability inloblolly pine basal area growth under unthinned control andlight thin treatments could be accounted for by competitioneffects. However, only one third of the variability could beexplained for loblolly pine under heavy thin treatment. Forhardwood species, the percentage of growth variation accountedfor by competition was about 45%, and did not change among thethinning treatments. Different resource demands between thetwo categories of tree species and a certain amount of thinningshock were suggested by the modelling results.Copyright 1994,1999 Academic Press Neighbourhood approach, competition index, hardwood, no-interaction model, basal area, reciprocal yield law     

Association Mapping of Quantitative Disease Resistance in a Natural Population of Loblolly Pine (Pinus taeda L.)

Genetic resistance to disease incited by necrotrophic pathogens is not well understood in plants. Whereas resistance is often quantitative, there is limited information on the genes that underpin quantitative variation in disease resistance. We used a population genomic approach to identify genes in loblolly pine (Pinus taeda) that are associated with resistance to pitch canker, a disease incited by the necrotrophic pathogen Fusarium circinatum. A set of 498 largely unrelated, clonally propagated genotypes were inoculated with F. circinatum microconidia and lesion length, a measure of disease resistance, data were collected 4, 8, and 12 weeks after inoculation. Best linear unbiased prediction was used to adjust for imbalance in number of observations and to identify highly susceptible and highly resistant genotypes (“tails”). The tails were reinoculated to validate the results of the full population screen. Significant associations were detected in 10 single nucleotide polymorphisms (SNPs) (out of 3938 tested). As hypothesized for genes involved in quantitative resistance, the 10 SNPs had small effects and proposed roles in basal resistance, direct defense, and signal transduction. We also discovered associated genes with unknown function, which would have remained undetected in a candidate gene approach constrained by annotation for disease resistance or stress response.GENETIC interactions between host and pathogen populations result in abundant natural variation in the genes involved in host disease resistance. Most of the studies leading to identification and cloning of disease resistance genes are focused on major gene disease resistance (Johal and Briggs 1992; Dangl and Jones 2001; Jones and Dangl 2006). In cases where resistance is associated with single genes, genetic effects are large in magnitude and detection is straightforward. In contrast, quantitative disease resistance is typically conditioned by many genes with relatively small effects. Quantitative resistance is generally considered to be more durable but also more difficult to investigate relative to major gene resistance, since the effects of individual genes are small and phenotyping experiments must be performed with high levels of precision. As a consequence, the genes and mechanisms of quantitative disease resistance are poorly understood, in part due to the smaller effect of individual genes on the resistance phenotype. Interactions between plants and necrotrophic pathogens often exhibit quantitative resistance (Balint-Kurti et al. 2008; Poland et al. 2009).Pitch canker disease of loblolly pine and other pine species is incited by the necrotrophic pathogen Fusarium circinatum and is manifest as resinous lesions in stems and branches (Dwinell et al. 1985; Enebak and Stanosz 2003; Carey et al. 2005; Sakamoto and Gordon 2006). There is evidence for heritable resistance to pitch canker in loblolly pine (Kayihan et al. 2005) as well as other pine species (Hodge and Dvorak 2000, 2007). In this article we report the first population-wide phenotypic screen of a clonally propagated population of loblolly pine for association testing (Eckert et al. 2010). Clonal propagation of this population enabled precise phenotyping, which was required to obtain the resolution needed to identify candidates for quantitative disease resistance loci.Pine species in general exhibit high levels of nucleotide variation and low linkage disequilibrium (LD) (Brown et al. 2004). An association genetic approach relies on the premise that historical, unrecorded recombination events over many generations have reduced LD between markers and quantitative trait loci such that only those marker-trait pairs that are tightly linked remain detectable; this may enable “fine mapping” to identify genes underlying quantitative variation (Flint-Garcia et al. 2003; Neale and Savolainen 2004). Association-based approaches have been used to identify candidate genes underlying traits in plants (Zhao et al. 2007; Stich et al. 2008; Wang et al. 2008; Yahiaoui et al. 2008; Inostroza et al. 2009; Stracke et al. 2009), based in part on applications in humans (D''alfonso et al. 2002; McGuffin et al. 2003; Easton et al. 2007; Lee et al. 2007), livestock (Martinez et al. 2006; Charlier et al. 2008; Goddard and Hayes 2009), and Drosophila (Kennington et al. 2007; Norry et al. 2007; Jiang et al. 2009). Recent association studies in tree species have evaluated single candidate genes or a modest number of candidate genes for association (Thumma et al. 2005; Gonzalez-Martinez et al. 2007, 2008; Ingvarsson et al. 2008; Eckert et al. 2009a). Association mapping has been used to identify disease resistance genes in several crop species including sugarcane, maize, barley, and potato (Flint-Garcia et al. 2005; Wei et al. 2006; Yu and Buckler 2006; Malosetti et al. 2007; Stich et al. 2008; Inostroza et al. 2009; Murray et al. 2009). The population analyzed in this study was genotyped at 3938 SNP loci that were selected without regard to the functional annotation of ESTs from which they were derived. Thus, we reasoned that the status of any particular marker as a candidate disease resistance gene would be determined by association testing, as opposed to previous studies in which markers were typically evaluated on the basis of their presumed roles in disease resistance in other species.Several different, but not mutually exclusive hypotheses have been proposed regarding the genetic origins of quantitative resistance (Poland et al. 2009), providing a useful framework for understanding evolution of resistance to necrotrophic pathogens. These six hypotheses proposed by Poland et al. (2009) predict that quantitative disease resistance is conditioned by: (1) genes regulating morphological and developmental phenotypes; (2) mutations in genes involved in basal defense causing small, incremental levels of resistance; (3) components of chemical warfare, through the action of genes producing antibiotic or antifungal compounds; (4) genes involved in defense signal transduction pathways; (5) weak forms of defeated R genes; and/or (6) genes not yet known to be involved in disease resistance.In this study, our main objective was to evaluate the genetic architecture of pitch canker disease resistance: to quantify the extent to which genes contribute to variation in the disease phenotype, to evaluate the hypothesis that disease resistance was quantitative, and to identify candidate genes for resistance as well as quantify their magnitude of effect. In the process of identifying candidate genes for resistance we were also able to evaluate support for hypotheses recently put forth by Poland et al. (2009) regarding the biological roles and origins of quantitative resistance genes.     

Limitations of Photosynthesis in Pinus taeda L. (Loblolly Pine) at Low Soil Temperatures

The relative importance of stomatal and nonstomatal limitations to net photosynthesis (A) and possible signals responsible for stomatal limitations were investigated in unhardened Pinus taeda seedlings at low soil temperatures. After 2 days at soil temperatures between 13 and 7°C, A was reduced by 20 to 50%, respectively. The reduction in A at these moderate root-chilling conditions appeared to be the result of stomatal limitations, based on the decrease in intercellular CO₂ concentrations (c_i). This conclusion was supported by A versus c_i analysis and measurements of O₂ evolution at saturating CO₂, which suggested increases in stomatal but not biochemical limitations at these soil temperatures. Nonuniform stomatal apertures, which were demonstrated with abscisic acid, were not apparent 2 days after root chilling, and results of our A versus c_i analysis appear valid. Bulk shoot water potential (ψ) declined as soil temperature dropped below 16°C. When half the root system of seedlings was chilled, shoot ψ and gas-exchange rates did not decline. Thus, nonhydraulic root-shoot signals were not implicated in stomatal limitations. The initial decrease in leaf conductance to water vapor after root chilling appeared to precede any detectable decrease in bulk fascicle ψ, but may be in response to a decrease in turgor of epidermal cells. These reductions in leaf conductance to water vapor, which occurred within 30 minutes of root chilling, could be delayed and temporarily reversed by reducing the leaf-to-air vapor-pressure deficit, suggesting that hydraulic signals may be involved in initiating stomatal closure. By independently manipulating the leaf-to-air vapor-pressure deficit of individual fascicles, we could induce uptake of water vapor through stomata, suggesting that nonsaturated conditions occur in the intercellular airspaces. There was an anomaly in our results on seedlings maintained for 2 days at soil temperatures below 7°C. Lower A appeared primarily the result of nonstomatal limitations, based on large increases in calculated c_i and A versus c_i analysis. In contrast, measurements of O₂ evolution at saturating CO₂ concentrations implied nonstomatal limitations per se did not increase at these temperatures. One explanation for this paradox is that calculations of c_i are unreliable at very low gas-exchange rates because of inadequate measurement resolution, and limitations of A are predominantly stomatal. An alternative interpretation is that increases in c_i are real and the results from O₂-evolution measurements are in error. The high CO₂ concentration used in O₂-evolution measurements (15%) may have overcome nonstomatal limitations by enzymes that were down-regulated by a feedback mechanism. In this scenario, carbohydrate feedback limitations may be responsible for nonstomatal reductions in A after 2 days at soil temperatures below 7°C.     

Elicitor-Induced Cinnamyl Alcohol Dehydrogenase Activity in Lignifying Wheat (Triticum aestivum L.) Leaves

The substrate-specific induction of wheat (Triticum aestivum L. cv Fenman) leaf cinnamyl alcohol dehydrogenase (CAD, EC 1.1.1.195) was examined in relation to its role in regulating the composition of defensive lignin induced at wound margins. Treatment of wounds with a partially acetylated chitosan hydrolysate or spores of the nonpathogen Botrytis cinerea elicited lignification at wound margins and invoked significant increases in phenylalanine ammonia-lyase (EC 4.3.1.5), peroxidase (EC 1.11.1.7), and CAD activities. The substrate-specific induction of CAD with time was determined in elicitor-treated leaves and in excised lignifying wounds. In whole leaf extracts no significant increases in p-cou-maryl and coniferyl alcohol dehydrogenase activities were detectable, but a significant 5-fold increase in sinapyl alcohol dehydrogenase activity was evident 32 h after elicitor treatment. Similarly, fungal challenge resulted in elevated levels of only sinapyl alcohol dehydrogenase in whole-leaf extracts. In excised lignifying tissues p-coumaryl alcohol dehydrogenase levels were similar to those observed in healthy tissue. A small yet significant increase in coniferyl alcohol dehydrogenase was apparent, but the most dramatic increase occurred in sinapyl alcohol dehydrogenase activity, which increased to values approximately 10 times higher than the untreated controls. Our results show for the first time that CAD induction in lignifying tissues of wheat is predominantly attributable to highly localized increases in sinapyl alcohol dehydrogenase activity.     

Assay and Electrophoresis of Superoxide Dismutase from Red Spruce (Picea rubens Sarg.), Loblolly Pine (Pinus taeda L.), and Scotch Pine (Pinus sylvestris L.) : A Method for Biomonitoring

This paper reports a method for extracting the antioxidant enzyme superoxide dismutase (SOD) from the needles of red spruce (Picea rubens Sarg.), loblolly pine (Pinus taeda L.), and scotch pine (Pinus sylvestris L.) with high efficiency and free from interfering compounds. The extraction employs phosphate buffer with polyvinylpolypyrrolidone and Triton X-100 followed by dialysis overnight. The isozymes of SOD in each species were separated electrophoretically and tested for their sensitivity to KCN and H₂O₂. An isozyme resistant to these inhibitors was found in the spruce but not the pine needles. The isozymes from the spruce needles were examined for individual responses to aging and H₂O₂ inhibition. Four of the five CuZn isozymes in spruce were found to have increased significantly but equally by October of their first year and two of those four isozymes were found to be more sensitive to H₂O₂. The response of the SOD isozymes in loblolly pine seedlings to O₃ was also examined and the isozymes were found to be induced equally. Because the SOD activity in the young pine needles was too low to electrophorese, the SOD activity from the pines in the O₃ experiment had to be partially purified using CHCl₃ and ethanol, then concentrated.     

Purification and Characterization of Cinnamyl Alcohol Dehydrogenase Isoforms from the Periderm of Eucalyptus gunnii Hook

Cinnamyl alcohol dehydrogenase (CAD, EC 1.1.1.195) isoforms were purified from the periderm (containing both suberized and lignified cell layers) of Eucalyptus gunnii Hook stems. Two isoforms (CAD 1P and CAD 2P) were initially characterized, and the major form, CAD 2P, was resolved into three further isoforms by ion-exchange chromatography. Crude extracts contained two aliphatic alcohol dehydrogenases (ADH) and one aromatic ADH, which was later resolved into two further isoforms. Aliphatic ADHs did not use hydroxycinnamyl alcohols as substrates, whereas both aromatic ADH isoforms used coniferyl and sinapyl alcohol as substrates but with a much lower specific activity when compared with benzyl alcohol. The minor form, CAD 1P, was a monomer with a molecular weight of 34,000 that did not co-elute with either aromatic or aliphatic ADH activity. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blot analysis demonstrated that this protein was very similar to another CAD isoform purified from Eucalyptus xylem tissue. CAD 2P had a native molecular weight of approximately 84,000 and was a dimer consisting of two heterogenous subunits (with molecular weights of 42,000 and 44,000). These subunits were differentially combined to give the heterodimer and two homodimers. SDS-PAGE, western blots, and nondenaturing PAGE indicated that the CAD 2P heterodimer was very similar to the main CAD isoform previously purified in our laboratory from differentiating xylem tissue of E. gunnii (D. Goffner, I. Joffroy, J. Grima-Pettenati, C. Halpin, M.E. Knight, W. Schuch, A.M. Boudet [1992] Planta 188: 48-53). Kinetic data indicated that the different CAD 2P isoforms may be implicated in the preferential production of different monolignols used in the synthesis of lignin and/or suberin.     

香蕉肉桂醇脱氢酶基因的克隆及表达分析

肉桂醇脱氢酶(CAD)在木质素合成过程中起关键作用。通过RACE(rapid-amplification of cDNA ends)方法从香蕉根系cDNA均一化全长文库中获得一个肉桂醇脱氢酶基因,命名为MaCAD1(GenBank登录号为KF582533)。MaCAD1是香蕉MYB基因编码框全长cDNA,包含一个1 077bp的最大开放阅读框(ORF),编码358个氨基酸。蛋白质序列同源比对发现,其含有完整的醇脱氧酶的典型保守结构域,属于典型的CAD蛋白。系统进化树比对分析表明,MaCAD1与水稻OsCAD6(CAD39907)的亲缘关系较近。组织特异性研究表明MaCAD1基因组成型表达于香蕉各个组织。在耐病和感病品种中,MaCAD1均上调表达,但在耐病品种中MaCAD1在所有时间点相对于对照增加的倍数均高于感病品种,表明MaCAD1基因在香蕉的抗病性中起着重要作用,MaCAD1可以作为一个新的响应枯萎病侵染的标记基因。     

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda,Pinaceae)

A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for >7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the >1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits.     

丹参肉桂醇脱氢酶基因（SmCAD）的克隆及表达分析

肉桂醇脱氢酶（cinnamyl alcohol dehydrogenase,CAD）依赖于NADPH还原肉桂醛及其衍生物,是催化木质素单体生物合成途径的最后一步关键酶。通过分析丹参转录组数据库,从丹参中获得一条肉桂醇脱氢酶基因,命名为SmCAD（Genebank注册号：HQ162287）。该序列包含一个长为1083 bp的开放阅读框,有3个内含子和4个外显子,编码360个氨基酸,含有NADP（H）结合域,Zn1和Zn2锌结合位点。利用BD walking的方法获得其启动子序列1202 bp,序列分析结果表明,SmCAD启动子区包含茉莉酸甲酯（MeJA）、脱落酸（ABA）、赤霉素（GA3）响应元件以及MYB结合位点。利用实时荧光定量PCR分析表明,该基因在丹参根、茎、叶中均有表达,且其表达受到MeJA的诱导和GA3的抑制,推测该基因可能参与了丹参对外源信号的应答反应。研究结果可为进一步研究SmCAD基因在丹参中的具体功能提供理论依据。     

Comparative mapping in Pinus: sugar pine (Pinus lambertiana Dougl.) and loblolly pine (Pinus taeda L.)

The majority of genomic research in conifers has been conducted in the Pinus subgenus Pinus mostly due to the high economic importance of the species within this taxon. Genetic maps have been constructed for several of these pines and comparative mapping analyses have consistently revealed notable synteny. In contrast, little genomic research has been conducted on the Pinus subgenus Strobus, even though these pines have strong ecological relevance. We report a consensus genetic linkage map for sugar pine (Pinus lambertiana Dougl.) constructed with 399 single nucleotide polymorphisms markers derived from annotated genes. The map is 1,231 cM in length and organized into 19 linkage groups. Two of the mapping populations were derived from trees that were segregating for the major gene of resistance (Cr1) to Cronartium ribicola, the fungal pathogen responsible for white pine blister rust. The third mapping population was derived from a full-sib cross segregating for partial resistance to white pine blister rust. In addition, we report the first comparative mapping study between subgenera Strobus and Pinus. Sixty mapped markers were found in common between sugar pine and the loblolly pine reference map with 56 of them (93%) showing collinearity. All 19 linkage groups of the sugar pine consensus map coaligned to the 12 linkage groups of the loblolly pine reference map. The syntenic relationship observed between these two clades of pines provides a foundation for advancing genomic research and genetic resources in subgenus Strobus.     

Induction of somatic embryogenesis in loblolly pine (Pinus taeda L.)

Summary Several factors that may affect induction of somatic embryogenesis in loblolly pine (Pinus taeda L.) were investigated in 1994 and 1995. Megagametophytes containing immature zygotic embryos were excised from seeds as explants. Potassium chloride, silver nitrate, myo-inositol, coconut water, or polyamine was added to the control media (U.S. patent no. 5,036,007) to determine the effects of each single ingredient or their combinations on the initiation of embryogenic tissue. Supplements of myo-inositol at 22.2 mM resulted in increases in frequencies of cell mass extrusion and proliferation compared with the control media in consecutive years. Addition of silver nitrate showed the potential to promote initiation of embryogenic culture. The combination of 10 mM potassium with 29.4 μM silver nitrate achieved the highest frequencies in both extrusion and proliferation of embryogenic tissue. The combination of silver nitrate at 29.4 μM with addition of myo-inositol at 11.1 or 22.2 mM achieved a higher conversion rate from extrusion to proliferation. Polyamine did not significantly affect the induction of somatic embryogenesis, but coconut water was inhibitory. Published with approval of the Director of Arkansas Agricultural Experimental Station.