No description available.

Pinus radiata is the dominant species of the plantations forests in New Zealand. The forest industry in New Zealand is heavily dependant on it. However, Pinus radiata can develop wood quality flaw called 'intra-ring checking'. The checks or splits appear in wood during kiln drying and usually affect the earlywood region of the wood. It lowers value of appearance grade timber leading to huge economic loses for the forest industry. This thesis presents a study that was undertaken as a part of ongoing collaborative work that is being carried out to understand wood quality issues in Pinus radiata, with a vision of improving its wood quality. This study was a part of that effort and was conducted with an aim to gain an insight into intra-ring checking, and the process of xylogenesis in Pinus radiata. The investigations for this study were carried out in two steps. The first step was to understand intra-ring checking. The location of intra-ring checking was determined by observing the checks using various microscopy techniques. Scanning electron microscopy confirmed that checking was as an intercell failure that usually occurs at the cm1/S1 boundary. A comparative study was also conducted to see if the checked wood had some inherent properties that made it more susceptible to checking. It was found that checking could be influenced by tracheid geometry and cell wall thickness. If the wood had large tracheids with thin walls, it was more likely to develop checks during drying. Lignin distribution in the cell wall layers was also seen to play an important role in checking. Lower lignin levels and disruption in the pattern of lignification of the cell wall layers increased the tendency of the wood to develop checks. Similarly, it the tracheids have larger pits then their tendency to check increases. Structural features that disrupt the uniformity of the interlocking pattern of the tracheid such as rays and resin canals could also play a role in checking. Checked wood tends to have more surface area occupied by ray tissue. However, resin canals do not seem to be directly involved in checking, though their arrangement could indicate disturbances during xylogenesis. The second step was to understand the process of xylogenesis in Pinus radiata especially with respect to the influence of auxin and boron on it. Nutrient and organ culture methods were manipulated and successfully used to study xylogenesis. An exhaustive comparative study was carried out to observe and measure selected wood properties. Microscopy and image analysis revealed that auxin and boron changes in the medium led to the alterations in the cell division, expansion and lignification. However, the analysis of the measurements and the observations displayed complex 'between-tree' and 'within-culture variations'. Clear trends did not emerge from the analysis hence, a confident conclusion on the association between auxin, boron and lignification could not be drawn from this organ culture study. The study has added to the knowledge about checking and wood properties associated with it. A new tool of organ culture had been established that can hlep future research on the process of xylogenesis in Pinus radiata.

Douglas-fir develops a megagametophyte regardless of the pollination state of the ovule, whereas many other conifers develop a megagametophye in response to polli- nation. Megagametophytes in unfertilized ovules degrade two weeks following fertil- ization of the surrounding population. This is mediated by programmed cell death (PCD). Pollinated and unpollinated megagametophytes were dissected from Douglas- fir cones and extracted for RNA, which was then used as input for sequencing. A transcriptome was assembled from this data and expression levels were calculated. The data were fitted to quadratic regressions to produce coexpression groups. There is no clear upregulation of PCD effectors in the unpollinated megagametophyte. Po- tential regulators of megagametophyte fate are present in the data. Some are as- sociated with ABA signalling and proanthocyanadin biosynthesis while others share similarity to known regulators of PCD. Seed development processes are represented in the expression data, which support current knowledge of conifer seed development and provide targets for research. / Graduate / 0369 / 0309 / 0817 / igboyes@gmail.com

Pinus radiata is the dominant species of the plantations forests in New Zealand. The forest industry in New Zealand is heavily dependant on it. However, Pinus radiata can develop wood quality flaw called 'intra-ring checking'. The checks or splits appear in wood during kiln drying and usually affect the earlywood region of the wood. It lowers value of appearance grade timber leading to huge economic loses for the forest industry. This thesis presents a study that was undertaken as a part of ongoing collaborative work that is being carried out to understand wood quality issues in Pinus radiata, with a vision of improving its wood quality. This study was a part of that effort and was conducted with an aim to gain an insight into intra-ring checking, and the process of xylogenesis in Pinus radiata. The investigations for this study were carried out in two steps. The first step was to understand intra-ring checking. The location of intra-ring checking was determined by observing the checks using various microscopy techniques. Scanning electron microscopy confirmed that checking was as an intercell failure that usually occurs at the cm1/S1 boundary. A comparative study was also conducted to see if the checked wood had some inherent properties that made it more susceptible to checking. It was found that checking could be influenced by tracheid geometry and cell wall thickness. If the wood had large tracheids with thin walls, it was more likely to develop checks during drying. Lignin distribution in the cell wall layers was also seen to play an important role in checking. Lower lignin levels and disruption in the pattern of lignification of the cell wall layers increased the tendency of the wood to develop checks. Similarly, it the tracheids have larger pits then their tendency to check increases. Structural features that disrupt the uniformity of the interlocking pattern of the tracheid such as rays and resin canals could also play a role in checking. Checked wood tends to have more surface area occupied by ray tissue. However, resin canals do not seem to be directly involved in checking, though their arrangement could indicate disturbances during xylogenesis. The second step was to understand the process of xylogenesis in Pinus radiata especially with respect to the influence of auxin and boron on it. Nutrient and organ culture methods were manipulated and successfully used to study xylogenesis. An exhaustive comparative study was carried out to observe and measure selected wood properties. Microscopy and image analysis revealed that auxin and boron changes in the medium led to the alterations in the cell division, expansion and lignification. However, the analysis of the measurements and the observations displayed complex 'between-tree' and 'within-culture variations'. Clear trends did not emerge from the analysis hence, a confident conclusion on the association between auxin, boron and lignification could not be drawn from this organ culture study. The study has added to the knowledge about checking and wood properties associated with it. A new tool of organ culture had been established that can hlep future research on the process of xylogenesis in Pinus radiata.

No description available.

Our understanding of the natural world is constantly evolving and strengthening as more observations are made and experiments are performed. For example, we understand that tree stems grow toward the light (positive phototropism; Darwin 1880, Loehle 1986, Christie et al. 2013) and against gravity (negative gravitropism; Knight 1806, Hashiguchi et al. 2013). We also know that plants respond to mechanical stimulus and perturbation (thigmotropism; Braam 2005). Genes and their resulting proteins have been described to uncover some of the mechanisms for these environmental responses, but relatively speaking, we have just scratched the surface (Wyatt et al. 2013). While the discovery of the molecular mechanisms responsible for these behaviors is certainly dependent on the ever-improving lab technology available, every molecular discovery is dependent on a macroscopic observation. In this manuscript I present the two novel macroscopic observations I made on members of Araucaria in the urban forest. The first describes a hemisphere-dependent lean in A. columnaris, and the second provides genetic and morphological evidence that hybrids exist between A. columnaris and A. heterophylla. Araucaria columnaris (J.R. Forst.) Hooker, or the Cook Pine is a conifer with a narrow native range that has been cultivated worldwide and grows unlike any other tree known. The initial observation we made was that trees in California and Hawaii lean south, and trees in California lean to a greater extent than trees in Hawaii. Measuring 250 trees in 16 regions worldwide, however, produced statistically significant evidence for a hemisphere dependent directional leaning pattern. Trees in the northern hemisphere lean south, and trees in the southern hemisphere lean north. Additionally, the lean becomes more pronounced at greater distances from the equator. We also gathered morphological and genetic evidence in the California urban forest that A. columnaris and A. heterophylla (Salisb.) Franco are hybridizing. Many individuals have intermediate characteristics of both species, which originally led me to believe that hybrids exist in cultivation. After analyzing several individuals with microsatellite genetic markers, I have enough evidence to conclude that hybrids between A. columnaris and A. heterophylla exist. This is an important observation mainly for municipalities and arborists interested in properly identifying trees in the urban forest. Knowing the proper identity of trees is imperative to informing decisions about their protection or removal. As we continue to ask questions about the inner workings of nature we will continue to gain a better appreciation for what we still do not know. The evidence provided in this manuscript better informs our future questions about a leaning pattern in A. columnaris and about the history of the cultivation of Araucaria.

Sequencing efforts for gymnosperm genomes typically focus on nuclear and chloroplast DNA, with only three complete mitochondrial genomes published as of 2017. The availability of additional mitochondrial genomes would aid biological and evolutionary understanding of gymnosperms. Identifying mtDNA from existing whole genome sequencing (WGS) data (i.e. contigs) negates the need for additional experimental work but previous classification methods show limitations in sensitivity or accuracy, particularly in difficult cases. In this thesis I present a classification pipeline based on (1) kmer probability scoring and (2) SVM classification applied to the available contigs. Using this pipeline the mitochondrial genomes of six gymnosperm species were obtained: Abies sibirica, Gnetum gnemon, Juniperus communis, Picea abies, Pinus sylvestris and Taxus baccata. Cross-validation experiments showed a satisfying and forsome species excellent degree of accuracy. / Vid sekvensering av gymnospermers arvsmassa har fokus oftast lagts på kärn- och kloroplast-DNA. Bara tre fullständiga mitokondriegenom har publicerats hittills (2017). Fler mitokondriegenom skulle kunna leda till nya kunskaper om gymnospermers biologi och evolution. Då mitokondriernas arvsmassa identifieras från tillgängliga sekvenser för hela organismen (så kallade “contiger”) behövs inget ytterligare laboratoriearbete, men detta förfarande har visat sig leda till bristfällig känslighet och korrekthet, särskilt i svåra fall. I denna avhandling presenterar jag en metod baserad på (1) kmer-sannolikheter och (2) SVM-klassificering applicerad på de tillgängliga contigerna. Med denna metod togs arvsmassan för mitokondrien hos sex gymnospermer fram: Abies sibirica, Gnetum gnemon, Juniperus communis, Picea abies, Pinus sylvestris och Taxus baccata. Korsvalideringsexperiment visade en tillfredställande och för vissa arter utmärkt precision.

Most gymnosperms produce a pollination drop that captures and transports pollen into the ovule. Pollination drops have other functions. These include influencing pollen germination and pollen tube growth, defending the ovule from pathogens and providing a food reward in insect-pollinated gymnosperms. Mineral and organic molecules, including proteins, are responsible for these additional functions. To date, pollination drops from a handful of conifers and one non-conifer gymnosperm, Welwitschia mirabilis, have been subjected to proteomic analysis. In the present study, tandem mass spectrometry was used to detect proteins in all gymnosperm lineages: cycads (Ceratozamia hildae, Cycas rumphii, Zamia furfuracea); Gnetales (Ephedra compacta, E. distachya, E. foeminea, E. likiangensis, E. minuta, E. monosperma, E. trifurca; Gnetum gnemon; Welwitschia mirabilis); Ginkgo biloba; conifers (Taxus x media). PEAKS 6 DB (Bioinformatics Solutions, Waterloo, ON, Canada) was used to make protein identifications. Proteins were detected in all gymnosperm species analyzed. The numbers of proteins identified varied between samples as follows: one protein in Welwitschia female; nine proteins in Cycas rumphii; 13 proteins on average in Ephedra spp.; 17 proteins in Gnetum gnemon; 38 proteins on average in Zamia furfuracea; 57 proteins in Ginkgo biloba; 61 proteins in Ceratozamia hildae; 63 in Taxus x media; 138 proteins in Welwitschia male. The types of proteins identified varied widely. Proteins involved in carbohydrate modification, e.g. galactosidase, chitinase, glycosyl hydrolase, glucosidase, were present in most gymnosperms. Similarly, defence proteins, e.g. reduction-oxidation proteins, lipid-transfer proteins and thaumatin-like proteins, were identified in many gymnosperms. Gymnosperms that develop a deep pollen chamber as the nucellus degrades, e.g., cycads, Ginkgo, Ephedra, generally contained higher proportions of proteins localized to intracellular spaces. These proteins represent the pollination drop degradome. Gymnosperms that either lack a pollen chamber, e.g. Taxus, or have a shallow pollen chamber, e.g. Gnetum, had greater proportions of extracellular proteins. These proteins represent the pollination drop secretome. Our proteomic analyses support the hypothesis that the pollination drops of all extant gymnosperms constitute complex reproductive secretions. / Graduate

From studies of the circadian clock in the plant model species Arabidopsis (Arabidopsis thaliana), a number of important properties and components have emerged. These include the genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), GIGANTEA (GI), ZEITLUPE (ZTL) and TIMING OF CAB EXPRESSION 1 (TOC1 also known as PSEUDO-RESPONSE REGULATOR 1 (PRR1)) that via gene expression feedback loops participate in the circadian clock. Here, we present results from ectopic expression of four Norway spruce (Picea abies) putative homologs (PaCCA1, PaGI, PaZTL and PaPRR1) in Arabidopsis, their flowering time, circadian period length, red light response phenotypes and their effect on endogenous clock genes were assessed. For PaCCA1-ox and PaZTL-ox the results were consistent with Arabidopsis lines overexpressing the corresponding Arabidopsis genes. For PaGI consistent results were obtained when expressed in the gi2 mutant, while PaGI and PaPRR1 expressed in wild type did not display the expected phenotypes. These results suggest that protein function of PaCCA1, PaGI and PaZTL are at least partlyconserved compared to Arabidopsis homologs, however further studies are needed to reveal the protein function of PaPRR1. Our data suggest that components of thethree-loop network typical of the circadian clock in angiosperms were present beforethe split of gymnosperms and angiosperms.

Almost all conifer ovules produce a liquid secretion as part of reproduction. This secretion, termed an ovular secretion, is produced during ovule receptivity and is involved in pollen capture and transport. Historically, examinations of the ovular secretion have focused on how they are part of pollination mechanisms. As a result, the chemical composition of the ovular secretion has not been examined systematically. Investigations into the constituents of the ovular secretion were limited to analyses for simple water soluble compounds such as sugars, minerals, amino acids and organic acids. More recently, the protein component of the secretion has been investigated using mass spectrometry-based proteomics. Proteins involved in processes such as carbohydrate modification, proteolysis, and defence have been identified in conifer ovular secretions. This biochemical complexity suggests a broader view of the function of the ovular secretion is warranted. However, protein identifications only provide putative information on function. Functional characterization of these proteins is needed in order to fully understand how they contribute to ovular secretion function. The research outlined in this dissertation describes the first functional characterizations of proteins found in conifer ovular secretions. Three proteins - invertase, chitinase, and thaumatin-like protein - were characterized in the ovular secretions of Douglas-fir (Pseudotsuga menziesii) and hybrid yew (Taxus × media). The Douglas-fir ovular secretion is capable of converting sucrose to glucose and fructose, confirming that invertases present in the secretion are functional. The invertase activity was maximal at pH 4.0. Activity was 77% of maximal at pH 4.5, the physiological pH. This indicates that post-secretory hydrolysis of sucrose occurs in situ in the Douglas-fir ovular secretion. Invertases in the ovular secretion are likely involved in controlling the movement of carbohydrates to developing pollen and could facilitate pollen selection. Chitinases present in the Douglas-fir ovular secretion are functional at physiological conditions. All three modes of chitinolytic activity, i.e. endochitinase, chitobiosidase and β-N-acetylglucosaminidase, were detected at physiological pH. β-N-acetylglucosaminidase activity was 80 % of maximal at physiological pH. Chitinases are pathogenesis-related proteins capable of hydrolysing chitin in fungal cell walls. These results suggest the ovular secretion is capable of defending the ovule against infection by phytopathogens. Thaumatin-like protein was immunolocalized to the cell wall and amyloplasts in Douglas-fir and yew nucellar tissue in a pattern consistent with a defensive role. It was also localized to the cell wall of fungal spores and germinating hyphae that were present in the micropyle of a yew ovule. These results provide additional evidence for an antifungal role for the ovular secretion. Functioning enzymes involved in pollen-ovule interactions and ovule defence are present in the conifer ovular secretion. The ovular secretion has functions beyond pollen capture. A revised functional model for the conifer ovular secretion is proposed. / Graduate / 2021-08-17