Thesis (MS)--Montana State University--Bozeman, 2009. / Typescript. Chairperson, Graduate Committee: Luther E. Talbert. Includes bibliographical references (leaves 46-52).

The introduction of dwarfing genes in wheat and rice enabled significant yield improvements and was later termed the “Green-Revolution”. Dwarfing genes in sorghum have not been accompanied by such increases in grain production. On the contrary, some of the commercially employed dwarfing genes in sorghum have been associated with negative effects on grain yield. A positive correlation between plant height and grain yield was also observed in trial data for a diverse range of hybrids tested within the Queensland Department of Primary Industries and Fisheries Sorghum Breeding Program in north-eastern Australia. No attempts have previously been made to examine the physiological basis of the relationship between plant height and grain yield in sorghum. The dwarfing genes that are commercially used in wheat, Rht-B1 and Rht-D1 (formerly known as Rht1 and Rht2, respectively), on the other hand, have been studied extensively. They have been shown to have substantial and positive effects on grain number and harvest index, while not considerably reducing plant biomass, increasing grain yield. Our objective in this study was to examine the effect of height on the physiological and genetic determinants of growth and yield in sorghum to determine whether there was scope to improve yield by increasing the height of sorghum. A positive correlation between plant height and yield was observed in a population that was fixed for the major dwarfing genes, but showed variation in peduncle and panicle length, which are under control of minor dwarfing genes. To study the effects of a single major dwarfing gene (dw3) on biomass production and grain yield, 2- and 3-dwarf isogenic contrasts were developed in three different genetic backgrounds (R931945-2-2, R955343-1, R955637). In some cases, dw3 led to a significant reduction in plant biomass, which was not sufficiently offset by increase in harvest index to avoid yield reduction. This is contrary to the situation in wheat. The observed reductions in plant biomass in sorghum were associated with reduced tiller number and a reduction in radiation use efficiency (RUE) in the short types. Subsequent experiments suggested that an increase in allocation of biomass to the roots, rather than differences in photosynthetic capacity or respiration, was the main cause for the apparent reduction in RUE. However, due to plant-to-plant variability and the difficulty in accurately measuring root-total biomass ratio, studies with greater replication are required to confirm this hypothesis. It was also found that interactions with genetic background (and environment) moderated the effects of dw3, resulting in smaller height, biomass and grain yield reductions in some isogenic pairs. The effects of dwarfing genes on grain yield therefore need to be assessed separately for different genetic backgrounds. As lodging may be controlled by means other than height reduction (e.g. stay-green), we suggest that yield of standard sorghum types used in industrialised countries may benefit from moderate increases in plant height.

Los cítricos son huéspedes naturales de diferentes especies de viroides, todos pertenecientes a la familia Pospiviroidae. Estudios preliminares para detectar viroides en especies y variedades comerciales dieron resultados erráticos, excepto cuando se utilizaba la especie indicadora cidro Etrog como huésped bioamplificador. Para evitar el uso de este huésped en los ensayos de detección, se desarrolló un método basado en la hibridación northern. El protocolo desarrollado consistía en: (i) extracción de ácidos nucleicos de muestras de corteza recolectadas en diferentes épocas y/o almacenadas en distintas condiciones; (ii) separación de los RNAs en 5% PAGE o 1% agarosa y transferencia a membranas; (iii) hibridación con sondas de DNA marcadas con digoxigenina (DIG) específicas para cada viroide, detección con un anticuerpo anti-DIG conjugado con fosfatasa alcalina y revelado con un substrato quimioluminiscente (CSPD). Con este método se pueden detectar viroides en todas las especies de cítricos ensayadas. La técnica es extremadamente sensible, y acorta el tiempo necesario para la detección fiable de los viroides de cítricos conocidos hasta el momento. La aplicación de esta técnica ha permitido realizar prospecciones en árboles cultivados en distintas regiones citrícolas de Colombia, Perú y Brasil. En limas Tahití de Colombia se han identificado infecciones múltiples con HSVd y CDVd o con CEVd, HSVd y CDVd. Las muestras procedentes del Banco de Germoplasma de Palmira estaban libres de viroides, excepto una fuente de cidro Etrog que estaba infectada con CEVd y CDVd. / Murcia Riaño, N. (2009). DETECCIÓN Y CARACTERIZACIÓN AGRONÓMICA DE VIROIDES DE CÍTRICOS. IDENTIFICACIÓN Y CARACTERIZACIÓN MOLECULAR Y BIOLOGÍCA DE VARIANTES DEL VIROIDE DEL ENANISMO DE LOS CÍTRICOS CDVd [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/6343 / Palancia

For millennia, scions have been grafted onto dwarfing apple rootstocks to reduce final tree size. However, it is unclear how scion architecture is first modified by the dwarfing apple rootstock, the time from grafting when this occurs and the endogenous hormonal signalling mechanisms that may cause the initial modifications in growth that then define the future architecture of the scion. In this study, the dwarfing (M.9) rootstock significantly decreased the mean total shoot length and node number of ‘Royal Gala’ apple scions by the end of the first year of growth from grafting when compared with rootstock(s) of greater vigour (MM.106, M.793 and a ‘Royal Gala’ rootstock control). Similarly, the auxin transport inhibitor 1-N-naphthylphthalamic acid (NPA) applied to the stem of vigorous rootstocks significantly decreased mean total shoot length and node number of the scion, and the architectural changes imposed were generally similar to those imposed by M.9. For example, both treatments decreased the mean length and node number of the primary shoot, reduced the formation of secondary axes on the primary shoot and caused a greater proportion of primary and secondary shoots (if present) to terminate growth early. Decreased formation of secondary axes imposed by both treatments was reversed by applying the cytokinin benzylaminopurine (BAP) repeatedly to the scion, whilst applications of gibberellins (GA4+7) reduced the proportion of primary and secondary shoots that terminated growth early, therefore increasing the final mean length and node number of these shoot types. Both M.9 and NPA also significantly decreased the final mean dry mass and length of the root system. Given these general similarities, it is proposed that the basipetal IAA signal is of central importance in rootstock-induced scion dwarfing, and that a shoot/root/shoot signalling mechanism may exist whereby the stem tissue of the M.9 rootstock decreases the basipetal transport of IAA to the root during summer, thereby decreasing root growth and the amount of rootproduced cytokinin and gibberellin transported to scion. Reduced amounts of cytokinin transported to the scion may decrease branching, whilst reduced amounts of gibberellins may decrease the duration for which a large proportion of primary and secondary shoots grow. Analysis of endogenous hormones for newly grafted composite ‘Royal Gala’ apple trees on rootstocks of different vigour provided some additional support for these ideas. It is recommended that future studies elucidate what unique properties of the M.9 bark act to restrict IAA transport, whilst it is concluded that gene(s) regulating rootstock-induced scion dwarfing are likely to control processes within the rootstock that modify the metabolism of IAA, its basipetal transport and the subsequent synthesis of root-produced vigour-inducing hormones including cytokinins and gibberellins.

<p>The Mediator (Med) complex comprises about 30 subunits and is a transcriptional co-regulator in eukaryotic systems. The core Mediator complex, consisting of the head, middle and tail modules, functions as a bridge between transcription factors and basal transcription machinery, whereas the CDK8 kinase module can attenuate Mediator’s ability to function as either a co-activator or co-repressor. Many Arabidopsis Mediator subunit has been functionally characterized, which reveals critical roles of Mediator in many aspects of plant growth and development, responses to biotic and abiotic stimuli, and metabolic homeostasis. Traditional genetic and biochemical approaches laid the foundation for our understanding of Mediator function, but recent transcriptomic and metabolomic studies have provided deeper insights into how specific subunits cooperate in the regulation of plant metabolism. In Chapter 1, we highlight recent developments in the investigation of Mediator and plant metabolism, with emphasis on the large-scale biology studies of <i>med</i> mutants.</p> <p>We previously found that MED5, an Arabidopsis Mediator tail subunit, is required for maintaining phenylpropanoid homeostasis. A semi-dominant mutation (<i>reduced epidermal fluorescence 4-3</i>, <i>ref4-3</i>) that causes a single amino acid substitution in MED5b functions as a strong suppressor of the pathway, leading to <a>decreased soluble phenylpropanoid accumulation, reduced lignin content and dwarfism</a>. In contrast, loss of MED5a and MED5b (<i>med5</i>) results in increased levels of phenylpropanoids. In Chapter 2, we present our finding that <i>ref4-3</i> requires CDK8, a Mediator kinase module subunit, to repress plant growth even though the repression of phenylpropanoid metabolism in <i>ref4-3 </i>is CDK8-independent. Transcriptome profiling revealed that salicylic acid (SA) biosynthesis genes are up-regulated in a CDK8-dependent manner in <i>ref4-3,</i> resulting in hyper-accumulation of SA and up-regulation of SA response genes. Both growth repression and hyper-accumulation of SA in <i>ref4-3</i> require CDK8 with intact kinase activity, but these SA phenotypes are not connected with dwarfing. In contrast, mRNA-sequencing (RNA-seq) analysis revealed the up-regulation of a DNA J protein-encoding gene in <i>ref4-3</i>, the elimination of which partially suppresses dwarfing. Together, our study reveals genetic interactions between Mediator tail and kinase module subunits and enhances our understanding of dwarfing in phenylpropanoid pathway mutants.</p> <p>In Chapter 3, we characterize other phenotypes of <i>med5</i> and <i>ref4-3</i>, and find that in addition to the up-regulated phenylpropanoid metabolism, <i>med5</i> show other interesting phenotypes including hypocotyl and petiole elongation as well as accelerated flowering, all of which are known collectively as the shade avoidance syndrome (SAS), suggesting that MED5 antagonize shade avoidance in wild-type plants. In contrast, the constitutive <i>ref4-3 </i>mutant protein inhibits the process, and the stunted growth of <i>ref4-3 </i>mutants is substantially alleviated by the light treatment that triggers SAS. Moreover, <i>ref4-3</i> mimics the loss-of-function <i>med5</i> mutants in maintaining abscisic acid (ABA) levels under both normal and drought growth conditions. The phenotypic characterization of <i>med5</i> mutants extend our understanding of the role of Mediator in SAS and ABA signaling, providing further insight into the physiological and metabolic responses that require MED5.</p> <p>In Chapter 4, we explore the function of MED5 and CDK8 in gene expression regulation by investigating the effect of mutations in Mediator including <i>med5</i>, <i>ref4-3</i>, <i>cdk8-1</i> and <i>ref4-3 cdk8-1</i> on genome-wide Pol II distribution. We find that loss of MED5 results in loss of Pol II occupancy at many target genes. In contrast, many genes show enriched Pol II levels in <i>ref4-3</i>, some of which overlap with those showing reduced Pol II occupancy in <i>med5</i>. In addition, Pol II occupancy is significantly reduced when CDK8 is disrupted in <i>ref4-3</i>. Our results help to narrow down the direct gene targets of MED5 and identify genes that may be closely related to the growth deficiency observed in <i>ref4-3</i> plants, providing a critical foundation to elucidate the molecular function of Mediator in transcription regulation.</p>