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Transcription Through The Eye Of A Needle: Daily And Annual Cyclic Gene Expression Variation In Douglas-Fir Needles, Peter Dolan

Computer Science Publications

Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using …

Enhancing Soybean Photosynthetic Co2 Assimilation Using A Cyanobacterial Membrane Protein, Ictb, William T. Hay, Saadia Bihmidine, Nedim Mutlu, Khang Le Hoang, Tala Awada, Donald P. Weeks, Thomas Clemente, Stephen P. Long

Center for Plant Science Innovation: Faculty Publications

Soybean C₃ photosynthesis can suffer a severe loss in efficiency due to photorespiration and the lack of a carbon concentrating mechanism (CCM) such as those present in other plant species or cyanobac-teria. Transgenic soybean (Glycine max cv. Thorne) plants constitutively expressing cyanobacterial ictB (inorganic carbon transporter B) gene were generated using Agrobacterium-mediated transformation. Although more recent data suggest that ictB does not actively transport HCO3-/CO2, there is nevertheless mounting evidence that transformation with this gene can increase higher plant photosynthesis. The hypothesis that expression of the ictB gene would improve photosynthesis, biomass production and seed yield in soybean …

A Multidomain Enzyme, With Glycerol-3-Phosphate Dehydrogenase And Phosphatase Activities, Is Involved In A Chloroplastic Pathway For Glycerol Synthesis In Chlamydomonas Reinhardtii, Daniela Morales-Sánchez, Yeongho Kim, Ee Leng Terng, Laura Peterson, Heriberto D. Cerutti

Center for Plant Science Innovation: Faculty Publications

Understanding the unique features of algal metabolism may be necessary to realize the full potential of algae as feedstock for the production of biofuels and biomaterials. Under nitrogen deprivation, the green alga C. reinhardtii showed substantial triacylglycerol (TAG) accumulation and up-regulation of a gene, GPD2, encoding a multidomain enzyme with a putative phosphoserine phosphatase (PSP) motif fused to glycerol-3-phosphate dehydrogenase (GPD) domains. Canonical GPD enzymes catalyze the synthesis of glycerol-3-phosphate (G3P) by reduction of dihydroxyacetone phosphate (DHAP). G3P forms the backbone of TAGs and membrane glycerolipids and it can be dephosphorylated to yield glycerol, an osmotic stabilizer and compatible …

Expression Of Cyanobacterial Fbp/Sbpase In Soybean Prevents Yield Depression Under Future Climate Conditions, Iris H. Köhler, Ursula M. Ruiz-Vera, Andy Vanloocke, Michell L. Thomey, Thomas Clemente, Stephen P. Long, Donald R. Ort, Carl J. Bernacchi

Center for Plant Science Innovation: Faculty Publications

Predictions suggest that current crop production needs to double by 2050 to meet global food and energy demands. Based on theory and experimental studies, overexpression of the photosynthetic enzyme sedoheptulose-1,7-bisphosphatase (SBPase) is expected to enhance C₃ crop photosynthesis and yields. Here we test how expression of the cyanobacterial, bifunctional fructose-1,6/sedoheptulose-1,7-bisphosphatase (FBP/SBPase) affects carbon assimilation and seed yield (SY) in a major crop (soybean, Glycine max). For three growing seasons, wild-type (WT) and FBP/SBPase-expressing (FS) plants were grown in the field under ambient (400 μmol mol⁻¹) and elevated (600 μmol mol⁻¹) CO₂ concentrations [CO …

Overexpression Of Sbmyb60 In Sorghum Bicolor Impacts Both Primary And Secondary Metabolism, Erin D. Scully, Tammy Gries, Nathan A. Palmer, Gautam Sarath, Deanna L. Funnell-Harris, Lisa Baird, Paul Twigg, Javier Seravalli, Thomas E. Clemente, Scott E. Sattler

Center for Plant Science Innovation: Faculty Publications

• Few transcription factors have been identified in C₄ grasses that either positively or negatively regulate monolignol biosynthesis.
• Previously, the overexpression of SbMyb60 in sorghum (Sorghum bicolor) has been shown to induce monolignol biosynthesis, which leads to elevated lignin deposition and altered cell wall composition. To determine how SbMyb60 overexpression impacts other metabolic pathways, RNA-Seq and metabolite profiling were performed on stalks and leaves.
• 35S::SbMyb60 was associated with the transcriptional activation of genes involved in aromatic amino acid, S-adenosyl methionine (SAM) and folate biosynthetic pathways. The high coexpression values between SbMyb60 and genes assigned to these pathways indicate …

Complete Mitochondrial Genomes From The Ferns Ophioglossum Californicum And Psilotum Nudum Are Highly Repetitive With The Largest Organellar Introns, Wenhu Guo, Andan Zhu, Weishu Fan, Jeffrey P. Mower

Center for Plant Science Innovation: Faculty Publications

• Currently, complete mitochondrial genomes (mitogenomes) are available from all major land plant lineages except ferns. Sequencing of fern mitogenomes could shed light on the major evolutionary transitions that established mitogenomic diversity among extant lineages.

• In this study, we generated complete mitogenomes from the adder’s tongue fern (Ophioglossum californicum) and the whisk fern (Psilotum nudum).

• The Psilotum mitogenome (628 kb) contains a rich complement of genes and introns, some of which are the largest of any green plant organellar genome. In the Ophioglossum mitogenome (372 kb), gene and intron content is slightly reduced, including the loss of …

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Plants With Useful Traits And Related Methods, Sally Ann Mackenzie, Roberto De La Rosa Santamaria

Center for Plant Science Innovation: Faculty Publications

The present invention provides methods for obtaining plants that exhibit useful traits by transient suppression of the MSH1 gene of the plants. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants.

Conventional And Unconventional Ubiquitination In Plant Immunity, Bangjun Zhou, Lirong Zeng

Center for Plant Science Innovation: Faculty Publications

Ubiquitination is one of the most abundant types of protein post-translational modification (PTM) in plant cells. The importance of ubiquitination in the regulation of many aspects of plant immunity has been increasingly appreciated in recent years. Most of the studies linking ubiquitination to the plant immune system, however, have been focused on the E3 ubiquitin ligases and the conventional ubiquitination that leads to the degradation of the substrate proteins by the 26S proteasome. By contrast, our knowledge about the role of unconventional ubiquitination that often serves as non-degradative, regulatory signal remains a sig- nificant gap. We discuss, in this review, …

Molecular Diversity Of Foliar Fungal Endophytes In Relation To Defense Strategies And Disease In Whitebark Pine, Lorinda Bullington

Graduate Student Theses, Dissertations, & Professional Papers

An invasive fungal pathogen, Cronartium ribicola (the causative agent of white pine blister rust) infects and kills whitebark pine (Pinus albicaulis) throughout the western US. Blister rust has decreased whitebark pine populations by over 90% in some areas. Whitebark pine, a keystone species, has been proposed for listing under the Endangered Species Act in the U.S., and the loss of this conifer is predicted to have severe impacts on forest composition and function in high elevations. Hundreds of asymptomatic fungal species live inside whitebark pine tissue, and recent studies suggest that these fungi can influence the frequency and …

Impact Of A High Oil And Protein On Agronomic Traits And Overall Seed Composition In Soybean, Maythem Al-Amery

Theses and Dissertations--Plant and Soil Sciences

New soybean lines have been developed with significantly higher oil, protein + oil and higher meal protein. These soybeans contain a VgD1 gene (highly active acyl-CoA:diacylglycerol acyltransferase, DGAT from Vernonia galamensis (VgDGAT1A) produces much higher oil synthesis and accumulation activity in soybean. Soybean with active DGAT from Vernonia galamensis (VgDGAT1A) has active TAG biosynthesis relative to other DGATs including from soybeans and Arabidopsis. DGATs catalyze the final step of TAG synthesis: DAG (diacylglycerol) + acyl-CoA → TAG + CoASH (Coenzyme A is notable for its role in the synthesis and oxidation of fatty acids, and the oxidation of pyruvate in …

Molecular Characterization Of Spot Blotch And Bacterial Leaf Streak Resistance In Bread Wheat, Girma Ayana

Electronic Theses and Dissertations

Spot blotch (SB), caused by Bipolaris sorokiniana (Sacc.) Shoem, and bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa (Smith et al.), two important foliar diseases of wheat in the major production regions of the US and the world. Deployment of adequate host resistance against them depends on determining the resistance genes or quantitative trait loci (QTLs) responsible for the trait and identification of genetic markers linked to QTL that facilitate markers assisted breeding. We conducted two independent studies and characterized QTLs for BLS and SB resistance. In the first study, we constructed a genetic linkage map of 1,211 …

Differential Gene Expression In Two Nodule Zones Of Soybean, Sunita Pathak

Electronic Theses and Dissertations

Soybean, a leguminous plant and rhizobia establishes symbiotic relationships, forming root nodules. Nodule organogenesis starts with cortical cell division forming infection and parenchyma zones which houses N-fixing bacteria and block O2 for nitrogenase enzyme function, respectively. The mechanism by which root cortical cells give rise to two structurally and functionally different nodule tissues is not known. One approach to address this knowledge gap is to evaluate global gene expression patterns in these two tissue types during nodule development. Using INTACT method, we developed two promoters, ENOD2 (nodule parenchyma) and ENOD40 (infection zone) driven nuclear envelope biotin tagging constructs and isolated …

Silencing Seed Dormancy Genes To Mitigate Risk Of Transgene Flow To Weedy Rice, Alexander Wireko Kena

Electronic Theses and Dissertations

The flow of fitness-enhancing transgenes from genetically modified crops into wild/weed relatives may cause serious ecological and economic consequences. Seed dormancy (SD) is a key adaptive trait that distributes germination over time, resulting in weed persistence in agroecosystems. Thus, silencing major genes controlling SD would reduce the adaptive fitness of weeds. SD-enhancing genes cloned from weedy rice include SD7-1, SD7-2, SD12a, SD12b, and SD12c. The goal of this study was to develop a transgenic mitigation (TM) strategy using SD gene-silencing structures as mitigating factors to reduce the risk of transgene flow to wild/weed populations. TM vector constructs consisted of the …

Primers For Castilleja And Their Utility Across Orobanchaceae: I. Chloroplast Primers, Maribeth Latvis, Sebastian M. E. Mortimer, Diego F. Morales-Briones, Samuel Torpey, Simon Uribe-Convers, Sarah J. Jacobs, Sarah Mathews, David C. Tank

Natural Resource Management Faculty Publications

Premise of the study: Chloroplast primers were developed from genomic data for the taxonomically challenging genus Castilleja. We further tested the broader utility of these primers across Orobanchaceae, identifying a core set of chloroplast primers amplifying across the clade.
Methods and Results: Using a combination of three low-coverage Castilleja genomes and sequence data from 12 Castilleja plastomes, 76 primer combinations were specifically designed and tested for Castilleja. The primers targeted the most variable portions of the plastome and were validated for their applicability across the clade. Of these, 38 primer combinations were subsequently evaluated in silico and then validated across …

Midwest Vegetable Trial Report For 2016, Elizabeth Maynard, Brad Bergefurd

Purdue Fruit and Vegetable Research Reports

This is a compilation of 21 research trial reports from six land-grant universities in the midwestern United States. Crops include dry beans, cantaloupe, cucumber, pepper, pumpkin, sweet corn, summer squash, winter squash, strawberry, tomato, watermelon, and winter melon. Several crops were evaluated in high tunnels or hoop houses. Most trials evaluated different cultivars or varieties. Three reports addressed specific growing practices: the use of poly-coated urea to supply nitrogen to sweet corn, potassium fertilization for high tunnel tomatoes, and use of cereal rye cover crop in butternut squash.

Midwest Vegetable Trial Report For 2016, Elizabeth Maynard, Brad Bergefurd

Midwest Vegetable Trial Reports

This is a compilation of 21 research trial reports from six land-grant universities in the midwestern United States. Crops include dry beans, cantaloupe, cucumber, pepper, pumpkin, sweet corn, summer squash, winter squash, strawberry, tomato, watermelon, and winter melon. Several crops were evaluated in high tunnels or hoop houses. Most trials evaluated different cultivars or varieties. Three reports addressed specific growing practices: the use of poly-coated urea to supply nitrogen to sweet corn, potassium fertilization for high tunnel tomatoes, and use of cereal rye cover crop in butternut squash.

Neutral And Adaptive Genetic Variation In North American Hardwood Tree Species, Sudhir Khodwekar

Dissertations, Master's Theses and Master's Reports

'Northern Hardwoods,’ are a characteristic composition of multiple tree species and a part of the rich and diverse northeastern forests. Hardwoods e.g. oaks (Quercus: Fagaceae and Sugar maple), serve as foundation species and offer ecological and economical gains to wildlife and humans. Most of the forest trees go through many biotic and abiotic stresses, for example climate change in their long life span. To overcome these threats and to adapt to changing conditions, tree species need to maintain variation especially in adaptive genes. Therefore, it is necessary to analyze genetic diversity within forest tree populations and take appropriate …

Association Mapping Of Seed Weight, Protein, And Sucrose Content; And Kinetics Of Edamame Under Infrared Treatment, Laura Melissa Lara Santisteban

Graduate Theses and Dissertations

Edamame is a specialty large-seeded soybean (Glycine max L. Merr.) harvested at an immature stage (R6) that has become the second largest consumed soyfood. Although United States is the largest soybean producer, majority of edamame is imported from Asia, highlighting the importance of developing new edamame varieties. Association mapping (AM) provides an alternative to bi-parental linkage mapping method to detect quantitative trait loci (QTL) adding higher resolution and broader germplasm information. Seed weight, sucrose, and protein are quantitative traits of value when selecting edamame lines. However molecular mechanisms controlling each of these traits are still inconclusive and have not been …

Development Of Highly Variable Microsatellite Markers For The Tetraploid Silene Stellata (Caryophyllaceae), Juannan Zhou, Michele R. Dudash, Charles B. Fenster, Elizabeth A. Zimmer

Natural Resource Management Faculty Publications

Premise of the study:We designed and tested microsatellite markers for the North American native species Silene stellata (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success.

Methods and Results: A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of S. stellata, with di- or trinucleotide repeats. Genotyping results showed the number of alleles per locus ranged from six to 45 and expected heterozygosity ranged from 0.511 to 0.951. Five of these loci were successfully amplified in S. …

Quantitative Trait Loci Mapping, Genome-Wide Association Analysis, And Gene Expression Of Salt Tolerance In Soybean, Ailan Zeng

Graduate Theses and Dissertations

Salt stress is a common abiotic stress causing yield reduction in soybean. There are differential responses, namely tolerance (excluder) and intolerance (includer), among soybean germplasm. However, the genetic and physiological mechanism for salt tolerance is not clear. Identification of novel QTL for salt tolerance and genes that are differentially expressed under salt stress would help elucidate the salt tolerance mechanism and facilitate the development of salt tolerant cultivars through marker assisted selection (MAS). The objectives of this study were to identify new QTL or genes responsible for salt tolerance using three approaches: QTL mapping, association analysis, and RNA sequencing (RNA-seq). …