Botany Commons^™

Next-Generation Biotechnology And Breeding Strategies For The Development Of Biotic Stress-Resistant Sugar Beet, Songül Gürel, Mehmet Cengi̇z Baloğlu, Pinar Baloğlu, Mehmet Kolçak, Ferhat Ulu, Ömer Can Ünüvar, Mehmet Örgeç, Özge Kaya, Ramazan Polat, Cemi̇le Köseoğlu, Yasemi̇n Çeli̇k Altunoğlu, Hati̇ce Korkmaz Güvenmez, Ekrem Gürel

Turkish Journal of Botany

Sugar beet is a high-sucrose crop primarily used for sugar production, and it is now gaining attention as a promising source for bioethanol production and cattle feed. This crop is also utilized for the extraction of pectin and the production of molasses. Despite its utilization across a wide range of industries, abiotic and biotic stress factors greatly reduce the productivity of the cash crop sugar beet. In this paper, we focus on the development of biotic stress-resistant sugar beet plants through various classical and biotechnological applications. In recent decades, omics technologies, next-generation sequencing, gene editing/silencing, and overexpression techniques have been …

Advanced Deep Learning Approaches For The Accurate Classification Of Phallaceae Fungi With Explainable Ai, Eda Kumru, Fati̇h Eki̇nci̇, Koray Açici, Ömer Burak Altindal, Mehmet Serdar Güzel, Ilgaz Akata

Turkish Journal of Botany

In this study, deep learning (DL)-based models were developed for the classification of 5 fungal species from the Phallaceae family (Clathrus ruber, Colus hirudinosus, Mutinus caninus, Phallus impudicus, and Pseudocolus fusiformis). ConvNeXT achieved the highest performance with 98% accuracy, 98% precision, 98% recall, and 98% F1-score. EfficientNetB4 and Xception also performed well with 96% accuracy. In contrast, lighter models such as MobileNetV2 and MixNet S showed significantly lower accuracy (84% and 80%, respectively). Among the explainable artificial intelligence (XAI) techniques, gradient-weighted class activation mapping (Grad-CAM) and Integrated Gradients showed that high-accuracy models focus more effectively on biologically meaningful regions. In …

Floral Trait Diversity Supports Multiple Pollination Systems Across Urban Habitats In One Of The World's Greenest Cities, Ana Paula Sales De Araujo Franco, Maxwell Da Rosa Oliveira, Evaldo Benedito De Souza, Ingrid Lohani Degering Brand, Marcus Paulo Goncalves Rosa, Bruno Henrique Dos Santos Ferreira, Maria Rosângela Sigrist

Turkish Journal of Botany

Green cities comprise a variety of habitats subject to different levels of anthropogenic pressure, ranging from completely unvegetated areas to vast green spaces such as linear parks. In this scenario, cities can support different ecological processes and ecosystem functions, which vary qualitatively and quantitatively between different habitat types along the urbanization gradient. Specifically, green spaces and ruderal plants can support pollination services in urban ecosystems, providing food resources (e.g., nectar, pollen, oil), reproduction supports (copulation sites), and nesting sites for pollinators. As a result, plant species and their floral resources are important for pollinator diversity and the maintenance of the …

Comparative Pollen Morphology Of The Genus Rhaponticoides Vaill. (Asteraceae) In Türkiye: Implications For Taxonomy And Phylogeny, Foroogh Tavakoli, Gürkan Semi̇z, Batikan Günal, Meryem Bozkurt, Tuna Uysal

Turkish Journal of Botany

The main focus of this research is the palynological investigation of Rhaponticoides Vaill. species naturally occurring in Türkiye. Light microscopy and scanning electron microscopy (SEM) were employed to examine the pollen morphology of nine Rhaponticoides species in detail. Hierarchical cluster analysis (HCA) was also conducted to identify closely related species and distinguish the investigated taxa based on palynological traits. The study found that the pollen grains were tricolporate, isopolar, monad, and radially symmetric, with an oblate-spheroidal shape as indicated by the polar/equatorial (P/E) ratio. The pollen measurements derived from the P/E ratio ranged between 0.85 and 1, values associated with …

Comparative Analysis Of The Complete Chloroplast Genome Of The Rare Endemic Palm Pinanga Arinasae Witono From Bali, Indonesia, Ni Putu Sri Asih, Risha Amilia Pratiwi, Istiana Prihatini, Paramita Cahyaningrum Kuswandi, Evy Yulianti, Arief Priyadi

Turkish Journal of Botany

Pinanga arinasae is an endangered species endemic to Bali, Indonesia. Our study aims to characterize its chloroplast genome, compare it with other chloroplast genomes, including its phylogenetic position within the Arecoideae subfamily, and identify potential molecular markers. P. arinasae chloroplast genomes characterization involves Illumina-based sequencing, de novo genome assembly, gene annotation, amino acid frequency, codon usage pattern analysis, and Simple Sequence Marker (SSR) identification. Comparative analysis include phylogenetic tree reconstruction, comparison of amino acid frequency, codon usage pattern, SSR number, inverted repeat junction arrangement, genome length, GC content, and gene number. Nucleotide diversity is calculated to identify substitution markers. The …

Erratum To “Anatomical And Palynological Studies On Turkish Primula Taxa (Primulaceae) And Their Taxonomic And Phylogenetic Significance [Turkish Journal Of Botany 49 (4) 2025 325-348 ] ”, Deni̇z Ulukuş, Esengül Özkaymakoğlu, Rebecca Stubbs, Hüseyi̇n Baykal, Kami̇l Coşkunçelebi̇, Osman Tugay, Barbara Keller, Elena Conti, Ferhat Celep

Turkish Journal of Botany

This erratum addresses an error concerning Figure 5 in the original published version of this article. During the typesetting process, Figure 5 was partially omitted, resulting in an incomplete figure being published.To correct this oversight and ensure the accuracy of the scholarly record, the complete Figure 5 is provided below for reference.

Link to the original article: https://doi.org/10.55730/1300-008X.2866

Optimizing Plant Nutrient Uptake: Cost Function Sensitivity Analysis Of The Fun Model, Gabriel Alpay, Joshua B. Fisher, Renato K. Braghiere, Edward R. Brzostek, Gabriella R. Dauber, Kara Allen, Rosemary A. Fisher

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

This study explores the cost functions of the Fixation & Uptake of Nutrients (FUN) model, which aims to optimize the amount of carbon used when plants acquire their necessary nutrients from the soil to maximize nitrogen (N) and phosphorus (P) uptake while minimizing the carbon cost. Specifically, we aimed to quantify the sensitivity of FUN outputs to the parameters belonging to the cost of nitrogen and phosphorus uptake functions by arbuscular mycorrhizal and ectomycorrhizal fungi. We present three dimensions of sensitivity analysis: (1) adjusting all parameters at the same time; (2) keeping one parameter constant while varying the other; and, …

Oregon State Rank Assessment For Split-Hair Paintbrush (Castilleja Schizotricha), Nora Dunkirk, Gabriel E. Campbell

Institute for Natural Resources Publications

Oregon state conservation status assessment for Split-hair paintbrush (Castilleja schizotricha) using NatureServe methodology, 2025.

The Evolution And Reproduction Of Andean Miconia (Melastomataceae), Juan Angulo

Dissertations, Theses, and Capstone Projects

Understanding the factors that shape diversification and distribution in tropical plant lineages is central to explaining the origins of Neotropical biodiversity. Assessing evolutionary history with trait evolution and climatic niche dynamics provides key insights into the drivers of diversification and biogeography, while natural history data remains critical for these evolutionary studies. The Tropical Andes, with its exceptional biodiversity and environmental heterogeneity, offers an ideal setting to explore these processes. In this dissertation, I investigate how reproductive systems, climatic niche dynamics, and pollination strategies influence the evolution and biogeography of Miconia III, a large and ecologically diverse clade in the …

Does Green Stem Photosynthesis Affect Plant Drought Tolerance And Recovery In Avocado?, Nadia A. Valverdi, Paula Guzmán-Delgado, Gregory R. Goldsmith, Eleinis Ávila-Lovera

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Woody plants with green stems may have advantages over non-green-stemmed plants in that extra photosynthetic carbon gain has the potential to improve plant drought tolerance and aid drought recovery. However, most studies relating to green stem photosynthesis and drought tolerance have been conducted on non-horticultural plants under natural growing conditions. We investigated whether avocado green stem photosynthesis enhances drought tolerance and recovery. We applied light exclusion and drought treatments to 3-year-old potted trees of cultivars ‘Hass’ and ‘Fuerte’. Measurements of soil moisture, midday stem water potential, stem photosynthesis, bark chlorophyll concentration, concentration of sugars + starch and stem hydraulic conductivity …

Large Scale Deletion And Rebalancing Within The K1c Kafirin Family In Sorghum, Tyler W. Ferris

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Sorghum bicolor (L.) Monech (sorghum) is cultivated as food for humans and livestock and is valued for its low input requirements. However, sorghum grain protein is deficient in the essential amino acid lysine and has poor protein digestibility because of the abundance of proline-rich kafirins that constitute >70% of proteins that form low-digestibility protein bodies. To reduce kafirin expression in the endosperm, and elicit wholesale proteome rebalancing to increase non-kafirin proteins, a single-guide RNA (sgRNA) Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) construct was previously used to target members of the highly-repetitive alpha-kafirin family, k1C in RTx430 sorghum. The …

Plant Reproductive Strategies Shift In Response To Restoration Using Beaver Dam Analogs, Laurel F. Martinez

Biology ETDs

As riparian communities become increasingly degraded, restoration treatments are being implemented in streams to recover ecosystem functions. In the Jemez Mountains, beaver dam analogs (BDAs) are used to restore degraded streams by connecting the floodplain and increasing the extent of anoxic soil conditions. These environmental disturbances are expected to alter how riparian plants recruit, particularly their allocation to seed-based and vegetative regeneration strategies. We investigated whether BDAs and associated changes in soil water filled pore space (WFPS) affected riparian plant recruitment. We investigated the number of flowering stems as a proxy for seed-based regeneration and rhizome length and mass as …

Anatomical And Palynological Studies On Turkish Primula Taxa (Primulaceae) And Their Taxonomic And Phylogenetic Significance, Deni̇z Ulukuş, Esengül Özkaymakoğlu, Rebecca Stubbs, Hüseyi̇n Baykal, Kami̇l Coşkunçelebi̇, Osman Tugay, Barbara Keller, Elena Conti, Ferhat Celep

Turkish Journal of Botany

Anatomical (scape, pedicel, leaf lamina, and leaf midrib) and pollen morphological features of 11 taxa belonging to the genus Primula subgen. Primula (P. vulgaris subsp. vulgaris, P. vulgaris subsp. rubra, and P.megaseifolia, P. meyeri,P. elatior subsp. pallasii, P. pseudoelatior, P. veris subsp. columnae, P. veris subsp. macrocalyx) and subgen. Aleurita (P. longipes, P. algida and P. auriculata) were examined using light and scanning electron microscopy to shed light on the existing taxonomic and phylogenetic relationships. The anatomical and palynological features of the majority of the taxa studied were revealed for the first time in this study. In anatomical studies, the …

Limited Soil Water Recharge In Summer Affects Seasonal Isotopic Signatures Of Tree Xylem Water, Marius G. Floriancic, Gregory R. Goldsmith, Harsh Beria, Scott T. Allen, James W. Kirchner

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Recent studies have reported that xylem waters in forest trees during the summer growing season are often isotopically similar to winter, rather than summer, precipitation. Several hypotheses have been proposed to explain this observation, which can be viewed as a form of ecohydrological separation, but empirical tests spanning space and time remain limited. We hypothesise that variations in the seasonal origin of precipitation found in tree xylem waters can be explained by seasonal differences in soil water recharge. We test this hypothesis by evaluating to what extent climatic aridity can explain seasonal signals in extensive surveys of the isotope ratios …

Bridging Prairie Restoration And Regenerative Agriculture With Compost Tea, April Hersey

2025 Symposium

Inland Pacific Northwest prairie is an endangered ecosystem that has been reduced by conversion to agriculture. There is growing interest in the role of soil microorganisms in prairie ecosystems, which may be crucial for restoration of the plant community through interspecies interactions within the soil near plant roots. One method for improving soil microorganism community composition is compost tea: enriched liquid compost extract. Compost tea is used in regenerative agriculture to improve crop yields and protect against pathogens, ostensibly through the activity of the added compost microbes. While research has supported compost tea application in regenerative agriculture, it has not …

Oregon State Rank Assessment For Limber Pine (Pinus Flexilis), Lindsey K. Wise

Institute for Natural Resources Publications

Oregon state conservation status assessment for limber pine (Pinus flexilis) using NatureServe methodology, 2025.

Oregon State Rank Assessment For Howell's Sandwort (Sabulina Howellii), Lindsey K. Wise, Nora Dunkirk

Institute for Natural Resources Publications

Oregon state conservation status assessment for Howell's sandwort (Sabulina howellii) using NatureServe methodology, 2025

Creek-Friendly Practices For Hoas, Plaster Creek Stewards

Print Materials

This booklet is intended to be a comprehensive guide to encourage Homeowner Associations (HOAs) in nurturing and safeguarding their local waterways. Within these pages the challenges facing our water ecosystems will be addressed, with particular focus being placed on the Plaster Creek Watershed in West Michigan. This booklet will also emphasize the role HOAs can play in fostering environmental stewardship and healthier, more resilient creek systems. This booklet contains practical strategies, from rain gardens to native plantings, that not only enhance the beauty of your HOA but extends care to downstream neighbors and the creek.

Soil Health In Nebraska: Exploring Practitioners' Needs And Insights From A Long-Term Organic Farm, Ingrids Isabel Mata Vigil

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Soil health is foundational to sustainable agriculture, environmental resilience, and long-term food security. Yet, the adoption of soil health assessments remains limited, often perceived as too technical, costly, or difficult to implement in real-world contexts. To better understand these challenges, the first chapter presents findings from a statewide survey of 41 soil health practitioners in Nebraska, including farmers, extension educators, NRCS staff, and conservation professionals. Respondents highlighted the need for simpler, more accessible, and context-specific tools for soil health assessment that help practitioners make informed decisions aligned with their management goals. Complementing these insights, the second chapter includes an independent, …

Scientific Note: Garden Loosestrife (Lysimachia Vulgaris, Primulaceae), An Emerging Invasive Plant Species Of Riparian Corridors In The Mid-Atlantic Region, Christopher T. Martine, Amy L. Jewitt, Claire M. Ciafre, Kaitlin G. Henry, Elizabeth H. Williams, Pj Newhart, Melody P. Sain

Faculty Journal Articles

Lysimachia vulgaris (garden loosestrife, Primulaceae) is an herbaceous perennial native to Europe that has been identified as an aggressive invasive species in parts of North America. The status of the species in the Mid-Atlantic region of the US, however, is poorly determined. Using recent field observations (from iNaturalist, iMapInvasives, and EDDMapS records) we here report localized incursions of L. vulgaris in the Susquehanna River Valley of central Pennsylvania, along with notes on its ecology, threats to native plant communities, and broader distribution in the state.

Catching A Fever: A Comparison Of Vachellia Xanthophloea Populations In The Limpopo And Luvuvhu River Floodplains Of The Makuleke Contractual Park, Kianie B. David

School of Natural Resources: Dissertations, Theses, and Student Research

This study investigates patterns of stand structure regeneration, growth characteristics, and coarse woody debris (CWD) patterns in Vachellia xanthophloea (fever tree) stands within the Makuleke Contractual Park (MCP), a semi-arid savanna system in northern Kruger National Park (KNP), South Africa. Fieldwork was conducted across two stand types: a monospecific fever tree stand in Rietbok Vlei and a mixed-species stand in the Western Nhlangaluwe Floodplain where fever tree is established with Faidherbia albida (ana tree). Data were collected from 20 total 1/4-acre (1,011 m²) circular plots between both stands in 2024 and 2025, including seedling root collar diameter (RCD), …

Insights Into The Floral Senescence Effects Of Nanoparticles, Vuk Uskoković

Administration and Staff Articles and Research

Flowers could be valuable addenda to nanomedicine labs as in vivo models crossing the gap between the cell culture and small mammals. However, as it is shown here, floral models continue to be predominantly utilized within resource-limited research environments and remain largely underrepresented in mainstream biomedical investigations conducted by well-funded institutions in the developed world. The ability to delay the senescence of Orange Jubilee wildflowers was tested here on three types of nanoparticles: selenite-doped hydroxyapatite (HAp), citrate-stabilized HAp, and superparamagnetic iron oxide. Integration of selenite into the HAp crystal lattice produced a mild increase in the senescence rate …

The Ecophysiology Of The Enigmatic Namib Succulent, Lithops Ruschiorum, Garrett Macleod Althausen

Environmental Studies Senior Theses

Water availability is the primary constraint for plant survival and reproduction in hyper-arid ecosystems. In such environments, plant fitness depends on an alignment between physiological traits and limited water resources. The Namib Desert of Namibia exemplifies this extreme selection pressure. Within the Namib Desert, Lithops ruschiorum, a succulent endemic to the gravel plains, exhibits habitat specificity and numerous physiological adaptations to cope with the hyper-aridity.

This research explores the intersection of two fitness strategies for L. ruschiorum: habitat selection and exploitation of alternative moisture sources. The first chapter explores the population dynamics and micro-site habitat conditions preferred by …

The Ethnobotany And Pharmacology Of Medicinal Plants For Caribbean Women’S Health, Ella Thomas Vardeman

Dissertations, Theses, and Capstone Projects

Approximately 55% of the world’s population lives in cities, and the United Nations estimates that this number will rise to 68% by 2050. Urban ethnobotany, the study of people’s traditional knowledge and use of plants in cities, is increasingly important as people adapt their cultural traditions to changing environments. In New York City (NYC), there have been several urban ethnobotany investigations in collaboration with Caribbean immigrant groups. However, there has yet to be an ethnobotanical survey that documents and botanically authenticates the medicinal plants used in the Haitian community. Previous collaborative research with women from the Caribbean in NYC has …

Subalpine And Alpine Plant Community Turnover In Yosemite National Park Following 30 Years Of Climate Warming, Rachel Friesen

Master's Theses

Subalpine and alpine regions in California are warming more rapidly than lower elevations. In response, high-elevation plants may acclimate or adapt to the new climate, move to higher elevations or latitudes, persist in refugia, or go extinct. While models predict substantial declines in subalpine and alpine plant communities due to discontinuous population distributions and lack of upslope area, actual responses may vary due to lags in dispersal, establishment, and extinction. Although shifts in high-elevation plant communities have been documented in other regions of the world, such changes have not yet been studied in Yosemite National Park. To assess high-elevation plant …

Fire Fossils: Biomineral Infrastructures In Untangling Climates, Tanmayee More

Masters Theses

Diatoms drift, sediments sink, wildfires generate their own weather. Lightning strikes can blast sand into glass, and microscopic organisms do the same in the cold recesses of the ocean. What alchemies and metabolisms catalyze space, time, and energy? What are the thermodynamics of infrastructure in Climate Change?

Places, materials, and beings are afterimages. Through alchemical experiments, and multi-scalar imaging, I develop simulations of wildfires, and their profound, reverberating effects. In this thesis, a glass-meets-landscape experimental process enters these obscured conditions and renders new material relations for the built environment.

Oregon State Rank Assessment For Maritime Goldfields (Lasthenia Maritima), Nora Dunkirk, Gabriel E. Campbell

Institute for Natural Resources Publications

Oregon state conservation status assessment for maritime goldfields (Lasthenia maritima) using NatureServe methodology, 2025.

Oregon State Rank Assessment For Siskiyou Iris (Iris Bracteata), Nora Dunkirk

Institute for Natural Resources Publications

Oregon state conservation status assessment for Siskiyou iris (Iris bracteata) using NatureServe methodology, 2025.

Oregon State Rank Assessment For Clackamas Iris (Iris Tenuis), Nora Dunkirk

Institute for Natural Resources Publications

Oregon state conservation status assessment for Clackamas iris (Iris tenuis) using NatureServe methodology, 2025.

Pollinator Plant Communities Within Restored Montane Longleaf Pine Ecosystems, Hanen Van Rossem

Master's Theses

Historically the fire-dependent and biodiverse longleaf pine (Pinus palustris) ecosystem was the dominant ecosystem of the Southeastern US. This ecosystem’s range was massively reduced due to land conversion and fire exclusion, causing the decline of many native species. Efforts to restore and protect longleaf pine stands are now ongoing with the goal of expanding habitat and refuge for threatened species. Differences in restoration practices and prior land use may influence the extent to which restored habitat patches can support pollinators and their plants. This study compared pollinator plant biodiversity between restored neighboring montane longleaf pine stands that differed in …