Genetics and Genomics Commons^™

With Love, ; An Interdisciplinary And Intersectional Look At Why Creativity Is Essential, Theo Starr Gardner

Whittier Scholars Program

My Whittier Scholars Program self-designed major, Teaching Creativity, is a mixture of Art, Literature, and Education classes. My research and praxis classes have been focused on the ‘how?’s and 'why?’s of creativity, so it felt only right that my project should be a constructivist, generative project. The project I have been working on throughout my time at Whittier, and that has just fully come to fruition on April 11th, 2024, was a solo art gallery/open mic event entitled ‘With Love,’. With Love, was conceptually inspired by the research I’ve conducted on creativity and creative arts education over the past few …

Pile Burning After Conifer Removal From Aspen Stands Affects Tree Mortality, Regeneration, And Understory Recovery, John-Pascal Berrill, Christa M. Dagley, Yoon G. Kim, J. Morgan Varner

Aspen Bibliography

Quaking aspen (Populus tremuloides Michx.) stands throughout the western United States provide valuable ecosystem services but can be lost via succession from aspen to conifer. Forest managers are cutting conifers, but disposal of cut wood can be challenging in remote or sensitive areas. Piling and burning is being tested within aspen stands but ecosystem responses to this treatment are understudied. We assessed aspen tree mortality, tree regeneration, and understory vegetation after forest restoration thinning followed by pile burning in seven aspen-conifer stands around Lake Tahoe, California and Nevada, USA. Pile burning was conducted after cut wood had dried (1.5–7.5 …

Aspen And Spruce Densities Affect Tree Size, Future Stand Volume, And Aboveground Carbon Following Precommercial Thinning, Philip G. Comeau, Mike Bokalo

Aspen Bibliography

Data collected over a 30-year period from an experiment replicated across 21 locations in western Canada are used to explore the effects of precommercial thinning of trembling aspen to a range of densities in combination with three initial white spruce densities on tree growth and stand dynamics. Increasing differentiation amongst the 15 treatments was observed with age after thinning for both spruce and aspen responses. Spruce height and diameter declined with increasing aspen density. At age 10 spruce diameter with no aspen was 1.5× that of spruce in unthinned while it was 2.6× that of spruce in unthinned at age …

Soybean Genetics, Genomics, And Breeding For Improving Nutritional Value And Reducing Antinutritional Traits In Food And Feed, William M. Singer, Yi-Chen Lee, Zachary Shea, Caio Canella Vieira, Dongho Lee, Xiaoying Li, Mia Cunicelli, Shaila S. Kadam, Mohammad Amir Waseem Khan, Grover Shannon, M. A. Rouf Mian, Henry T. Nguyen, Bo Zhang

Agriculture Faculty Publications

Soybean [Glycine max(L.) Merr.] is a globally important crop due to its valuable seed composition, versatile feed, food, and industrial end-uses, and consistent genetic gain. Successful genetic gain in soybean has led to widespread adaptation and increased value for producers, processors, and consumers. Specific focus on the nutritional quality of soybean seed composition for food and feed has further elucidated genetic knowledge and bolstered breeding progress. Seed components are historical and current targets for soybean breeders seeking to improve nutritional quality of soybean. This article reviews genetic and genomic foundations for improvement of nutritionally important traits, such as protein and …

Genetic Evaluation Of Enteric Methane For Sustainable Irish Beef Cattle, Clodagh Ryan

ORBioM (Open Research BioSciences Meeting)

Background:

Globally, livestock agriculture significantly contributes to human-induced greenhouse gas emissions, particularly through methane production. A potential approach to effectively, durably, and progressively reduce enteric methane emissions at a reasonable cost is through animal breeding.

Methods:

Individual animal methane records were available from 1,508 multi-breed growing beef cattle using GreenFeed Emission Monitoring systems. The objective of this study was to derive genetic parameters for a series of definitions of enteric methane, carbon dioxide, and dry matter intake (DMI). Estimated breeding values (EBVs) were generated for nine alternative definitions of enteric methane and EBVs were validated against phenotypic performance (adjusted for …

Forest Composition Change And Biophysical Climate Feedbacks Across Boreal North America, Richard Massey, Brendan M. Rogers, Logan T. Berner, Sol Cooperdock, Michelle C. Mack, Xanthe J. Walker, Scott J. Goetz

Aspen Bibliography

Deciduous tree cover is expected to increase in North American boreal forests with climate warming and wildfire. This shift in composition has the potential to generate biophysical cooling via increased land surface albedo. Here we use Landsat-derived maps of continuous tree canopy cover and deciduous fractional composition to assess albedo change over recent decades. We find, on average, a small net decrease in deciduous fraction from 2000 to 2015 across boreal North America and from 1992 to 2015 across Canada, despite extensive fire disturbance that locally increased deciduous vegetation. We further find near-neutral net biophysical change in radiative forcing associated …

Genomic And Transcriptomic Analyses Reveal Polygenic Architecture For Ecologically Important Traits In Aspen (Populus Tremuloides Michx.), Jennifer F. L. Riehl, Christopher T. Cole, Clay J. Marrow, Hilary L. Barker, Carolina Bernhardsson, Kennedy Rubert-Nason, Pär K. Ingvarsson, Richard L. Lindroth

Aspen Bibliography

Intraspecific genetic variations in foundation species such as aspen (Populus tremuloides Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspect through genomic and transcriptomic analyses. A multilocus association model revealed …

Bison Alter The Northern Yellowstone Ecosystem By Breaking Aspen Saplings, Luke E. Painter, Robert L. Beschta, William J. Ripple

Aspen Bibliography

The American bison (Bison bison) is a species that strongly interacts with its environment, yet the effects of this large herbivore on quaking aspen (Populus tremuloides) have received little study. We documented bison breaking the stems of aspen saplings (young aspen > 2 m tall and ≤ 5 cm in diameter at breast height) and examined the extent of this effect in northern Yellowstone National Park (YNP). Low densities of Rocky Mountain elk (Cervus canadensis) after about 2004 created conditions conducive for new aspen recruitment in YNP's northern ungulate winter range (northern range). We sampled …

Upland Cotton And Nematodes: An Analysis Of Historical Resistance, Upcoming Threats, And Co-Inoculation Effects, Amanda Gaudin

Theses and Dissertations

Upland cotton (Gossypium hirsutum ) is an important fiber crop grown throughout the southern United States. Plant-pathogenic nematodes are worm-like animals that feed on the roots of most agronomic crops, including cotton. The southern root-knot nematode (Meloidogyne incognita, RKN) and the reniform nematode (Rotylenchulus reniformis, RN) cause significant yield losses in cotton every year. Current sources of resistance are effective but limited, therefore historical screenings of cotton accessions were revisited in search for novel resistance sources. None were identified but many of the screened accessions possessed markers of known root-knot nematode and reniform nematode resistance. …

Mid-Gestation Maternofetal Inflammation Impacts Growth, Skeletal Muscle Glucose Metabolism, And Inflammatory Tone In The Ovine Fetus During Late Gestation, Zena Hicks

Department of Animal Science: Dissertations, Theses, and Student Research

Our 1^st and 2^nd studies assessed the impact of mid-gestation maternofetal inflammation on growth, skeletal muscle glucose metabolism, and inflammatory tone in the late gestation ovine fetus. The objective was to determine if inducing maternofetal inflammation during peak placental growth would lead to more profound IUGR characteristics in the fetus. MI-IUGR fetuses exhibited reduced body and skeletal muscle weights and hallmark asymmetric growth at late gestations. Fetuses had higher baseline glucose:insulin ratios and reduced glucose-stimulated insulin secretion. Moreover, hindlimb glucose oxidation was impaired independent of glucose uptake. Skeletal muscle specific glucose uptake and oxidation was reduced in MI-IUGR …

Variable Synchrony In Insect Outbreak Cycling Across A Forest Landscape Gradient: Multi-Scale Evidence From Trembling Aspen In Alberta, Barry J. Cooke, Jens Roland

Aspen Bibliography

Using multi-scale trembling aspen tree-ring width data from Alberta, we show that scaling has a profound influence on dendroecological inferencing. At all scales of sampling, there is a significant climatological signal whose strength is nevertheless superseded by the pervasive effect of insect herbivory. At the smallest spatial scale, 20 km x 20 km, we demonstrate a quasi-periodic pattern of sharp growth reductions and the existence of negative spatial correlations among successive outbreaks. At the intermediate spatial scale of 20 km x 80 km, we show that the period 1930-1963 was marked by extremely low correlations in aspen ring widths, with …

Genome-Wide Association Study For Agronomic Traits In Bermudagrass (Cynodon Spp.), Lovepreet Singh

Theses and Dissertations

Bermudagrass (Cynodon spp.) breeding and cultivar development is hampered by limited information regarding its genetic and phenotypic diversity. A germplasm collection of 206 bermudagrass accessions from 29 countries was genotyped with high-throughput genotyping-by-sequencing technique. Genomic diversity in this diverse germplasm panel was assessed with multifaceted approaches including population structure, phylogenetic analysis, principal component analysis, and genetic diversity parameters. This study revealed substantial genetic variation in the Cynodon accessions, demonstrating the potential of this germplasm panel for further genetic studies and cultivar development in breeding programs. Another critical issue in turfgrass breeding is the lack of information regarding the genetic …

Sequence Analysis Of Herbicide Target Genes In Herbicide-Tolerant Rice, Jonathan Kearney, Nilda R. Burgos, Gulab D. Rangani

Biological Sciences Undergraduate Honors Theses

The tolerance of mutagenized rice (Oryza sativa) lines to selector herbicides was investigated and the sequence of ALS gene was analyzed in plants that survived treatment with 4x the label rate of imazethapyr herbicide. This was done to determine if insensitivity to imazethapyr is due to mutation(s) in the herbicide binding site. Seedlots previously treated with ethyl-methyl sulfonate were planted in the field and 3-leaf seedlings were treated with various herbicides to screen for herbicide-tolerant mutants. Seeds from survivors composed the rice lines tested in the current research. Seeds were planted in the greenhouse and 3-leaf seedlings were …

Remote Sensing In Mapping Biodiversity – A Case Study Of Epiphytic Lichen Communities, Ida Palmroos, Veera Norros, Sarita Keski-Saari, Janne Mäyrä, Topi Tanhuanpää, Sonja Kivinen, Juha Pykälä, Peter Kullberg, Timo Kumpula, Petteri Vihervaara

Aspen Bibliography

In boreal forests, European aspen (Populus tremula L.) is a keystone species that hosts a variety of accompanying species including epiphytic lichens. Forest management actions have led to a decrease in aspen abundance and subsequent loss of suitable habitats of epiphytic lichens. In this study, we evaluate the environmental responses of epiphytic lichen species richness and community composition on aspen, focusing on the potential of remote sensing by combined hyperspectral imaging and airborne laser scanning to identify suitable habitats for epiphytic lichens. We measured different substrate and habitat parameters in the field (e.g., aspen diameter and bark pH) …

Genetic Markers And Tree Properties Predicting Wood Biorefining Potential In Aspen (Populus Tremula) Bioenergy Feedstock, Sacha Escamez, Kathryn M. Robinson, Mikko Luomaranta, Madhavi Latha Gandla, Niklas Mähler, Zakiya Yassin, Thomas Grahn, Gerhard Scheepers, Lars-Göran Stener, Stefan Jansson, Leif J. Jönsson, Nathaniel R. Street, Hannele Tuominen

Aspen Bibliography

Background Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.

Results We recorded 65 wood-related and growth traits in a population of 113 natural aspen genotypes from Sweden (https://doi.org/10.5061/dryad.gtht76hrd). These traits included three growth and field performance traits, 20 traits for wood chemical composition, 17 traits for wood anatomy …

Less Fuel For The Next Fire? Short-Interval Fire Delays Forest Recovery And Interacting Drivers Amplify Effects, Kristin H. Braziunas, Nathan G. Kiel, Monica G. Turner

Aspen Bibliography

As 21st-century climate and disturbance dynamics depart from historic baselines, ecosystem resilience is uncertain. Multiple drivers are changing simultaneously, and interactions among drivers could amplify ecosystem vulnerability to change. Subalpine forests in Greater Yellowstone (Northern Rocky Mountains, USA) were historically resilient to infrequent (100–300 year), severe fire. We sampled paired short-interval (<30-year) and long-interval (>125-year) post-fire plots most recently burned between 1988 and 2018 to address two questions: (1) How do short-interval fire, climate, topography, and distance to unburned live forest edge interact to affect post-fire forest regeneration? (2) How do forest biomass and fuels vary following short-interval versus long-interval severe fires? …

Regeneration Strategies And Forest Resilience To Changing Fire Regimes: Insights From A Goldilocks Model, Tanjona Ramiadantsoa, Zak Ratajczak, Monica G. Turner

Aspen Bibliography

Disturbances are ubiquitous in ecological systems, and species have evolved a range of strategies to resist or rebound following disturbance. Understanding how the presence and complementarity of regeneration traits will affect community responses to disturbance is increasingly urgent as disturbance regimes shift beyond their historical ranges of variability. We define "disturbance niche" as a species' fitness across a range of disturbance sizes and frequencies that can reflect the fundamental or realized niche, that is, whether the species occurs alone or with other species. We developed a model of intermediate complexity (i.e., a Goldilocks model) to infer the disturbance niche. We …

Revisiting Trophic Cascades And Aspen Recovery In Northern Yellowstone, Robert L. Beschta, Luke E. Painter, William J. Ripple

Aspen Bibliography

We revisit the nature and extent of trophic cascades and quaking aspen (Populus tremuloides) recovery in the northern range of Yellowstone National Park (YNP), where studies have reported on Rocky Mountain elk (Cervus canadensis) browsing and young aspen heights following the St. John, 1995-96 reintroduction of gray wolves (Canis lupus). A recent study by Brice et al. (2021) expressed concerns about methodologies employed in earlier aspen studies and that results from those studies exaggerated the extent to which a trophic cascade has benefitted aspen, concerns such as: (a) the selection of aspen stands, (b) …

Validation Of Newly Designed Ssr Markers For Eight Rice (Oryza Sativa L.) Genotypes With Variable Heat Tolerance Responses Based On Agromorphic Data And Pollen Fertility Analysis [Research Note], Monaliza B. Magat, Norvie L. Manigbas, Jessica D. Rey

The Philippine Agricultural Scientist

Rice is one of the most valuable staple food crops in the world. However, several challenges greatly affect production, one of which is the threat imposed by heat stress. To address this, researchers are developing varieties that are heat stress tolerant with genetic markers aid. In this study, eight rice genotypes, namely Dular, Nagina 22, NSIC Rc 222, Milyang 23, EL15, EL92, EL85, and IR52 were observed for agromorphic data, which included plant height, panicle length, filled and unfilled grains, and grain yield. Flower samples were collected to determine the effect of heat stress on pollen fertility. Molecular markers were …

Bison Influences On Composition And Diversity Of Riparian Plant Communities In Yellowstone National Park, J. Boone Kauffman, Dian Lyn Cummings, Cimarron Kauffman, Robert L. Beschta, Jeremy Brooks, Keeley Macneill, William J. Ripple

Aspen Bibliography

Riparian zones are among the most biologically diverse ecosystems in the Intermountain West, USA, and provide valuable ecosystem services, including high rates of biotic productivity, nutrient processing, and carbon storage. Thus, their sustainability is a high priority for land managers. Large ungulates affect composition and structure of riparian/stream ecosystems through herbivory and physical effects, via trailing and trampling. Bison (Bison bison) in Yellowstone National Park (YNP) have been characterized as "ecosystem engineers" because of their demonstrated effects on phenology, aboveground productivity of grasses, and woody vegetation structure. Bison have greatly increased in numbers during the last two decades …

Assessment Of Carbon Productivity Dynamics In Aspen Stands Under Climate Change Based On Forest Inventories In Central Siberia, Andrey Andreevich Vais, Valentina Valerievna Popova, Alina Andreevna Andronova, Viktor Nikolaevich Nemich, Artem Gennadievich Nepovinnykh, Pavel Vladimirovich Mikhaylov

Aspen Bibliography

The aim of the present research was to study the dynamics of growth and conditions of aspen stands under climate change, according to different periods of forest inventory. The study was conducted in modal aspen forests growing in the subtaiga/forest steppe region of Central Siberia. Aspen forests grow intensively at young age, which allows them to realize maximum carbon sequestration potential. The research was based on forest inventory data from 1972, 1982, 2002, and 2021 (the study was conducted on a limited territory). There was a steady increase in temperatures in the growing season from 1982 to 2002. The amount …

Morphological And Genetic Analysis Of The Root System In Two American Grapevines (Vitis Species), Parinaz Mohtasebi

MSU Graduate Theses

The North American grapes species Vitis rupestris Scheele and Vitis riparia Michx have been the pillars of rootstock breeding for many decades. Though a large body of viticultural knowledge has been accumulated on their impact on grafted scions, the genetic basis of their root system architecture (RSA) has received limited scientific attention. In this study, I generated and analyzed adventitious root systems from dormant cuttings of 22 V. riparia and 19 V. rupestris accessions, as well as 162 interspecific F1 hybrid progeny from a cross between V. rupestris (♀) and V. riparia (♂). I photographed the roots and then extracted …

Big Meadows Mountain Meadow & Aspen Restoration Project 2017 – 2023 Summary Report, Scott River Watershed Council

Aspen Bibliography

Big Meadows Mountain Meadow and Aspen Restoration Project is designed to enhance aspen and mountain meadow habitats at Big Meadows, a property that is privately owned by Ecotrust Forest Management (EFM). EFM owns approximately 40,000 acres in the Klamath Mountains of Siskiyou County, known as the Scott River Headwaters Property. The Scott River Headwaters Property Management Plan, developed by EFM, specifically identifies and prioritizes the restoration of aspen woodlands. As such, EFM and Scott River Watershed Council (SRWC) partnered with the goal of improving these critical habitats. The Big Meadows complex is one of the largest mountain meadow systems within …

Enhancement Of Developmental Defects In The Boron-Deficient Maize Mutant Tassel-Less1 By Reduced Auxin Levels, Michaela S. Matthes, Norman B. Best, Janlo M. Robil, Paula Mcsteen

Biology Faculty Publications

Background

Plant responses to deficiencies of the micronutrient boron are diverse and go beyond the well-characterized function of boron in cell wall crosslinking. To explain these phenotypic discrepancies, hypotheses about interactions of boron with various phytohormones have been proposed, particularly auxin. While these hypotheses are intensely tested in the root meristem of the model species, Arabidopsis thaliana, studies in crop species and the shoot are limited.

Aims

To address potential boron–auxin interactions during the vegetative and reproductive development of the crop maize (Zea mays), we utilized the boron-deficient tassel-less1 (tls1) mutant and the auxin-deficient vanishing tassel2 (vt2) mutant. We investigated …

Tree Biomass – A Fragile Carbon Storage In Old-Growth Birch And Aspen Stands In Hemiboreal Latvia, Laura Ķēniņa, Didzis Elferts, Ieva Jaunslaviete, Endijs Bāders, Guntars Šņepsts, Āris Jansons

Aspen Bibliography

Birch (Betula pendula Roth, Betula pubescens Ehrh.) and European aspen (Populus tremula L.) stands dominate the deciduous forests of Northern Europe. Due to increasing forest protections, more deciduous stands will reach the old-growth stage. Thus, data on the carbon storage potential in such areas are essential. We aimed to establish a benchmark for carbon stocks of the main carbon pools in old-growth deciduous hemiboreal stands. Carbon pools were calculated from measurements in forty old-growth (104–148 years-old) deciduous stands in forests on fertile mineral soil. The carbon stock in these stands is distributed across tree biomass (~ 60%), mineral soil (~ …

Aspen Leaves As A "Chemical Landscape" For Fungal Endophyte Diversity - Can Nitrogen And Herbivory Shape The Community Composition In Controlled Conditions?, Johanna Witzell, Vicki Huizu Guo Decker, Marta Agostinelli, Carmen Romeralo Tapia, Michelle Cleary, Benedicte Riber Albrectsen

Aspen Bibliography

The endophytic microbiome may influence the ecological performance of plants, including forest trees. Various abiotic and biotic factors may shape the endophyte communities directly but also indirectly, by modifying the quality of host plants as a substrate. We hypothesized that potentially antifungal or fungistatic condensed tannins (CTs) would determine the quality of aspen (Populus tremula) leaves as a substrate for endophytic fungi. By subjecting the plants to nitrogen fertilization (N) or herbivory (H; leaf beetles) we aimed to change the internal “chemical landscape”, especially the CT levels, in aspen leaves. We expected that this would lead to changes in the …

Connections Between Mechanosensitive Ion Channel Msl10 And Er-Plasma Membrane Contact Sites, Jennette Marie Codjoe

Arts & Sciences Electronic Theses and Dissertations

Mechanosensitive (MS) ion channels are an evolutionarily conserved way for cells to sense mechanical forces and transduce them into ionic signals. A plasma membrane-localized MS channel from Arabidopsis thaliana, MscS-Like (MSL)10, senses cell swelling and initiates a signaling cascade that triggers programmed cell death. Whereas the channel properties of MSL10 have been well studied, how MSL10 signals remains largely unknown. I worked collaboratively to show that important lesions for cell death signaling in the cytosolic N- and C-terminal domains of MSL10 interact genetically. I also helped show that ionic flux through MSL10 is dispensable for signaling, which suggested that MSL10 …

Development Of Functional Markers For Resistance To Smut And Identification Of Genes Differentially Expressed In Response To Brown Rust In Sugarcane, Jose David Cortes

LSU Doctoral Dissertations

Smut, caused by Sporisorium scitamineum and brown rust, caused by Puccinia melanocephala, are two of the most important diseases that affect sugarcane production in Louisiana and worldwide. Smut continues to cause losses in the breeding program in Louisiana. Therefore, a QTL analysis was conducted to identify molecular markers associated with resistance in F₁ progeny (162) of a biparental cross between susceptible cultivar L 99-233 and resistant HoCP 96-540. Using 1,574 single-dose SNP markers, a total of 253 linkage groups (LG) were obtained with a genome coverage of 24,580.15 cM. Six QTLs were localized on five LGs. The highest …

Deciphering The Genetic Architecture Of Key Female Floral Traits For Hybrid Wheat Seed Production, Juan Jimenez

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

Wheat (Triticum aestivum L.) is a staple cereal that provides 20% of the calories and proteins in human intake (Ray et al., 2013). Global population is projected to increase to 9.7 billion by 2050. Food production must increase by 70% to feed this future population. Wheat production is in crisis due to political and environmental challenges and is projected to decline by 0.8% in 2022 (FAO, 2022). To ensure food security yield genetic gain must increase by around 1.4% annually. Taking advantage of heterosis, hybrid wheat has the potential to boost grain yield. However, hybrid wheat seed production systems …

Ungulate Herbivores As Drivers Of Aspen Recruitment And Understory Composition Throughout Arid Montane Landscapes, Elizabeth S. Reikowski, Tyler Refsland, J. Hall Cushman

Aspen Bibliography

Herbivory by wild and domestic ungulates can influence tree recruitment and understory forest communities throughout the world. Herbivore-driven declines in tree recruitment have been observed for quaking aspen (Populus tremuloides), a foundation species whose health and management is recognized as a critical priority throughout much of its range. Livestock fencing is commonly used to promote aspen regeneration, but its effectiveness is rarely assessed, especially across large spatial scales. Using a livestock-reduction experiment, we evaluated the effects of ungulate herbivory on aspen in the Great Basin and southern Cascades, an expansive and environmentally heterogeneous region where aspen faces the …