Botany Commons^™

Editorial: New Insights Into Mechanisms Of Epigenetic Modifiers In Plant Growth And Development, Volume Ii, Ming Luo, Tomasz Jacek Sarnowski, Marc Libault, Gabino Ríos, Jean-Benoit Charron, Nitin Mantri, Shoudong Zhang

Department of Agronomy and Horticulture: Faculty Publications

As we have learned, chromatin modifications, including histone modifications and DNA methylation, play a key role in plant development (Ng and Bird, 1999). However, accumulated evidence shows that, besides chromatin biochemical modifications, other epigenetic regulations such as chromatin architecture also function at a pivot point to regulate plant development (Zhang et al., 2021). In this Research Topic, five research papers describe multiple developmental facets mediated by different epigenetic mechanisms besides histone modifications. These manuscripts report experimental evidence or summarize recent advances in epigenetic regulations of some important developmental genes or development-related mechanisms. This Research Topic allows readers to learn of …

A Complete Telomere-To-Telomere Assembly Of The Maize Genome, Jian Chen, Zijian Wang, Kaiwen Tan, Wei Huang, Junpeng Shi, Tong Li, Jiang Hu, Kai Wang, Chao Wang, Beibei Xin, Haiming Zhao, Weibin Song, Matthew B. Hufford, James C. Schnable, Weiwei Jin, China Agricultural University, Hainan Yazhou Bay Seed Laboratory

Department of Agronomy and Horticulture: Faculty Publications

A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of genomic research. Through generating deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads, we report here a complete genome assembly of maize with each chromosome entirely traversed in a single contig. The 2,178.6 Mb T2T Mo17 genome with a base accuracy of over 99.99% unveiled the structural features of all repetitive regions of the genome. There were several super-long simple-sequence-repeat arrays having consecutive thymine–adenine– guanine (TAG) tri-nucleotide repeats up to 235 kb. The assembly of the entire nucleolar organizer region of the 26.8 Mb array with …

Genome-Wide Association Analysis For Emergence Of Deeply Sown Rice (Oryza Sativa) Reveals Novel Aus-Specific Phytohormone Candidate Genes For Adaptation To Dry-Direct Seeding In The Field, Sandeep A. Sakhale, Shailesh Yadav, Lindsay V. Clark, Alexander E. Lipka, Arvind Kumar, Erik J. Sacks

Department of Agronomy and Horticulture: Faculty Publications

Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, an understanding of the genomic regions and underlying genes that confer emergence in deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide …

Updating The Dual C And O Isotope—Gas-Exchange Model: A Concept To Understand Plant Responses To The Environment And Its Implications For Tree Rings, Rolf T. W. Siegwolf, Marco M. Lehmann, Gregory R. Goldsmith, Olga V. Churakova (Sidorova), Cathleen Mirande-Ney, Galina Timoveeva, Rosmarie B. Weigt, Matthias Saurer

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The combined study of carbon (C) and oxygen (O) isotopes in plant organic matter has emerged as a powerful tool for understanding plant functional responses to environmental change. The approach relies on established relationships between leaf gas exchange and isotopic fractionation to derive a series of model scenarios that can be used to infer changes in photosynthetic assimilation and stomatal conductance driven by changes in environmental parameters (CO₂, water availability, air humidity, temperature, nutrients). We review the mechanistic basis for a conceptual model, in light of recently published research, and discuss where isotopic observations do not match our …

Nature As Material, Time As Tool, Chuchu Chen

Masters Theses

No building stands forever. Over time, the natural environment acts upon the outer surface of the building, leading to the failure of materials and the final dissolution of the structure itself, leading to ruin. In order to prevent this or retard its occurrence, we constantly maintain and renew the things we build. Nature seems to stand in opposition to architecture. The passage of time is constantly subtracting from the building. However, what differentiates nature from architecture? This thesis questions whether these two are not opposed, but on a continuous spectrum. Approaching the building as part of the overall environment that …

Arkansas Soybean Performance Tests 2022, J. F. Carlin, R. B. Mulloy, R. D. Bond

Arkansas Agricultural Experiment Station Research Series

Soybean variety and strain performance tests are conducted each year in Arkansas by the University of Arkansas System Division of Agriculture’s Arkansas Crop Variety Improvement Program. The tests provide information to companies developing varieties and/ or marketing seed within the state, and aid the Arkansas Cooperative Extension Service in formulating variety recommendations for soybean producers.

Fluidity And Inconstancy: Australian Bush Tomatoes As An Exemplar Of Non-Normative Sex Expression, Christopher T. Martine

Faculty Journal Articles

Solanum, a genus of ~1500 global species, is one of the more interesting plant groups in which to study reproductive biology and ecology. Overwhelmingly, species in this group express full cosexuality, where individual plants have flowers containing both fully-functioning “male” (staminate) and “female” (carpellate) organs. However, there have been multiple and widespread evolutionary transitions within the genus to non-normative variations on this ancestral condition. Australian bush tomatoes (ca. 40 species) are especially diverse in this regard, with uncommon variation and combinations of unisexuality and cosexuality -- including, most notably, two sexual systems known as dioecy (unisexual male or female …

Do Cover Crop Mixtures Improve Soil Physical Health More Than Monocultures?, Humberto Blanco-Canqui

Department of Agronomy and Horticulture: Faculty Publications

Rationale and Purpose — Adding multispecies cover crop (CC) mixtures could diversify the current simplified crop rotations and enhance soil health more than monoculture CCs. Further, CC mixtures with diverse plant species could adapt better to changing climatic and environmental conditions than monoculture CCs. However, our current understanding of the soil benefits of CC mixtures is still limited. This review discussed whether CC mixtures are better than monoculture CCs to improve soil physical health.

Methods — All studies published up to May 25, 2023, comparing soil physical properties between CC mixtures and their constituents grown as monocultures were searched in …

Impact Of Nitrogen Availability On The Accumulation Of Vegetative Lipids In Sorghum, Leticia Felicio Pasqualino

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

Sorghum (Sorghum bicolor (L.) Moench) is a versatile and prosperous feedstock crop for renewable energy production. With the increase in bioenergy demand, the production of higher oil content per biomass in a feedstock crop is a highly desirable trait for the biofuel conversion process yield. Especially if this outcome can be achieved using fewer inputs in the field, such as nitrogen. In microalgae species, nitrogen limitation has been associated with changes in the carbon storage metabolic pathway favoring triacylglycerol (TAG) accumulation. In this context, this study aimed to assess whether nitrogen starvation would result in a similar outcome in …

A Foundational Population Genetics Investigation Of The Sexual Systems Of Solanum (Solanaceae) In The Australian Monsoon Tropics Suggests Dioecious Taxa May Benefit From Increased Genetic Admixture Via Obligate Outcrossing, Jason T. Cantley, Ingrid E. Jordon-Thaden, Morgan Roche, Daniel S. Hayes, Stephamie Kate, Christopher T. Martine

Faculty Journal Articles

Solanum section Leptostemonum is an ideal lineage to test the theoretical framework regarding proposed evolutionary benefits of outcrossing sexual systems in comparison to cosexuality. Theoretically, non-cosexual taxa should support more genetic diversity within populations, experience less inbreeding, and have less genetic structure due to a restricted ability to self-fertilize. However, many confounding factors present challenges for a confident inference that inherent differences in sexual systems influence observed genetic patterns among populations. This study provides a foundational baseline of the population genetics of several species of different sexual systems with the aim of generating hypotheses of any factor—including sexual system—that influences …

2018–2019 Field Seasons Of The Maize Genomes To Fields (G2f) G X E Project, Dayane Dayane Lima, Alejandro Castro Aviles, Ryan Timothy Alpers, Bridget A. Mcfarland, Shawn Kaeppler, David Ertl, Maria Cinta Romay, Joseph L. Gage, James Holland, Timothy Beissinger, Martin Bohn, Edward Buckler, Jode Edwards, Sherry Flint‑Garcia, Candice N. Hirsch, Elizabeth Hood, David C. Hooker, Joseph E. Knoll, Judith M. Kolkman, Sanzhen Liu, John Mckay, Richard Minyo, Danilo E. Moreta, Seth C. Murray, Rebecca Nelson, James C. Schnable, Rajandeep S. Sekhon, Maninder P. Singh, Peter Thomison, Addie Thompson, Mitchell Tuinstra, Jason Wallace, Jacob D. Washburn, Teclemariam Weldekidan, Randall J. Wisser, Wenwei Xu31, Natalia De Leon

Department of Agronomy and Horticulture: Faculty Publications

Objectives This report provides information about the public release of the 2018–2019 Maize G X E project of the Genomes to Fields (G2F) Initiative datasets. G2F is an umbrella initiative that evaluates maize hybrids and inbred lines across multiple environments and makes available phenotypic, genotypic, environmental, and metadata information. The initiative understands the necessity to characterize and deploy public sources of genetic diversity to face the challenges for more sustainable agriculture in the context of variable environmental conditions.

Data description Datasets include phenotypic, climatic, and soil measurements, metadata information, and inbred genotypic information for each combination of location and year. …

A Most Surprising Fern: Serendipity And Browsing In Botanical Search, Douglas Tuers

Journal of the South Carolina Academy of Science

This article is a case study of botanical field work in the eastern United States in the early twentieth century. These cases will be analyzed as instances of browsing and serendipity. Browsing and serendipity have a rich literature in information science and this article will draw on this literature in order to better understand serendipity in botany. This article will show how botanical localities support browsing and serendipity for the botanists who search them. This article will also show how botanical institutions and botanists interface with localities in order to further support browsing and serendipity. As a whole this article …

Creeper Legume, In Conjunction With Biochar, Is A Potential Tool To Minimize Soil Erosion, Sujani De Silva, Priyantha Indralal Yapa, Kushani Mahatantila, Saurav Das, Bijesh Maharjan

Department of Agronomy and Horticulture: Faculty Publications

Accelerated soil erosion and landslides are destructive consequences of road development and intensive agriculture in the central highlands of Sri Lanka. Properly designed vegetation covers can play a vital role in erosion control. Identifying a plant that can adapt to eroded land with a low-nutrient supply is critical for natural erosion management. A perennial creeper legume, Vigna marina, adaptable for marginal lands and used to control soil erosion in Australia, was introduced to Sri Lanka via the 2004 tsunami. The objective of this study was to assess V. marina under five different soil substrates, including a reference treatment (RT) …

Effectiveness Of Tadreb-B1 And 1-Feh W3 Kasp Markers In Spring And Winter Wheat Populations For Marker-Assisted Selection To Improve Drought Tolerance, Shamseldeen Eltaher, Mostafa Hashem, Asmaa A. M. Ahmed, P. Stephen Baenziger, Andreas Börner, Ahmed Sallam

Department of Agronomy and Horticulture: Faculty Publications

Due to the advances in DNA markers, kompetitive allele-specific PCR (KASP) markers could accelerate breeding programs and genetically improve drought tolerance. Two previously reported KASP markers, TaDreb-B1 and 1-FEH w3, were investigated in this study for the markerassisted selection (MAS) of drought tolerance. Two highly diverse spring and winter wheat populations were genotyped using these two KASP markers. The same populations were evaluated for drought tolerance at seedling (drought stress) and reproductive (normal and drought stress) growth stages. The single-marker analysis revealed a high significant association between the target allele of 1-FEH w3 and drought susceptibility in the spring …

Mowing Cattail Cover To Increase Aquatic Vegetation Diversity On The Coeur D’Alene River Floodplain In Cataldo, Idaho, Makenna J. Tabino

2023 Symposium

The Schlepp Easement is a 400 acre wetland on the Coeur D’Alene River floodplain, near Cataldo, Idaho. The wetland has been restored to protect it from heavy metal pollution transported downstream from mining sites near Kellogg, Idaho, the location of the Bunker Hill EPA Superfund Site. This wetland was restored to provide safe habitats and feeding grounds for migratory waterfowl and to maintain wetland biodiversity. However, cattail is prone to becoming overdominant and outcompeting other plants, which greatly limits a wetland’s biodiversity. Our objectives were to test whether aquatic boat mowing can reduce cattail cover, improving species diversity and cover …

Long-Term Conservation And Conventional Tillage Systems Impact Physical And Biochemical Soil Health Indicators In A Corn–Soybean Rotation, Anuoluwa O. Sangotayo, Jemila Chellappa, Udayakumar Sekaran, Sangeeta Bansal, Padma Angmo, Paul J. Jasa, Sandeep Kumar, Javed Iqbal

Department of Agronomy and Horticulture: Faculty Publications

Agricultural management practices tend to influence soil structure stabilization, mediating many physical, chemical, and biological processes in soils. Therefore, understanding the long-term effects of management practices on various soil health indicators is crucial to develop sustainable agricultural practices. This study aimed to assess the long-term conventional and conservation tillage effects on soil physical (aggregates) and biochemical (soil organic carbon [SOC], enzymes, and microbial biomass) parameters under a range of tillage practices in a corn–soybean rotation in Nebraska. The experiment was conducted at two locations as follows: (1) Concord site (36 years) with the three treatments: no-till (NT), disk, and moldboard …

Hybrid Allele‑Specific Chip‑Seq Analysis Identifies Variation In Brassinosteroid‑Responsive Transcription Factor Binding Linked To Traits In Maize, Thomas Hartwig, Michael Banf, Gisele Passaia Prietsch, Jia‑Ying Zhu, Isabel Mora‑Ramírez, Jos H. M. Schippers, Samantha J. Snodgrass, Arun S. Seetharam, Bruno Huettel, Judith M. Kolkman, Jiashi Yang, Julia Engelhorn, Zhi‑Yong Wang

Department of Agronomy and Horticulture: Faculty Publications

Background: Genetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. Genetic variation in brassinosteroidresponsive cis-elements likely contributes to trait variation. Pinpointing such regulatory variations and quantitative genomic analysis of the variation in TF-target binding, however, remains challenging. How variation in transcriptional targets of signaling pathways such as the brassinosteroid pathway contributes to phenotypic variation is an important question to be investigated with innovative approaches.

Results: Here, we use a hybrid allele-specific chromatin binding sequencing (HASChseq) approach and …

Factors Affecting Apothecia Production And Primary Infection By Monilinia Vaccinii-Corymbosi On Vaccinium Angustifolium, Ian Leonard

Electronic Theses and Dissertations

Mummy berry, caused by Monilinia vaccinii-corymbosi (MVC), is a prolific disease of Vaccinium angustifolium (wild blueberry) leading to decreased yield in wild blueberry fields throughout the Downeast (DE) and Midcoast (MC) regions of Maine (ME). This study aimed to identify factors affecting primary inoculum production and infection by MVC on wild blueberry, and what bud stages of wild blueberry are most susceptible to infection. Through common garden (CGE), field and incubation experiments conducted in 2021 and 2022, factors affecting carpogenic germination of MVC pseudosclerotia and relationships between susceptible wild blueberry buds and environmental factors were analyzed. The CGE conducted in …

Evaluating Planting Green And Herbicides For Integrated Weed Management And Their Effect On Soil Properties In Corn And Soybean In Nebraska, Trey Stephens

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

Producers across the Midwest are finding new ways to implement cover crops into cropping systems and the practice of “Planting Green” is one of the newest uses of cover crops. When planting green, producers plant their row crops into actively growing cover crops and terminate the cover crop at time of planting or shortly after planting. This practice would allow for higher biomass accumulation of the cover crop and could aid in weed management of herbicide-resistant weeds. The objective of the first two studies was to evaluate planting green and its effect on soil-applied residual herbicides, weed management, dicamba/glyphosate-resistant soybean …

Effects Of Nonnative Plants On Space-Use In Eastern Box Turtles, Emily Ilene Crago

Graduate Theses

Introduction of nonnative plants outside their natural range has caused widespread reduction in the abundance and diversity of native plant species. Nonnative plants typically form dense, often monotypic, thickets that affect the ability of animals to find food, reproduce, avoid predation risk, and thermoregulate. By doing so, nonnative plants have the potential to displace resident animals from areas otherwise suitable as animal habitat. However, limited studies have investigated whether resident animals avoid areas dominated by nonnative plants. This study investigated impacts of nonnative plants on eastern box turtles (Terrapene carolina carolina), a species that has been declining throughout their range. …