Botany Commons^™

Combination Of Biological And Chemical Soil Tests Best Predict Maize Nitrogen Response, M. D. Mcdaniel, Daniel T. Walters, L. G. Bundy, Xiaofei Li, Rhae A. Drijber, John E. Sawyer, Michael J. Castellano, C. A.M. Laboski, Peter C. Scharf

Department of Agronomy and Horticulture: Faculty Publications

Soil tests can help optimize nitrogen (N) fertilizer rates, thereby improving farmer profitability and environmental performance. In US Midwest maize (Zea mays) production, however, most soil N tests have limited accuracy to predict N fertilizer requirements. Here we tested the individual and combined ability of 30 soil tests (12 rapid N extractions, seven biological carbon or N tests, six long-term incubation kinetic parameters, and five other routine soil tests), as well as environmental and management data, to predict maize response to N fertilizer across 56 site-years in the US Midwest. Out of 30 soil tests, and across all …

Soybean Response To Water: Trait Identification And Prediction, Shawn Jenkins

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

The rising demand for soybean [Glycine Max (L.) Merrill] taken in consideration with current climatic trends accentuates the importance of improving soybean seed yield response per unit water (WP). To further our understanding of the quantitative WP trait, a multi-omic approach was implemented for improved trait identification and predictive modeling opportunities. Through the evaluation of two recombinant inbred line populations jointly totaling 439 lines subjected to contrasting irrigation treatments, informative agronomic, phenomic, and genomic associations were identified. Across both populations, relationships were identified between lodging at maturity (r = -0.58, H = 0.86), canopy to air temperature differential …

Availability Of Soil Mutualists May Not Limit Non‐Native Acacia Invasion But Could Increase Their Impact On Native Soil Communities, Elizabeth M. Wandrag, Christina Birnbaum, Metha M. Klock, Luke G. Barrett, Peter H. Thrall

Faculty Publications, Environmental Studies

1. The availability of compatible mutualistic soil microbes could influence the invasion success of non-native plant species. Specifically, there may be spatial variation in the distribution of compatible microbes, and species-specific variation in plant host ability to associate with available microbes. Although either or both factors could promote or limit invasion, the scale over which most studies are conducted makes it difficult to examine these two possibilities simultaneously. However, this is critical to identifying a role of soil microbes in invasion.
2. A series of recent research projects focused on interactions between Australian Acacia and nitrogen-fixing bacteria (rhizobia) at multiple spatial scales, …

Enhancing Hybrid Prediction In Pearl Millet Using Genomic And/Or Multi- Environment Phenotypic Information Of Inbreds, Diego Jarquin, Reka Howard, Zhikai Liang, Shashi K. Gupta, James C. Schnable, Jose Crossa

Department of Agronomy and Horticulture: Faculty Publications

Genomic selection (GS) is an emerging methodology that helps select superior lines among experimental cultivars in plant breeding programs. It offers the opportunity to increase the productivity of cultivars by delivering increased genetic gains and reducing the breeding cycles. This methodology requires inexpensive and sufficiently dense marker information to be successful, and with whole genome sequencing, it has become an important tool in many crops. The recent assembly of the pearl millet genome has made it possible to employ GS models to improve the selection procedure in pearl millet breeding programs. Here, three GS models were implemented and compared using …

A List Of The Rare, Endangered, & Threatened Vascular Plants Of California, James P. Smith Jr

Botanical Studies

No abstract provided.

List Of The Federal And State-Listed Rare, Endangered, & Threatened Plants Of California, James P. Smith Jr

Botanical Studies

No abstract provided.

Long-Term Ecological Research In Southern Brazil Grasslands: Effects Of Grazing Exclusion And Deferred Grazing On Plant And Arthropod Communities, Pedro M.A. Ferreira, Bianca O. Andrade, Luciana R. Podgaiski, Amanda C. Dias, Valerio D. Pillar, Gerhard E. Overbeck, Milton De S. Mendonca Jr., Ilsi I. Boldrini

Department of Agronomy and Horticulture: Faculty Publications

Grazing exclusion may lead to biodiversity loss and homogenization of naturally heterogeneous and species-rich grassland ecosystems, and these effects may cascade to higher trophic levels and ecosystem properties. Although grazing exclusion has been studied elsewhere, the consequences of alleviating the disturbance regime in grassland ecosystems remain unclear. In this paper, we present results of the first five years of an experiment in native grasslands of southern Brazil. Using a randomized block experimental design, we examined the effects of three grazing treatments on plant and arthropod communities: (i) deferred grazing (i.e., intermittent grazing), (ii) grazing exclusion and (iii) a control under …

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

Department of Agronomy and Horticulture: Faculty Publications

In eukaryotic cells, chromatin, a highly dynamic nucleoprotein complex, plays a critical role in controlling gene expression notably by regulating the interaction between transcription factors and regulatory elements. The structure of the chromatin is determined by epigenetic mechanisms, including DNA methylation, histone modifications, and chromatin remodeling. A growing body of evidence indicates that epigenetic regulations are involved in plant adaptation to environmental stresses, and in plant development, including flowering control, fruit and root development, as well as seed maturation and germination. Furthermore, epigenetic mechanisms have the potential to stabilize cell identity and maintain tissue organization. Hence, epigenetic diversity is now …

Yield And Quality In Purple-Grained Wheat Isogenic Lines, Alexey Morgounov, Yasar Karaduman, Beyhan Akin, Sinan Aydogan, Peter Stephen Baenziger, Madhav Bhatta, Vladimir Chudinov, Susanne Dreisigacker, Velu Govindan, Safure Güler, Carlos Guzman, Ajit Nehe, Rachana Poudel, Devin J. Rose, Elena Gordeeva, Vladimir Shamanin, Kemal Subasi, Yuriy Zelenskiy, Elena Khlestkina

Department of Agronomy and Horticulture: Faculty Publications

Breeding programs for purple wheat are underway in many countries but there is a lack of information on the effects of Pp (purple pericarp) genes on agronomic and quality traits in variable environments and along the product chain (grain-flour-bread). This study was based on unique material: two pairs of isogenic lines in a spring wheat cv. Saratovskaya-29 (S29) background differing only in Pp genes and grain color. In 2017, seven experiments were conducted in Kazakhstan, Russia, and Turkey with a focus on genotype and environment interaction and, in 2018, one experiment in Turkey with a focus on grain, flour, and …

The Land Variational Ensemble Data Assimilation Framework: Lavendar V1.0.0, Ewan Pinnington, Tristan Quaife, Amos Lawless, Karina Williams, Tim Arkebauer, David Scoby

Department of Agronomy and Horticulture: Faculty Publications

The Land Variational Ensemble Data Assimilation Framework (LAVENDAR) implements the method of fourdimensional ensemble variational (4D-En-Var) data assimilation (DA) for land surface models. Four-dimensional ensemble variational data assimilation negates the often costly calculation of a model adjoint required by traditional variational techniques (such as 4D-Var) for optimizing parameters or state variables over a time window of observations. In this paper we present the first application of LAVENDAR, implementing the framework with the Joint UK Land Environment Simulator (JULES) land surface model. We show that the system can recover seven parameters controlling crop behaviour in a set of twin experiments. We …

Adaptive Capacity In Ecosystems, David G. Angeler, Hannah Fried-Petersen, Craig R. Allen, Ahjond Garmestani, Dirac L. Twidwell Jr, H.E. Birgé, W. Chuang, V. M. Donovan, T. Eason, C.P. Roberts, S.M. Sundstrom, C.L. Wonkka

Department of Agronomy and Horticulture: Faculty Publications

Understanding the adaptive capacity of ecosystems to cope with change is crucial to management. However, unclear and often confusing definitions of adaptive capacity make application of this concept difficult. In this paper, we revisit definitions of adaptive capacity and operationalize the concept. We define adaptive capacity as the latent potential of an ecosystem to alter resilience in response to change. We present testable hypotheses to evaluate complementary attributes of adaptive capacity that may help further clarify the components and relevance of the concept. Adaptive sampling, inference and modeling can reduce key uncertainties incrementally over time and increase learning about adaptive …

Characterization Of The Transcriptional Divergence Between The Subspecies Of Cultivated Rice (Oryza Sativa), Malachy T. Campbell, Qian Du, Kan Li, Sandeep Sharma, Chi Zhang, Harkamal Walia

Agronomy & Horticulture -- Faculty Publications

Background: Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1).

Results: The transcriptomes of the two subspecies of rice are highly divergent. Japonica have significantly lower expression and genetic diversity relative to Indica, which is likely a consequence of a population bottleneck during Japonica domestication. We leveraged high-density genotypic data and …

Spatial Distribution And Risk Area Assessment Of Aphelenchoides Besseyi Using Geostatistical Approaches In Giridih District Of Jharkhand, India, Sandip Mondal, Matiyar Rahaman Khan, Abhishek Mukherjee

ISI Best Publications

Distributed widely across the rice growing regions of India, the rice leaf and bud nematode (Aphelenchoides besseyi Christie 1942) can cause substantial yield loss in rice. Whitening of leaf tips is the characteristics damage symptom of this nematode and therefore it is popularly referred to as the rice white tip nematode (RWTN). While information on the damage severity of RWTN is available from others parts of the country, to date, no information is available from the state of Jharkhand. In order to generate a detailed information on spatial distribution of this nematode and to identify infestation hotspots, extensive field sampling …

A Preliminary Checklist Of Lichens From Kamiak Butte County Park, Washington State, Emma Sell, Amanda Chandler

2020 Symposium Posters

The semiarid Palouse ecoregion of North America was once dominated by temperate prairies and connects areas of southeast Washington, north-central Idaho, and northeast Oregon. Transformation of nearly all habitats comprising this ecosystem into agricultural lands has drastically reduced extant native grasslands to small, highly fragmented pieces. These land conversion practices, coupled with the subsequent takeover of invasive plant species, have placed the Palouse ecoregion among the most critically endangered ecosystems in the United States, with < 1% of land remaining that is suitable to host native species. The enormous loss of biodiversity across the Palouse has prompted a need for further study regarding a wide variety of organisms. In particular, lichen diversity of the Palouse ecoregion has never been formally characterized, and there are overall very few detailed studies of lichens throughout eastern Washington. To improve knowledge of Palouse lichen diversity, we first reviewed collection data from historical herbarium specimens via the Consortium of North American Lichen Herbaria (CNALH) database. We then collected lichen voucher specimens from Kamiak Butte County Park (KBCP), one of the largest contiguous natural areas within the Palouse ecoregion as its relatively steep, rocky slopes make it ill-suited for agricultural conversion. KBCP consists of 298 acres of mixed Pinus ponderosa (ponderosa pine) and Pseudotsuga menziesii (Douglas fir) forest and native grassland that rises above the surrounding farmland, as well as an east-west ridgeline …

Annonex2embl: Automatic Preparation Of Annotated Dna Sequences For Bulk Submissions To Ena, Michael Gruenstaeudl

Biological Sciences Faculty Publications

The submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research. The surge of novel DNA sequences awaiting database submission due to the application of next-generation sequencing has increased the need for software tools that facilitate bulk submissions. This need has yet to be met with the concurrent development of tools to automate the preparatory work preceding such submissions.The author introduce annonex2embl, a Python package that automates the preparation of complete sequence flatfiles for large-scale sequence submissions to the European Nucleotide Archive. The tool enables the conversion of DNA sequence alignments that are co-supplied …

Wood Anatomy Of Argophyllaceae (Asterales): Adaptation In A Small Clade, Sherwin Carlquist, Mark E. Olson

Aliso: A Journal of Systematic and Floristic Botany

Argophyllaceae (Argophyllum, 14 spp.; Corokia, 6 spp.; Lautea, 1 sp.), are shrubs that occur in the southwestern Pacific and eastern Australia. They occur in habitats where moisture is relatively common but dry days and mild frost may occur. The woods of these genera show enough distinctive features to justify their grouping in a single family: perforation plates with 10–20 bars, vessel elements narrow and numerous per mm², imperforate tracheary elements about 50% longer than the vessel elements, axial parenchyma scarce, diffuse, multiseriate rays narrow and heterocellular (upright cells common in uniseriate rays), crystals absent, …

Justicieae Ii: Resolved Placement Of Many Genera And Recognition Of A New Lineage Sister To Isoglossinae, Lucinda A. Mcdade, Carrie A. Kiel, Thomas F. Daniel, Iain Darbyshire

Aliso: A Journal of Systematic and Floristic Botany

We present phylogenetic results for Justicieae, the largest of the major lineages of Acanthaceae. With 300% more sequence data and a similarly increased but also more geographically representative taxon sample compared to the only previous study of the lineage as a whole, we confirm the existence of the Pseuderanthemum Lineage, Isoglossinae, the Tetramerium Lineage and the Justicioid Lineage. To the last three lineages, we add a number of taxa with the goal of advancing our knowledge of genera (e.g., Isoglossa, Rhinacanthus) and of geographic areas (e.g., Malagasy and Asian Acanthaceae). These added taxa are accommodated within the phylogenetic …

The Influences Of Green Infrastructure On Levels Of Somatic And Male-Specific Coliphages At Shadyside Park, Oula Salih

Student Papers and Reports

Microbial contamination is still considered one of the major causes of diminished function and quality of urban rivers and streams in Michigan. Floodplains, a type of green infrastructure used to reduce flooding after large amounts of rainfall, were reported to have variable effects of reducing levels of stormwater runoff within these bodies of water ( Hubbart et al., 2011 ). Viral indicators of fecal contamination in bodies of water include male-specific and somatic coliphages. Water samples from Plaster Creek were collected before and after the floodplain in order to identify the levels of somatic and male-specific coliphages during dry and …

Ms Environmental Biology Capstone Project, Alexandra Sorenson

Regis University Student Publications (comprehensive collection)

• Chapter 1. Literature Review: Invasive Plant Considerations in Alpine Restoration Project Planning
• Chapter 2. Grant Proposal: Success Rates of Native See Germination on Esplanade-Treated Plots
• Chapter 3. Journal Manuscript: Meta-Analysis of Cheatgrass (Bromus Tectorum) Control with Three Commonly Used Herbicides
• Chapter 4. Stakeholder Analysis: Stakeholder Analysis: Recommendation for Herbicide Use at Lippincott Ranch

Biology 4920g: Companion Planting In The Community, Jacquline A. Nathaniel

Community Engaged Learning Final Projects

LIFE*SPIN is a local organization in London, Ontario that provides resources to individuals and families dependent on low income to ultimately break the poverty cycle by encouraging sustainable living and self-sufficiency. For this Seminar in Biology course, Maria Bata and I partnered with LIFE*SPIN to plan and execute a "Seeding Planting Party" to teach children about basic botany, nutrition, and leadership. The following final paper for this seminar discusses the project deliverables and efforts, biological research concerning companion planting, and personal reflection on this experience.