Botany Commons^™

2010 Lilley Cornett Woods Overstory Data, Ryan W. Mcewan, Julia I. Chapman, Robert N. Muller

Data Files: Big Everidge Hollow Permanent Plots

Data collected in 2010 on the overstory in the Big Everidge Hollow portion of the Lilley Cornett Woods Appalachian Ecological Research Station in southeastern Kentucky. Data key is provided in a supplemental file.

Accompanying photo by Julia I. Chapman.

DOI: https://doi.org/10.26890/lcw.s3l6btsgv3

1999 Lilley Cornett Woods Overstory Data, Ryan W. Mcewan, Julia I. Chapman, Robert N. Muller

Data Files: Big Everidge Hollow Permanent Plots

Data collected in 1999 on the overstory in the Big Everidge Hollow portion of the Lilley Cornett Woods Appalachian Ecological Research Station in southeastern Kentucky. Data key is provided in a supplemental file.

Accompanying photo by Ryan W. McEwan.

DOI: https://doi.org/10.26890/lcw.5pn95oc6d7

1989 Lilley Cornett Woods Overstory Data, Ryan W. Mcewan, Julia I. Chapman, Robert N. Muller

Data Files: Big Everidge Hollow Permanent Plots

Data collected in 1989 on the overstory in Big Everidge Hollow portion of the Lilley Cornett Woods Appalachian Ecological Research Station in southeastern Kentucky. Data key is provided in a supplemental file.

Accompanying photo by Ryan W. McEwan.

DOI: https://doi.org/10.26890/lcw.jt5ds3db92

Overstory 2017, Mitchell J. Kukla, Corey M. Kuminecz, Julia I. Chapman, Taylor M. Sparbanie, Katherine Schrader, Michelle N. Little, Keith E. Gilland, Ryan W. Mcewan

Data Files: Drew Woods Permanent Plots

Overstory data (woody species ≥2.5 centimeters in diameter at breast height) collected in 2017 at Drew Woods State Nature Preserve in Darke County, OH. Data key is provided in a supplemental file.

Saplings 2017, Mitchell J. Kukla, Corey M. Kuminecz, Julia I. Chapman, Ryan W. Mcewan

Data Files: Drew Woods Permanent Plots

Sapling data (woody species >50 centimeters in height and <2.5 cm diameter at breast height) collected in 2017 at Drew Woods State Nature Preserve in Darke County, OH. Data key is provided in a supplemental file.

Instructions For Authors, Discovery Editors

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Local Wind Monitoring Matched With Lichen Pseudevernia Furfuracea (L.) Zopf Transplantation Technique To Assess The Environmental Impact Of A Biomass Power Plant, Lucio Lucadamo, Anna Corapi, Luana Gallo

Turkish Journal of Botany

The potential environmental impact of a biomass power plant (BPP) was evaluated by transplanting thalli of the lichen Pseudevernia furfuracea (L.) Zopf in the surrounding area for 3 months. Four meteorological stations were placed at four sites to monitor local winds. At the end of the period, thalli were retrieved and electrical conductivity percentage (EC%), lipid peroxidation, lichen vitality, photosynthetic efficiency, chlorophylls, xanthophylls+carotenoids, OD435/OD415, and concentrations of some elements frequently emitted by BPPs were measured. A univariate-multivariate analysis revealed clusters of sites with dissimilar mean values of ecophysiological parameters. They were merged, when not significantly differing, and classified as different …

Characterization Of The Beta1 Gene, Which Might Play A Role In Beta Vulgaris Subsp. Maritima Salt Tolerance, Özge Uysal, Çi̇ğdem Çakiroğlu, Ahmet Koç, Hüseyi̇n Çağlar Karakaya

Turkish Journal of Botany

Salinity stress has a negative impact on plant growth, which affects homeostasis and productivity. The uptake of nonessential salt ions changes the osmotic balance of the cell and causes dehydration. Higher plants develop salt tolerance mechanisms to avoid dehydration. Sea beet (Beta vulgaris subsp. maritima) is a halophytic ancestor of cultivated sugar beet that displays salt stress tolerance. In this study, we screened a B. vulgaris subsp. maritima cDNA library in Saccharomyces cerevisiae strain Ab11c (ena1Δ, nha1/4Δ, nhx1Δ), which is deficient in sodium transport, to find sodium-detoxifying genes. We identified a cDNA construct, named BETA1, providing salt tolerance to yeast …

The Effect Of Artificial Selection On Phenotypic Plasticity In Maize, Joseph L. Gage, Diego Jarquin, Cinta Romay, Aaron Lorenz, Edward S. Buckler, Shawn Kaeppler, Naser Alkhalifah, Martin Bohn, Darwin A. Campbell, Jode Edwards, David Ertl, Sherry Flint-Garcia, Jack Gardiner, Byron Good, Candice N. Hirsch, Jim Holland, David C. Hooker, Joseph Knoll, Judith Kolkman, Greg Kruger, Nick Lauter, Carolyn J. Lawrence-Dill, Elizabeth Lee, Jonathan Lynch, Seth C. Murray, Rebecca Nelson, Jane Petzoldt, Torbert Rocheford, James C. Schnable, Patrick S. Schnable, Brian Scully, Margaret Smith, Nathan M. Springer, Srikant Srinivasan, Renee Walton, Teclemariam Weldekidan, Randall J. Wisser, Wenwei Xu, Jianming Yu, Natalia De Leon

Department of Agronomy and Horticulture: Faculty Publications

Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize …

Allelic Variants Of Oshkt1;1 Underlie The Divergence Between Indica And Japonica Subspecies Of Rice (Oryza Sativa) For Root Sodium Content, Malachy T. Campbell, Nonoy Bandillo, Fouad Razzaq A. Al Shiblawi, Sandeep Sharma, Kan Liu, Qian Du, Aaron J. Schmitz, Chi Zhang, Anne-Alienor Very, Aaron J. Lorenz, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

Salinity is a major factor limiting crop productivity. Rice (Oryza sativa), a staple crop for the majority of the world, is highly sensitive to salinity stress. To discover novel sources of genetic variation for salt tolerance-related traits in rice, we screened 390 diverse accessions under 14 days of moderate (9 dS m^-1) salinity. In this study, shoot growth responses to moderate levels of salinity were independent of tissue Na⁺ content. A significant difference in root Na+ content was observed between the major subpopulations of rice, with indica accessions displaying higher root Na⁺ and japonica …

Jasmonoyl-L-Tryptophan Disrupts Iaa Activity Through The Aux1 Auxin Permease, Paul E. Staswick, Martha Rowe, Edgar P. Spalding, Bessie L. Splitt

Department of Agronomy and Horticulture: Faculty Publications

Amide-linked conjugates between tryptophan (Trp) and jasmonic (JA) or indole-3- acetic (IAA) acids interfered with gravitropism and other auxin-dependent activities in Arabidopsis, but the mechanism was unclear. To identify structural features necessary for activity several additional Trp conjugates were synthesized. The phenylacetic acid (PAA) conjugate was active, while several others were not. Common features of active conjugates is that they have ring structures that are linked to Trp through an acetic acid side chain, while longer or shorter linkages are inactive or less active. A dominant mutant, called tryptophan conjugate response1-D that is insensitive to JA-Trp, but still sensitive …

Tgbs® Genotyping-By-Sequencing Enables Reliable Genotyping Of Heterozygous Loci, Alina Ott, Sanzhen Liu, James C. Schnable, Cheng-Ting 'Eddy' Yeh, Kai-Sin Wang, Patrick S. Schnable

Department of Agronomy and Horticulture: Faculty Publications

Conventional genotyping-by-sequencing (cGBS) strategies suffer from high rates of missing data and genotyping errors, particularly at heterozygous sites. tGBS® genotyping-by-sequencing is a novel method of genome reduction that employs two restriction enzymes to generate overhangs in opposite orientations to which (single-strand) oligos rather than (double-stranded) adaptors are ligated. This strategy ensures that only doubledigested fragments are amplified and sequenced. The use of oligos avoids the necessity of preparing adaptors and the problems associated with inter-adaptor annealing/ligation. Hence, the tGBS protocol simplifies the preparation of high-quality GBS sequencing libraries. During polymerase chain reaction (PCR) amplification, selective nucleotides included at the 3'-end …

Plantcv V2: Image Analysis Software For High-Throughput Plant Phenotyping, Malia A. Gehan, Noah Fahlgren, Arash Abbasi, Jeffrey C. Berry, Steven T. Callen, Leonardo Chavez, Andrew N. Doust, Max J. Feldman, Kerrigan B. Gilbert, John G. Hodge, J. Steen Hoyer, Andy Lin, Suxing Liu, César Lizárraga, Argelia Lorence, Michael Miller, Eric Platon, Monica Tessman, Tony Sax

Department of Agronomy and Horticulture: Faculty Publications

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major …

Leveraging Agroecology For Solutions In Food, Energy, And Water, Marcia Delonge, Andrea D. Basche

Department of Agronomy and Horticulture: Faculty Publications

Global agriculture is facing growing challenges at the nexus of interconnected food, energy and water systems, including but not limited to persistent food insecurity and diet-related diseases; growing demands for energy and consequences for climate change; and declining water resources, water pollution, floods and droughts. Further, soil degradation and biodiversity loss are both triggers for and consequences of these problems. In this commentary, we argue that expanding agroecological principles, tools, and technologies and enhancing biological diversity can address these challenges and achieve better socioeconomic outcomes. Agroecology is often described as multi- or transdiscplinary, and applies ecological principles to the design …

Improving Water Resilience With More Perennially Based Agriculture, Andrea D. Basche, Oliver F. Edelson

Department of Agronomy and Horticulture: Faculty Publications

Land conversion from natural to managed ecosystems, while necessary for food production, continues to occur at high rates with significant water impacts. Further, increased rainfall variability exposes agricultural systems to impacts from flood and drought events. In many regions, water limitations are overcome through technological approaches such as irrigation and tile drainage, which may not be sustainable in the long term. A more sustainable approach to combat episodes of floods and droughts is to increase soil water storage and the overall green water efficiency of agroecosystems. Agricultural practices that promote “continuous living cover,” such as perennial grasses, agroforestry and cover …

Using An Active-Optical Sensor To Develop An Optimal Ndvi Dynamic Model For High-Yield Rice Production (Yangtze, China), Xiaojun Liu, Richard B. Ferguson, Hengbiao Zheng, Qiang Cao, Yongchao Tian, Weixing Cao, Yan Zhu

Department of Agronomy and Horticulture: Faculty Publications

The successful development of an optimal canopy vegetation index dynamic model for obtaining higher yield can offer a technical approach for real-time and nondestructive diagnosis of rice (Oryza sativa L) growth and nitrogen (N) nutrition status. In this study, multiple rice cultivars and N treatments of experimental plots were carried out to obtain: normalized difference vegetation index (NDVI), leaf area index (LAI), above-ground dry matter (DM), and grain yield (GY) data. The quantitative relationships between NDVI and these growth indices (e.g., LAI, DM and GY) were analyzed, showing positive correlations. Using the normalized modeling method, an appropriate NDVI simulation model …

Genomic Prediction With Pedigree And Genotype X Environment Interaction In Spring Wheat Grown In South And West Asia, North Africa, And Mexico, Sivakumar Sukumaran, José Crossa, Diego Jarquin, Marta Lopes, Matthew P. Reynolds

Department of Agronomy and Horticulture: Faculty Publications

Developing genomic selection (GS) models is an important step in applying GS to accelerate the rate of genetic gain in grain yield in plant breeding. In this study, seven genomic prediction models under two cross-validation (CV) scenarios were tested on 287 advanced elite spring wheat lines phenotyped for grain yield (GY), thousand-grain weight (GW), grain number (GN), and thermal time for flowering (TTF) in 18 international environments (year-location combinations) in major wheat-producing countries in 2010 and 2011. Prediction models with genomic and pedigree information included main effects and interaction with environments. Two random CV schemes were applied to predict a …

Validation Of Qtl Mapping And Transcriptome Profiling For Identification Of Candidate Genes Associated With Nitrogen Stress Tolerance In Sorghum, Malleswari Gelli, Anji Reddy Konda, Kan Liu, Chi Zhang, Thomas E. Clemente, David R. Holding, Ismail M. Dweikat

Department of Agronomy and Horticulture: Faculty Publications

Background: Quantitative trait loci (QTLs) detected in one mapping population may not be detected in other mapping populations at all the time. Therefore, before being used for marker assisted breeding, QTLs need to be validated in different environments and/or genetic backgrounds to rule out statistical anomalies. In this regard, we mapped the QTLs controlling various agronomic traits in a recombinant inbred line (RIL) population in response to Nitrogen (N) stress and validated these with the reported QTLs in our earlier study to find the stable and consistent QTLs across populations. Also, with Illumina RNA-sequencing we checked the differential expression of …

Drivers And Feedbacks Of The Fire-Grazing Interaction In The Northern Great Plains, Jacob E. Powell

Graduate Student Theses, Dissertations, & Professional Papers

The fire-grazing interaction is well studied in mesic grasslands worldwide, but research is lacking in semiarid systems. In addition, the fire-grazing interaction reduces the invasion of exotic forage species in mesic grasslands by increasing the scale of grazing selection and may be a tool to control invasive plants in other grasslands. We examined the principal drivers and feedbacks of the fire-grazing interaction on the strength of cattle grazing selection, forage quantity and quality, and vegetation structure and composition in two pastures in northeast Montana at The Nature Conservancy’s Matador Ranch. We also determined the influence of time since fire, within …

Classification Of Plant Communities Along Postfire Succession In Pinus Brutia (Turkish Red Pine) Stands In Antalya (Turkey), Ali̇ Kavgaci, Urban Silc, Sai̇me Başaran, Aleksander Marinsek, Mehmet Ali̇ Başaran, Petra Kosir, Nesli̇han Balpinar, Münevver Arslan, Özge Ergüler, Andraz Carni

Turkish Journal of Botany

The paper deals with the classification of plant communities that appear along postfire succession of Pinus brutia forests (Turkish red pine). The research took place in the Antalya region in the southern part of Turkey. Samplings were performed in nine areas, with different periods after fire: 1, 2, 3, 4, 7, 12, 20, 40 years, and a mature forest with an estimated age of 60 years. Numerical classification and ordination analysis were used to determine the communities and to understand the temporal changes. The vegetation classification showed that separate plant communities can be distinguished along the succession line. It was …

Zn-Use Efficiency For Optimization Of Symbiotic Nitrogenfixation In Chickpea (Cicer Arietinum L.), Igor Kryvoruchko

Turkish Journal of Botany

Zn deficiency is widespread in traditional areas of chickpea cultivation worldwide. It limits chickpea productivity and causes significant losses to the economies of the world?s largest chickpea exporters. This review may be of interest to researchers who would like to contribute to the improvement of chickpea cultivation on Zn-depleted soils in an environmentally sustainable manner, namely via identification of genotypes with superior symbiotic performance under Zn-limited conditions. The primary aim of the current work is to familiarize the readers with the biology and symbiotic characteristics of chickpea, and also to provide the necessary background on Zn as an essential nutrient …

Bioaccumulation And Oxidative Stress Impact Of Pb, Ni, Cu, And Cr Heavy Metals In Two Bryophyte Species, Pleurochaete Squarrosa And Timmiella Barbuloides, Serap Aydoğan, Bengi̇ Erdağ, Lale Aktaş

Turkish Journal of Botany

This study was conducted to evaluate the bioaccumulation and oxidative stress impact of lead (Pb), nickel (Ni), copper (Cu), and chromium (Cr) in bryophyte species Pleurochaete squarrosa and Timmiella barbuloides exposed to Pb, Ni, Cu, and Cr at 1 mM concentration for 48 h. Bioaccumulation ratios in the non-Fenton metals Ni and Pb were found to be higher than in Fenton metals Cu and Cr for both moss species. Except for Cu, high levels of heavy metal accumulation caused a slight increase in dry weights of both species. Total chlorophyll and carotenoid contents of both species showed variations under Ni, …

Pollen-Mediated Gene Flow From Glyphosate-Resistant Common Waterhemp (Amaranthus Rudis Sauer): Consequences For The Dispersal Of Resistance Genes, Debalin Sarangi, Andrew J. Tyre, Eric L. Patterson, Todd A. Gaines, Suat Irmak, Stevan Z. Knezevic, John L. Lindquist, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

Gene flow is an important component in evolutionary biology; however, the role of gene flow in dispersal of herbicide-resistant alleles among weed populations is poorly understood. Field experiments were conducted at the University of Nebraska-Lincoln to quantify pollen-mediated gene flow (PMGF) from glyphosate-resistant (GR) to -susceptible (GS) common waterhemp using a concentric donorreceptor design. More than 130,000 common waterhemp plants were screened and 26,199 plants were confirmed resistant to glyphosate. Frequency of gene flow from all distances, directions, and years was estimated with a double exponential decay model using Generalized Nonlinear Model (package gnm) in R. PMGF declined by 50% …

Estimating Yield Gaps At The Cropping System Level, Nicolas Guilpart, Patricio Grassini, Victor O. Sadras, Jagadish Timsina, Kenneth Cassman

Department of Agronomy and Horticulture: Faculty Publications

Yield gap analyses of individual crops have been used to estimate opportunities for increasing crop production at local to global scales, thus providing information crucial to food security. However, increases in crop production can also be achieved by improving cropping system yield through modification of spatial and temporal arrangement of individual crops. In this paper we define the cropping system yield potential as the output from the combination of crops that gives the highest energy yield per unit of land and time, and the cropping system yield gap as the difference between actual energy yield of an existing cropping system …

Modeling Pollen-Mediated Gene Flow From Glyphosate-Resistant To -Susceptible Giant Ragweed (Ambrosia Trifida L.) Under Field Conditions, Zahoor A. Ganie, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

A field experiment was conducted to quantify pollen mediated gene flow (PMGF) from glyphosateresistant (GR) to glyphosate-susceptible (GS) giant ragweed under simulated field conditions using glyphosate resistance as a selective marker. Field experiments were conducted in a concentric design with the GR giant ragweed pollen source planted in the center and GS giant ragweed pollen receptors surrounding the center in eight directional blocks at specified distances (between 0.1 and 35 m in cardinal and ordinal directions; and additional 50 m for ordinal directions). Seeds of GS giant ragweed were harvested from the pollen receptor blocks and a total of 100,938 …

Gene Silencing Of Argonaute5 Negatively Affects The Establishment Of The Legume-Rhizobia Symbiosis, Maria Del Rocio Reyero-Saavedra, Zhenzhen Qiao, Maria Del Socorro Sanchez-Correa, M. Enrique Diaz-Pineda, Jose L. Reyes, Alejandra A. Covarrubias, Marc Libault, Oswaldo Valdes-Lopez

Department of Agronomy and Horticulture: Faculty Publications

The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also …

Phytoplankton Dynamics And Structure, And Ecological Status Estimation By The Q Assemblage Index: A Comparative Analysis In Two Shallow Mediterranean Lakes, Tuğba Ongun Sevi̇ndi̇k, Hati̇ce Tunca, Ari̇f Gönülol, Ni̇sa Gürsoy, Şeyma Nur Küçükkaya, Zuhal Kinali

Turkish Journal of Botany

The aim of this research was to compare the phytoplankton structure on the basis of environmental variables and test the Q assemblage index based on phytoplankton functional groups in two shallow Mediterranean lakes [Lake Taşkısığı (LT) and Lake Little Akgöl (LLA)] in the north of Turkey. Variations in the phytoplankton structure and environmental parameters were analyzed monthly at two stations of each lake between January 2013 and December 2013. We showed that total phosphorus (TP) values were vital in shaping phytoplankton biomass in eutrophic LLA. Nitrate-nitrogen (NO3-N), TP, zmix/zeu, and macrophyte coverage are important in shaping the differences in dominant …

Relationships Between Sorghum Bicolor (Poaceae) And Its Closerelatives Based On Genomic In Situ Hybridization Evidence, Qing Liu, H L, Jun Wen

Turkish Journal of Botany

Sorghum bicolor (L.) Moench (sorghum) is a naturally well-established diploid species with 2n = 2x = 20. Here we provide evidence to identify the genomic relationships of S. bicolor and its extant relatives using genomic in situ hybridization. The genomic divergences between S. bicolor and its close relatives may be presented as: S. bicolor-S. x drummondii (Nees ex Steud.) Millsp. & Chase < S. bicolor-S. x almum Parodi < S. bicolor S. arundinaceum (Desv.) Stapf < S. bicolor-S. propinquum (Kunth) Hitchc. Sorghum arundinaceum probe signals showed spotted or painted patterns on the S. bicolor chromosomes, indicating that the degree of genomic divergence between S. bicolor and S. arundinaceum is distinct. It is reasonable to infer that S. bicolor might have diverged from S. arundinaceum in the early diversification history of the subgenus. The probe signal intensity of S. arundinaceum and S. propinquum is greater on the 17 chromosomes than on the remaining 23 chromosomes of S. halepense (L.) Pers., whereas S. bicolor and S. propinquum probes produced spotted or patchy signals on the 40 S. halepense chromosomes. Therefore, the degree of genomic divergence may be presented as: S. halepense-S. bicolor < S. halepense-S. arundinaceum < S. halepense-S. propinquum.

Scilla Bilgineri (Asparagaceae: Scilloideae): A New Species Ofscilla L. From Eastern Turkey, Hasan Yildirim, Yusuf Altioğlu

Turkish Journal of Botany

Scilla bilgineri Yıldırım (Asparagaceae) is described here as a new species. Diagnostic morphological characters, a full description, and detailed illustrations are provided on the basis of the type specimens and observations of wild populations. The new species is characterized by whitish to very pale lilac tepals, variegated ovary; style 5-6 mm long; oblong, straw to pale yellow and cucullate seed; pale creamy-white elaiosome, which is adherent to the testa; and pinkish to reddish, fleshy bulb scales. It belongs to Scilla bifolia agg. and is related to S. bifolia and S. albinerve within. It is easily distinguished from all other species …

Leaf Morpho-Physiological Dynamics In Salvia Officinalis L. Var. Purpurascens, Filipa Martins, Ivo Oliveira, Ana Barros, Carla Amaral, Sílvia Afonso, Helena Ferreira, José Moutinho-Pereira, Berta Gonçalves

Turkish Journal of Botany

Salvia officinalis L. var. purpurascens is one of the most insufficiently studied varieties of the genus Salvia. Hence, the study and characterization of this plant, as well as the monitoring of changes occurring during leaf ontogeny, are of great importance and interest. For this purpose, young and adult leaves of Salvia officinalis L. var. purpurascens collected in two different seasons and in two different years were analyzed, considering morpho-anatomical traits but also leaf gas exchange and chlorophyll a fluorescence parameters. Leaf age was found to have significant effects on several of the analyzed parameters, including the parenchyma, mesophyll, xylem, and …