Digital Commons Network^™

Semantic Segmentation Of Sorghum Using Hyperspectral Data Identifies Genetic Associations, Chenyong Miao, Alejandro Pages, Zheng Xu, Eric Rodene, Jinliang Yang, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

This study describes the evaluation of a range of approaches to semantic segmentation of hyperspectral images of sorghum plants, classifying each pixel as either nonplant or belonging to one of the three organ types (leaf, stalk, panicle). While many current methods for segmentation focus on separating plant pixels from background, organ-specific segmentation makes it feasible to measure a wider range of plant properties. Manually scored training data for a set of hyperspectral images collected from a sorghum association population was used to train and evaluate a set of supervised classification models. Many algorithms show acceptable accuracy for this classification task. …

Isoseq Transcriptome Assembly Of C3 Panicoid Grasses Provides Tools To Study Evolutionary Change In The Panicoideae, Daniel S. Carvalho, Aime V. Nishimwe, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses—Poaceae—have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C₄ photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C₃ panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and …

Oxidosqualene Cyclases Involved In The Biosynthesis Of Triterpenoids In Quercus Suber Cork, Lucas Busta, Olga Serra, Ok Tae Kim, Marisa Molinas, Irene Peré-Fossoul, Mercè Figueras, Reinhard Jetter

Center for Plant Science Innovation: Faculty Publications

Cork is a water-impermeable, suberin-based material harboring lignin, (hemi)cellulose, and extractable small molecules (primarily triterpenoids). Extractables strongly influence the properties of suberin-based materials. Though these previous findings suggest a key role for triterpenoids in cork material quality, directly testing this idea is hindered in part because it is not known which genes control cork triterpenoid biosynthesis. Here, we used gas chromatography and mass spectrometry to determine that the majority (>85%) of non-polar extractables from cork were pentacyclic triterpenoids, primarily betulinic acid, friedelin, and hydroxy-friedelin. In other plants, triterpenoids are generated by oxidosqualene cyclases (OSCs). Accordingly, we mined Quercus suber …

Plant Segmentation By Supervised Machine Learning Methods, Jason Adams, Yumou Qiu, Yuhang Xu, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

High-throughput phenotyping systems provide abundant data for statistical analysis through plant imaging. Before usable data can be obtained, image processing must take place. In this study, we used supervised learning methods to segment plants from the background in such images and compared them with commonly used thresholding methods. Because obtaining accurate training data is a major obstacle to using supervised learning methods for segmentation, a novel approach to producing accurate labels was developed. We demonstrated that, with careful selection of training data through such an approach, supervised learning methods, and neural networks in particular, can outperform thresholding methods at segmentation.

Advances In Plant Phenomics: From Data And Algorithms To Biological Insights, Sunil Kumar Kenchanmane Raju, Addie M. Thompson, James Schnable

Center for Plant Science Innovation: Faculty Publications

The measurement of the characteristics of living organisms is referred to as phenotyping (Singh et al., 2016). While the use of phenotyping in plant biology and genetics can be traced back at least to Gregor Mendel sorting and counting peas by shape and pod color 160 years ago, addressing current questions in plant biology, genetics, and breeding often requires increasingly precise phenotyping of a wide range of traits. Accurate phenotyping has played a role in both novel discoveries about the fundamental biology of plants and the development of improved crop varieties around the world. With the advent of inexpensive genotyping …

Leaf Angle Extractor: A High-Throughput Image Processing Framework For Leaf Angle Measurements In Maize And Sorghum, Sunil Kumar Kenchanmane Raju, Miles Adkins, Alex Enersen, Daniel Santana De Carvalho, Anthony J. Studer, Baskar Ganapathysubramanian, Patrick S. Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

PREMISE: Maize yields have significantly increased over the past half-century owing to advances in breeding and agronomic practices. Plants have been grown in increasingly higher densities due to changes in plant architecture resulting in plants with more upright leaves, which allows more efficient light interception for photosynthesis. Natural variation for leaf angle has been identified in maize and sorghum using multiple mapping populations. However, conventional phenotyping techniques for leaf angle are low throughput and labor intensive, and therefore hinder a mechanistic understanding of how the leaf angle of individual leaves changes over time in response to the environment.

METHODS …

Methods And Compositions For Obtaining Useful Plant Traits, Sally Mackenzie, Michael Fromm, Kamaldeep Viridi, Yashitola Wamboldt

Center for Plant Science Innovation: Faculty Publications

The present invention provides methods for obtaining plants that exhibit useful traits by perturbation of plastid function in plant rootstocks and grafting the rootstocks to scions. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for plastid perturbation are also provided.

Interspecific Analysis Of Diurnal Gene Regulation In Panicoid Grasses Identifies Known And Novel Regulatory Motifs, Xianjun Lai, Claire Bendix, Lang Yan, Yang Zhang, James C. Schnable, Frank G. Harmon

Center for Plant Science Innovation: Faculty Publications

Background: The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum.

Results: Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in …

Voxel Carving-Based 3d Reconstruction Of Sorghum Identifies Genetic Determinants Of Light Interception Efficiency, Mathieu Gaillard, Chenyong Miao, James C. Schnable, Bedrich Benes

Center for Plant Science Innovation: Faculty Publications

Changes in canopy architecture traits have been shown to contribute to yield in- creases. Optimizing both light interception and light interception efficiency of agri- cultural crop canopies will be essential to meeting the growing food needs. Canopy architecture is inherently three-dimensional (3D), but many approaches to measuring canopy architecture component traits treat the canopy as a two-dimensional (2D) structure to make large scale measurement, selective breeding, and gene identifi- cation logistically feasible. We develop a high throughput voxel carving strategy to reconstruct 3D representations of sorghum from a small number of RGB photos. Our approach builds on the voxel carving …

Compounds For Increasing Lipid Synthesis And Storage, Concetta Dirusso, Nishikant Wase

Center for Plant Science Innovation: Faculty Publications

This invention relates to methods for increasing lipid accumulation and lipid production in cells. Methods of producing biofuel from cells and preparing nutraceuticals comprising lipids produced according to a method provided herein are also provided.

Non-Homology-Based Prediction Of Gene Functions In Maize (Zea Mays Ssp. Mays), Xiuru Dai, Zheng Xu, Zhikai Liang, Xiaoyu Tu, Silin Zhong, James C. Schnable, Pinghua Li

Center for Plant Science Innovation: Faculty Publications

Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions. As a result, homology is widely used for gene function pre- diction. This means functional annotation errors also propagate from one species to another. Several approaches based on machine learning classification algorithms were evaluated for their ability to accurately predict gene function from non-homology gene features. Among the eight supervised classification algorithms evaluated, random- forest-based prediction consistently provided the most accurate gene …

A High-Throughput Phenotyping Pipeline For Image Processing And Functional Growth Curve Analysis, Ronghao Wang, Yumuo Qiu, Yuzhen Zhou, Zhikai Liang, James Schnable

Center for Plant Science Innovation: Faculty Publications

High-throughput phenotyping system has become more and more popular in plant science research. The data analysis for such a system typically involves two steps: plant feature extraction through image processing and statistical analysis for the extracted features. The current approach is to perform those two steps on different platforms. We develop the package “implant” in R for both robust feature extraction and functional data analysis. For image processing, the “implant” package provides methods including thresholding, hidden Markov random field model, and morphological operations. For statistical analysis, this package can produce nonparametric curve fitting with its confidence region for plant growth. …

Leaf Angle Extractor: A High-Throughput Image Processing Framework For Leaf Angle Measurements In Maize And Sorghum, Sunil Kumar Kenchanmane Raju, Miles Adkins, Alex Enersen, Daniel Santana De Carvalho, Anthony J. Studer, Baskar Ganapathysubramanian, Patrick Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

PREMISE: Maize yields have significantly increased over the past half-century owing to advances in breeding and agronomic practices. Plants have been grown in increasingly higher densities due to changes in plant architecture resulting in plants with more upright leaves, which allows more efficient light interception for photosynthesis. Natural variation for leaf angle has been identified in maize and sorghum using multiple mapping populations. However, conventional phenotyping techniques for leaf angle are low throughput and labor intensive, and therefore hinder a mechanistic understanding of how the leaf angle of individual leaves changes over time in response to the environment.

METHODS: High-throughput …

Advances In Plant Phenomics: From Data And Algorithms To Biological Insights, Sunil K. Kenchanmane Raju, Addie M. Thompson, James Schnable

Center for Plant Science Innovation: Faculty Publications

The measurement of the characteristics of living organisms is re- ferred to as phenotyping (Singh et al., 2016). While the use of phe- notyping in plant biology and genetics can be traced back at least to Gregor Mendel sorting and counting peas by shape and pod color 160 years ago, addressing current questions in plant biology, genet- ics, and breeding often requires increasingly precise phenotyping of a wide range of traits. Accurate phenotyping has played a role in both novel discoveries about the fundamental biology of plants and the development of improved crop varieties around the world. With the advent …

Metabolic Profiles Of Six African Cultivars Of Cassava (Manihot Esculenta Crantz) Highlight Bottlenecks Of Root Yield, Toshihiro Obata, Patrick A.W. Klemens, Laise Rosado-Souza, Armin Schlereth, Andreas Gisel, Livia Stavolone, Wolfgang Zierer, Nicolas Morales, Lukas A. Mueller, Samuel C. Zeeman, Frank Ludewig, Mark State, Uwe Sonnewald, H. Ekkehard Neuhaus, Alisdair R. Femie

Center for Plant Science Innovation: Faculty Publications

Cassava is an important staple crop in sub-Saharan Africa, due to its high productivity even on nutrient poor soils. The metabolic characteristics underlying this high productivity are poorly understood including the mode of photosynthesis, reasons for the high rate of photosynthesis, the extent of source/sink limitation, the impact of environment, and the extent of variation between cultivars. Six commercial African cassava cultivars were grown in a greenhouse in Erlangen, Germany, and in the field in Ibadan, Nigeria. Source leaves, sink leaves, stems and storage roots were harvested during storage root bulking and analyzed for sugars, organic acids, amino acids, phosphorylated …

Increased Power And Accuracy Of Causal Locus Identification In Time Series Genome-Wide Association In Sorghum1[Open], Chenyong Miao, Yuhang Xu, Sanzhen Liu, Patrick S. Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

The phenotypes of plants develop over time and change in response to the environment. New engineering and computer vision technologies track these phenotypic changes. Identifying the genetic loci regulating differences in the pattern of phenotypic change remains challenging. This study used functional principal component analysis (FPCA) to achieve this aim. Time series phenotype data were collected from a sorghum (Sorghum bicolor) diversity panel using a number of technologies including conventional color photography and hyperspectral imaging. This imaging lasted for 37 d and centered on reproductive transition. A new higher density marker set was generated for the same population. Several genes …

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

The Coordinate Regulation Of Digestive Enzymes In The Pitchers Of Nepenthes Ventricosa, Zephyr Anne Lenninger

Honors Program Theses

Many species of plants have adopted carnivory as a way to obtain supplementary nutrients from otherwise nutrient deficient environments. One such species, Nepenthes ventricosa, is characterized by a pitcher shaped passive trap. This trap is filled with a digestive fluid that consists of many different digestive enzymes, the majority of which seem to have been recruited from pathogen resistance systems. The present study attempted to determine whether the introduction of a prey stimulus will coordinately up-regulate the enzymatic expression of a chitinase and a protease while also identifying specific chitinases that are expressed by Nepenthes ventricosa. We were able to …

Virus-Induced Changes In Nuclear Proteins And Membranes In Nicotiana Benthamiana Cells, Caleb Mathias

Theses and Dissertations--Plant Pathology

Viruses rely on host proteins to complete their life cycles. This results in alterations to normal cell physiology to processes which benefit viral processes such as replication and movement to other cells. This may involve the relocalization of host proteins away from their original subcellular targets to sites which may benefit the virus, a process that is not as well understood as it relates to the nucleus. To identify nuclear proteins that may be involved in such processes, a library of random Nicotiana benthamiana cDNAs were expressed as GFP fusions in a transgenic marker lines expressing a histone 2B:RFP nuclear …

Dicamba Retention In Commercial Sprayers Following Triple Rinse Cleanout Procedures, And Soybean Response To Contamination Concentrations, Frances B. Browne, Xiao Li, Katilyn J. Price, Jianping Wang, Yi Wang, Greg R. Kruger, Jeff Golus, Gabrielle De Castro Macedo, Bruno C. Vieira, Tyler Sandlin

Department of Agronomy and Horticulture: Faculty Publications

The commercial launch of dicamba‐tolerant (DT) crops has resulted in increased dicamba usage and a high number of dicamba off‐target movement complaints on sensitive soybeans (Glycine max L.). Dicamba is a synthetic auxin and low dosages as 0.028 g ae ha−1 can induce injury on sensitive soybean. Tank contamination has been identified as one of the sources for unintended sensitive crop exposure. The labels of new dicamba formulations require a triple rinse cleanout procedure following applications. Cleanout efficacy might vary based on the sprayer type and procedure followed. This study was performed to quantify dicamba retention in commercial sprayers and …

Improving On Modis Mcd64a1 Burned Area Estimates In Grassland Systems: A Case Study In Kansas Flint Hills Tall Grass Prairie, Rheinhardt Scholtz, Jayson Prentice, Yao Tang, Dirac Twidwell

Department of Agronomy and Horticulture: Faculty Publications

Uncertainty in satellite-derived burned area estimates are especially high in grassland systems, which are some of the most frequently burned ecosystems in the world. In this study, we compare differences in predicted burned area estimates for a region with the highest fire activity in North America, the Flint Hills of Kansas, USA, using the moderate resolution imaging spectroradiometer (MODIS) MCD64A1 burned area product and a customization of the MODIS MCD64A1 product using a major ground-truthing effort by the Kansas Department of Health and Environment (KDHE-MODIS customization). Local-scale ground-truthing and the KDHE-MODIS product suggests MODIS burned area estimates under predicted fire …

Habitat Assessment Of Suitable Areas For Three Rare Plant Species (Layia Carnosa, Erysimum Menziesii, And Gilia Millefoliata) In The Barr Parcel On Friends Of The Dunes Property, Sophia Grubb, Almond Dodge, Jeremy Cashen

Environmental Science & Management Senior Capstones

Native rare plants are an important component of ecosystems. It is critical to preserve these species because it facilitates growth of native plants. Ecological restoration provides the necessary conditions to encourage native plant growth. Gilia millefoliata, Erysimum menziesii, and Layia carnosa are three rare plants found on the Friends of the Dunes property in Arcata, CA. In this assessment, we surveyed these three rare plants and came up with a management plan for the Barr Parcel on the Friends of the Dunes property. Friends of the Dunes recently acquired the Barr Parcel and are waiting for restoration permits …

A Comparison Of Media To Determine Optimal Growth In Aquaponics, Rachel L. Fogle, Andrea Nagy, Allison Bernard, Jordan Brown, Samantha Delvalle-Trinh, James Shuler

Harrisburg University Presidential Research Grants

No abstract provided.

Functional Analysis Of Squamosa-Promoter Binding Protein Like 13 In Controlling Flowering Time, Plant Architecture, Grain Size, And Grain Number In Wheat, Ajay Gupta

Electronic Theses and Dissertations

Higher and stable yield is always a major objective of wheat genetic improvement programs. The SQUAMOSA-promoter binding protein-like (SPL) genes constitute a small family of plant-specific transcription factors with diverse functions in plant development and growth and have great potential in improving yield and other major agronomic traits. However, the functional characterization of the SPL gene family in wheat is far behind other cereal crops such as rice. Using phylogenetic analysis, we identified 56 wheat orthologues of rice SPL genes belonging to 19 homoeologous groups. Among these 19 orthologous TaSPL genes, nine harbor the micro RNA 156 recognition element (MRE) …

Developing Microbial Based Process To Produce High Value Natural Antimicrobial (Glyceollin) In Soybeans And Pullulan From Sucrose, Andrea Zavadil

Electronic Theses and Dissertations

Glyceollin is a secondary metabolite produced under stress conditions by soybean to act as a plant defender to pathogen attack. The antimicrobial nature of glyceollin makes it a promising natural alternative to antibiotics if incorporated into livestock feed. However, production of glyceollin is highly variable, dependent on soybean variety, and fungal elicitor used as inoculum. Our study compares two fungal spore elicitors, Trichoderma reesei and Aspergillus sojae on soybeans of diverse maturity level, and fungal susceptibility to determine highest glyceollin titer. Spore inoculation with T. reesei elicited highest glyceollin titers of 2.42±0.20 mg/g at 120 h, while A. sojae elicited …

A Global Database Of Soil Nematode Abundance And Functional Group Composition, Johan Van Den Hoogen, Stefan Geisen, Thomas W. Crowther, Peter Mullin, Many Co-Authors

Department of Plant Pathology: Faculty Publications

As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into …

Effects Of Chemical Variation On Competition And Insect Communities Across Solidago Altissima Genotypes, Bryan Scott Foster Ii

Masters Theses

Individuals within a plant species can differ greatly from one another, especially regarding the range of chemical compounds produced. However, the functions of many of these chemicals are unknown, but likely include defenses against herbivores, attractants for pollinators and seed dispersers, as well as mechanisms for resource competition. To assess the effects of foliar chemical composition on interspecific plant competition and insect communities, I conducted a common garden and greenhouse experiment using 24 genotypes of the allelopathic species Solidago altissima for which the foliar chemistry had been characterized. Using these data and chemical profiles of S. altissima, I linked …

The Origin And Evolution Of Flower Characters In Angiosperms With A Case Study On The Genetic Basis Of Zygomorphic Corolla Development In Bee And Hummingbird Pollinated Species Of Schizanthus (Solanaceae), Ghadeer Bukhari

Theses and Dissertations

This Ph.D. dissertation investigates two main projects separated into two chapters, one for each. The first chapter explores the evolution of flowering plants (angiosperms), a macro-scale study. The second project is on a micro-scale that focus on exploring the genes that regulate the similarities and the differences of flower morphology reflecting their different pollination syndromes in two species of Schizanthus (Solanaceae), i.e., S. pinnatus, a bee-pollinated flower, and S. grahamii, a hummingbird- pollinated flower.

In the first chapter, I used floral diagrams to study the origin and the evolution of floral traits in angiosperms, a new set of morphological data …

Non-Homology-Based Prediction Of Gene Functions In Maize (Zea Mays Ssp. Mays), Xiuru Dai, Zheng Xu, Zhikai Liang, Xiaoyu Tu, Silin Zhong, James Schnable, Pinghua Li

Center for Plant Science Innovation: Faculty Publications

Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions.As a result, homology is widely used for gene function prediction. This means functional annotation errors also propagate from one species to another. Several approaches based on machine learning classification algorithms were evaluated for their ability to accurately predict gene function from non-homology gene features. Among the eight supervised classification algorithms evaluated, random forest-based prediction consistently provided the most accurate gene function prediction. …

Characterization Of Bacterial Endophytes Isolated From Brassica Carinata And Their Potential Use To Decrease Nutrient Requirements In Crops, Alex Soupir

Electronic Theses and Dissertations

Bacterial endophytes have the capability to enhance plant growth by producing plant growth hormones, solubilizing phosphates, suppressing pathogenic fungi, and reducing plant stress hormones. These capabilities make them desirable limiting the amount of nutrients and pesticides that are applied to crops. Through these assays and isolations, it is possible to identify novel bacterial species. In-vitro testing had shown 9 of the 20 isolates possess the ability to produce indole-3-acetic acid (IAA) with Pantoea agglomerans BC09 producing a concentration of 30.2 ng/μl over 4 days. BC09, Bacillus subilis BC10, and Pantoea sp. BC12 were able to solubilize calcium phosphate, 7 endophytes …