Plant Biology Commons^™

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 …

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 …

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.

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 …

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. …

Principles, Applications, And Biosafety Of Plant Genome Editing Using Crispr-Cas9, Kaoutar El-Mounadi, María Luisa Morales-Floriano, Hernan Garcia-Ruiz

Department of Plant Pathology: Faculty Publications

The terms genome engineering, genome editing, and gene editing, refer to modifications (insertions, deletions, substitutions) in the genome of a living organism. The most widely used approach to genome editing nowadays is based on Clustered Regularly Interspaced Short Palindromic Repeats and associated protein 9 (CRISPR-Cas9). In prokaryotes, CRISPR-Cas9 is an adaptive immune system that naturally protects cells from DNA virus infections. CRISPR-Cas9 has been modified to create a versatile genome editing technology that has a wide diversity of applications in medicine, agriculture, and basic studies of gene functions. CRISPR-Cas9 has been used in a growing number of monocot and dicot …

Variation Profile Of The Orthotospovirus Genome, Deepti Nigam, Hernan Garcia Ruiz

Department of Plant Pathology: Faculty Publications

Orthotospoviruses are plant-infecting members of the family Tospoviridae (order Bunyavirales), have a broad host range and are vectored by polyphagous thrips in a circulative- propagative manner. Because diverse hosts and vectors impose heterogeneous selection constraints on viral genomes, the evolutionary arms races between hosts and their pathogens might be manifested as selection for rapid changes in key genes. These observations suggest that orthotospoviruses contain key genetic components that rapidly mutate to mediate host adaptation and vector transmission. Using complete genome sequences, we profiled genomic variation in orthotospoviruses. Results show that the three genomic segments contain hypervariable areas at homologous locations …

Mutations In Virus-Derived Small Rnas, Deepti Nigam, Katherine Latourrette, Hernan Garcia Ruiz

Department of Plant Pathology: Faculty Publications

RNA viruses exist as populations of genome variants. Virus-infected plants accumulate 21–24 nucleotide small interfering RnAs (siRnAs) derived from viral RnA (virus-derived siRnAs) through gene silencing. This paper describes the profile of mutations in virus-derived siRNAs for three members of the family Potyviridae: Turnip mosaic virus (tuMV), Papaya ringspot virus (pRSV) and Wheat streak mosaic virus (WSMV). for tuMV in Arabidopsis thaliana, profiles were obtained for mechanically inoculated rosette leaves and systemically infected cauline leaves and inflorescence. Results are consistent withselection pressure on the viral genome imposed by local and systemic movement. By genetically removing gene silencing in the plant …

Metabolite Profiling Of Ganoderma-Infected Oil Palm Tree Grown On Ultisol And Oxisol Soil, Ahmad Muhamad Fadhil

Student Works (2020-2029)

The oil palm industry is a pillar of the Malaysian economy and plays a pivotal role in feeding and fueling a growing global population. In 2018, oil palm contributed 37.9% or RM37.7 billion to the country's' Gross Domestic Products (GDP) of agriculture sector. Despite achieving significant achievements in the industry, Ganoderma sp. infection that cause basal stem rot (BSR) and upper stem rot (USR) disease are considered a threat. The palm oil industry is expected to experience significant losses, thereby affecting yield production and ultimately the dead of trees. Some factors have been reported to affect the occurrence of the …

Can Precision Farming Technologies Be Applied To Grazing Management?, S. Mark Rutter

IGC Proceedings (1977-2023)

In arable farming, precision is used to monitor and manage crop variability. The same precision approach can be used to manage grassland, by using crop sensing, targeted fertilizer/herbicide/pesticide application and forage yield measurement when it is harvested mechanically. An additional challenge in grassland agriculture is developing precision approaches to manage the grazing process. This requires technologies to determine where an animal is, when, what and how much it is grazing which the system then needs to use in conjunction with other sources of information to control where the animal grazes next. This paper reviews the existing technologies in these …

Manipulation Of The Spatial Grazing Behaviour Of Livestock In Extensive Grassland Systems, Derek W. Bailey, Mitch B. Stephenson, Milton G. Thomas, Juan F. Medrano, Gonzalo Rincon

IGC Proceedings (1977-2023)

Spatial behaviour of livestock is a critical factor in grassland management. Recent and ongoing research suggests that new approaches can be used to manipulate where cattle graze. The combination of strategic supplement placement and low-stress herding can be used to target cattle grazing and potentially may be useful for managing fine fuels. A phenotype to genotype association study of cattle spatial behavior suggests that use of rugged terrain and areas far from water is inherited. Although more research is needed, selection for animals specifically adapted for mountainous terrain or extensive paddocks may be an alternative for managing grasslands in the …

Case Studies Which Demonstrate The Financial Viability Of Precision Dairy Farming, Ian Yule, Hayden Lawrence, Craige Mackenzie, Carolyn Hedley, Miles Grafton

IGC Proceedings (1977-2023)

A number of case studies are used to demonstrate the financial viability of precision farming methods for intensively managed pastures. Precision farming has sometimes been criticized as being technology-led where the management goals and desired outcomes are sometimes poorly defined. Case studies presented in this paper demonstrate a strong management approach where appropriate technologies are selected to contribute to the financial success of the farm. The first case study farm has increased milk production by 70% in four years, increased pasture production by 43%, reduced fertilizer costs to 43% of previous levels and has successfully predicted annual production to within …

Opportunities For Improving Livestock Production With E-Management Systems, Dave L. Swain, Rebecca N. Handcock, Greg J. Bishop-Hurley, Don Menzies

IGC Proceedings (1977-2023)

There is increased interest in hardware and software that can support e-Management for grassland-based livestock industries. Managers of grazing livestock were early adopters of radio frequency identification (RFID) technologies automatically monitoring individual animal performance. Recent developments of remote sensing, automated individual recording and management, location based systems, improved data transfer and technologies that can be used in more extensive grazing systems are providing new opportunities for the development of e-Management systems. There is a need for better data integration and systems that can provide the best available information to enable better decision-making. For greater industry adoption of more integrated e-Management …

Growth Of Bali Bulls Fattened With Forage Tree Legumes In Eastern Indonesia: Leucaena Leucocephala In Sumbawa, Tanda Panjaitan, Muhammad Fauzan, H. Dahlanuddin, Michael J. Halliday, H. Max Shelton

IGC Proceedings (1977-2023)

The contribution of West Nusa Tenggara Province to domestic beef supply in Indonesia is relatively small, however, beef cattle are very important for the livelihoods of smallholder farmers in the region.

Bali cattle (Boss javanicus) are the predominant breed as they are adapted to harsh nutritional conditions, are highly fertile and have low calf mortality (Toelihere 2003). While genetically capable of achieving a growth rate of 0.85 kg/d (Mastika 2003), Panjaitan (2012) identified poor nutrition as a severe limitation to animal growth in traditional village systems. Improving feed quality and supply is vital to increasing growth rates and …

Effect Of High Se And Co Alfalfa Forage On Animal Production, Xiao-Lei Jie, Xiao Guo, Hua-Feng Hu

IGC Proceedings (1977-2023)

Total and available selenium (Se) and cobalt (Co) concentrations are low in Chinese soils, especially those found in mainly in temperate humid sub-humid conditions in the northeast to the southwest band across China (Tan et al. 2002). The levels of Se and Co are marginally deficit in the brown soil of the Yellow River region which causes lower production level and quality in forage and crop plants. Application of Se and Co fertilizers to arable lands is essential to produce high Se and Co forages. Henan is a Province where produce high-quality grass forages are used to support dairy …

Pre-Conditioned Cattle Sales For Forage-Based Cow-Calf Management Systems, C. P. Bagley, L. S. Dale, B. C. Housewright

IGC Proceedings (1977-2023)

Demand for preconditioned feeder cattle continues to increase in the beef industry as value-based marketing and information flow expands indicating preconditioned forage-raised calves require less management, fewer losses due to illness and deaths, and increased profitability to both buyer and seller. The goal of a preconditioning program is to increase the value of weaned cattle (Bailey, 2002). The Northeast Texas Beef Improvement Organization (NET-BIO) is comprised of commercial cow/calf and stocker operators and various agribusinesses with the same interest. The objective of this study is to determine if prices received for preconditioned NETBIO stocker cattle increase the net income above …

Performance, Carcass Characteristics And Meat Quality Of Grazing Lambs Finished On Tropical Grasses, Cesar H. E. C. Poli, Samuel Carnesella, Fernando M. Souza, Concepta Mcmanus, Zélia M. S. Castilhos, Liris Kindlein, Jaime U. Tarouco

IGC Proceedings (1977-2023)

Brazil is a country of continental size, and more than seven million ha are occupied with tropical pasture. Worldwide animal production from tropical pastures is also very significant where Cynodon, Panicum and Paspalum are important genus. These grasses are widely used in the production of cattle, and are growing in importance for sheep production, but their potential for producing quality lamb is not fully known.

The objective of this study was to evaluate the potential of two tropical grasses for finishing lambs in autumn to reduce the seasonality of production of lamb for meat.

Alternative Pasture Development System And Breeding Weight For Beef Heifers, H. A. Lardner, Daalkhaijav Damiran, Steve Hendrick, Kathy Larson

IGC Proceedings (1977-2023)

Proper development of replacement beef heifers is critical and needs to be accomplished at lower costs without sacrificing reproductive performance. The current recommendations indicate heifers should reach approximately 65% of mature body weight (MBW) at breeding for successful reproduction (Patterson et al. 1992; NRC 1996). Meeting heifer maintenance and gestation nutrient requirements are getting more economically challenged for beef producers in western Canada. Therefore, producers are moving from drylot development systems where cattle are housed and fed in pens to the adoption of extensive grazing systems (Kelln et al. 2011) in field paddocks. Limited research has been conducted …

Variation Of Rumen Bacterial Diversity In Steers After The Beginning Of Grazing, Miwa Nakano, Satoshi Haga, Masanori Tohno, Kazuhiro Matoba, Ryuichi Uegaki, Hiroshi Ishizaki

IGC Proceedings (1977-2023)

Holstein heifers before or after puberty often are herded on public pastures in Japan. The herbage intake and rumen fermentation of grazing heifers that are not adapted for fresh herbage decreases due to a change of feed from stall-fed dried forage to fresh herbage. This limits their performance during the first several weeks on pasture. Thus, the feeding program such as supplementation before and after the beginning of grazing is important. An increase in ammonia concentration and a decline in fibre degradation in the rumen of a heifer (both of which occur simultaneously with low herbage intake and rumen fermentation) …

Forage Systems Effect On Forage-Fed Beef Production, Guillermo Scaglia, Basu Bhandari, Jeffrey M. Gillespie, Jim J. Wang

IGC Proceedings (1977-2023)

Locally produced forage-finished beef offers high value while enhancing economic, environmental, and social sustainability. It enhances environmental quality and the natural resource base, and makes good use of resources both on and off-farm. On the farm, it makes the most of the ability of cattle to convert grass to meat in a low-input system, making efficient use of solar energy, improving soil nutrient cycling, conserving soil and water, and limiting reliance on non-renewable resources (DeRamus 2004). Although the major causes of increased greenhouse gas emissions are due to population growth and industrialization, agriculture contributes to carbon dioxide (CO2) emissions through …