Plant Biology Commons^™

Variations An Α-Tocopherol And Β-Carotene Concentrations In Forage Legumes And Grasses Harvested At Different Sites And Maturity Stages, Elisabet Nadeau, Hanna Lindqvist, Søren Krogh Jensen, Nilla Nilsdotter-Linde, Anne-Maj Gustavsson

IGC Proceedings (1977-2023)

Forage is a major source of natural α-tocopherol and β-carotene for dairy cows. This study examined vitamin concentrations of birdsfoot trefoil (Bft), red clover (Rc), timothy (Ti) and meadow fescue (Mf) at different sites, years and cutting dates. Mixtures of Bft+Ti, Rc+Ti and Rc+Mf were established at Skara (58°21’N; 13°08’E) and Umeå (63°45’N; 20°17’E) in Sweden. First-year leys were cut on three occasions in spring (Umeå 2005, Skara 2005 and 2007); one week before heading of timothy, at heading and one week after heading. Birdsfoot trefoil had higher α-tocopherol concentration at Skara than at Umeå in the first two cuts …

Comparing Drying Protocols For Perennial Ryegrass Samples In Preparation For Chemical Analysis, Marion Beecher, Deirdre Hennessy, Tommy M. Boland, Michael O’Donovan, Eva Lewis

IGC Proceedings (1977-2023)

Diet formulation for animals requires accurate estimation of feed nutritive value. In order to determine the nutritive value of grass, the moisture in the samples must be removed, with minimum damage to cell structure, and then the dried samples milled, prior to chemical analysis. Generally samples are oven dried. The aim of this study was to verify if differing drying protocols gave diverging results when drying grass samples. The drying protocols investigated were 40°C for 48 hours, 60°C for 48 hours and 95°C for 15 hours in forced convection ovens. Four perennial ryegrass samples were cut to 4 cm from …

Remote Sensing Of Pasture Quality, Reddy R. Pullanagari, Robyn A. Dynes, Warren M. King, Ian Yule, Susanne Thulin, Nichola M. Knox, Abel Ramoelo

IGC Proceedings (1977-2023)

Worldwide, farming systems are undergoing significant changes due to economic, environmental and social drivers. Agribusinesses must increasingly deliver products specified in terms of safety, health and quality. Increasing constraints are being placed on them by the market, the community and by government to achieve a financial benefit within social and environmental limits (Dynes et al. 2003).

In order to meet these goals, producers must know the quantity and quality of the inputs into their feeding systems, be able to reliably predict the products and by-products being generated, and have the skills to be able to manage their business accordingly. …

Infrastructure To Improve Beef Business Outcomes In The Queensland Gulf, Kiri C. Broad, Bernie H. English, Rebecca A. Gunther, Emma S. Hegarty, Joe W. Rolfe, Steven G. Bray

IGC Proceedings (1977-2023)

There are significant economic and environmental issues impacting on the short and long term viability of family-run breeding enterprises in the Queensland Gulf. Falling cattle prices and increased business costs threaten the social and financial well-being of many beef producers. Set stocking and overgrazing combine to reduce native 3P (productive, palatable and perennial) grass frequency and herd productivity. The Ryan family on Greenhills Station at George-town in the Queensland Gulf embarked on a 5 year water and fencing infrastructure development program aiming to improve pasture utilisation, land condition and long term carrying capacity.

A Technique For Measurement Of Cattle Form Using A Trail 3d Digital Camera, Tamaki Kida, Shigeki Tejima, Toshitaka Uchino, Fumihiko Tanaka

IGC Proceedings (1977-2023)

Measurement of weight and form are important for the management of grazing cattle; however, form measurement is seldom carried out. Recently, use of 3D digital cameras has been increasing, and 3D-technology for reconstruction of 3D pictures has been developed. The measurement of withers and hip height of cattle from 3D pictures using the image-analysis technique has been reported (Kida et al. 2012). However, time and effort are required to obtain 3D images of grazing cattle in pastures.

Here, we examined an automatic photographic technique using a sensor camera.

Modelling Complex Sheep Systems Using Ausfarm, Susan M. Robertson, Michael A. Friend

IGC Proceedings (1977-2023)

Simulation modelling can be a valuable method for extrapolating experimental findings to different weather or management conditions. However, most of the decision support tools which are available for sheep grazing systems, for example GrassGro® (Donnelly et al. 1997), are limited to modelling of relatively simple sheep management. This makes validation of simulations against experimental results difficult where management changes from year to year, and where more complex sheep management is used. This study evaluated the use of the AusFarm® decision support tool (Moore et al. 2007) to model a split-joined sheep system, using different ram breeds against experimental …

Does Targeted Short-Term Grazing Of Lucerne Increase Twinning Rates In Unsynchronised Merino Ewes?, Jessica M. Rummery, Susan M. Robertson, Belinda J. King, Michael A. Friend

IGC Proceedings (1977-2023)

Reproduction is one of the key profit drivers in the sheep industry and increased reproductive output is needed to address the decline in sheep numbers in Australia to maintain supply to export markets (Curtis 2009). Increased nutrition around mating, or ‘flushing’, is a well-known means of increasing twinning rates. Studies using synchronisation methods have shown that short-term (acute) supplementation can increase prolificacy if targeted at days 9-14 of the oestrous cycle (Stewart and Oldham 1986). However, synchronisation involves increased chemical and labour costs, so may not suit extensive production systems. This study aimed to test whether an increase in twinning …

Evaluating Rangeland's Grazing Capacity For Livestock And Wild Herbivores Using The Delta Diet Tool And Gis Technology, Sandra A. Santos, Arnaud L. J. Desbiez, Humberto L. Perotto-Baldivieso, Juliana M. Alvarez

IGC Proceedings (1977-2023)

Rangelands are dynamic and complex systems requiring appropriate adaptive decision-making to calculate grazing capacity integrating livestock and herbivore wildlife. This work describes the development and application of an integrated framework using the microhistological analysis (DeltaDiet tool) to identify key forage used by different herbivores from the same area associated with GIS technology to mapping landscape containing forage productivity and quality information. This study was conducted in a management unit, representative of the Nhecolândia sub-region landscape, Pantanal. During the dry period, representative fecal samples were collected from cows, capybaras and deer grazing in the same management unit for diet analysis, using …

Soybean Nodule-Associated Non-Rhizobial Bacteria Inhibit Plant Pathogens And Induce Growth Promotion In Tomato, Serkan Tokgöz, Dilip K. Lakshman, Mahmoud H. Ghozlan, Hasan Pinar, Daniel P. Roberts, Amitava Mitra

Department of Plant Pathology: Faculty Publications

The root nodules are a unique environment formed on legume roots through a highly specific symbiotic relationship between leguminous plants and nodule-inducing bacteria. Previously, Rhizobia were presumed to be the only group of bacteria residing within nodules. However, recent studies discovered diverse groups of bacteria within the legume nodules. In this report soybean nodule-associated bacteria were studied in an effort to identify beneficial bacteria for plant disease control and growth promotion. Analysis of surface-sterilized single nodules showed bacterial diversity of the nodule microbiome. Five hundred non-rhizobial colonies from 10 nodules, 50 colonies per nodule, were tested individually against the tomato …

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 …

Drought In Temperate Mesic Regions Leads To Micro-Density Anomalies In White Pine, Elise Miller

CSB and SJU Distinguished Thesis

Wood density and wood volume determine the amount of carbon fixed by trees; however, while we are beginning to understand normal seasonal variation in wood density, anomalies are common, and their drivers are poorly understood. In conifers, wood density normally increases continuously throughout the season, but intra-annual fluctuations in wood density can occur and have been linked to climatic events. The causes of these fluctuations in density at the micro-scale (hereafter micro-density anomalies) are still debated.

Mesic regions are experiencing more droughts, but micro-density anomalies are rarely studied in these ecosystems. This study examined micro-density anomaly distribution within the boles …

Subalpine Forest Tree Seedling Response To Drought, Alex Goke

Electronic Theses and Dissertations

Knowledge of tree species’ ability to tolerate drought is necessary to anticipate future forest dynamics with climate change, especially at the seedling stage given their role in shaping forest structure. We used precipitation reduction shelters to mimic drought for subalpine conifer seedlings (A. lasiocarpa and P. engelmannii) in the Rocky Mountains and compared survivorship and morphological and physiological responses to assess relative degrees of drought tolerance. We detected no significant investment in morphological tolerance traits (e.g. root biomass, leaf:stem area ratio) but substantial reductions in net photosynthesis. While shading partially ameliorated drought effects when precipitation reduction was moderate, …

A Rubric For Grading Laboratory Research Paper Writing Assignments In Plant Biology, David Rhoads

Q2S Enhancing Pedagogy

Writing a research paper based on a course laboratory research project is challenging for many students. In addition to providing a 3 page summary on how to write the paper (with details on the type and format of the content to be included for each section), I provide a detailed grading rubric that also contains an outline of the topics to be included in the paper. This rubric was further refined in the Winter 2020 (Q2S) Writing Intensive Faculty Learning Community (WI FLC).

Seed Source Regions Drive Fitness Differences In Invasive Macrophytes, Morgane B. Gillard, Rebecca E. Drenovsky, Gabrielle Thiébaut, Michèle Tarayre, Caryn J. Futrell, Brenda J. Grewell

2020 Faculty Bibliography

Premise Worldwide, ecosystems are threatened by global changes, including biological invasions. Invasive species arriving in novel environments experience new climatic conditions that can affect their successful establishment. Determining the response of functional traits and fitness components of invasive populations from contrasting environments can provide a useful framework to assess species responses to climate change and the variability of these responses among source populations. Much research on macrophytes has focused on establishment from clonal fragments; however, colonization from sexual propagules has rarely been studied. Our objective was to compare trait responses of plants generated from sexual propagules sourced from three climatic …

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 …