Plant Biology Commons^™

Overlapping Residual Herbicides For Control Of Photosystem (Ps) Ii- And 4-Hydroxyphenylpyruvate Dioxygenase (Hppd)-Inhibitor-Resistant Palmer Amaranth (Amaranthus Palmeri S. Watson) In Glyphosate-Resistant Maize, Parminder S. Chahal, Zahoor Ahmad Ganie, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

A Palmer amaranth (Amaranthus palmeri S. Watson) biotype has evolved resistance to photosystem (PS) II- (atrazine) and 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides (mesotrione, tembotrione, and topramezone) in maize seed production field in Nebraska, USA. The objectives of this study were to determine the effect of soil residual pre-emergence (PRE) herbicides followed by (fb) tank-mixture of residual and foliar active post-emergence (POST) herbicides on PS-II- and HPPD-inhibitor-resistant Palmer amaranth control, maize yield, and net economic returns. Field experiments were conducted in a grower’s field infested with PS II- and HPPD-inhibitor-resistant Palmer amaranth near Shickley in Fillmore County, Nebraska, USA in 2015 …

Evaluation Of Bacillus Strains For Plant Growth Promotion And Predictability Of Efficacy By In Vitro Physiological Traits, Rufus J. Akinrinlola, Gary Y. Yuen, Rhae A. Drijber, Anthony O. Adesemoye

Department of Plant Pathology: Faculty Publications

Bacilli are commonly used as plant growth-promoting agents but can be limited in effectiveness to certain crop and soil environments. The objectives of this study were to (1) identify Bacillus strains that can be consistent in promoting the growth of corn, wheat, and soybean and (2) determine whether physiological traits expressed in vitro can be predictive of growth promotion efficacy/consistency and be used for selecting effective strains. Twelve Bacillus strains isolated from wheat rhizospheres were evaluated in greenhouse pot tests with nonsterile soil for their effects on the growth of corn, soybean, and wheat. The strains also were assessed in …

Chapter 008 - Tropics, Janice M. Glime

Bryophyte Ecology Volume 4: Habitat and Role

Explore the contents of Bryophyte Ecology, Volume 4, Chapter 8 - Tropics by clicking the links above. For the Contents section of this ebook, as well as Volumes 1 through 5, please visit the Bryophyte Ecology Main Page.

Use CTRL+F to easily search within PDF files.

Ebook sponsored by Michigan Technological University and the International Association of Bryologists.

Bulked-Segregant Analysis Coupled To Whole Genome Sequencing (Bsa-Seq) For Rapid Gene Cloning In Maize, Harry Klein, Yuguo Xiao, Phillip A. Conklin, Rajanikanth Govindarajulu, Jacob A. Kelly, Michael J. Scanlon, Clinton J. Whipple, Madelaine Bartlett

Faculty & Staff Scholarship

Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can …

Field Evaluation Of Commercially Available Small Unmanned Aircraft Crop Spray Systems, Wayne Woldt, D. Martin, M. Latheef, Greg Kruger, Robert J. Wright, Justin Mcmechan, Christopher A. Proctor, Tamra Jackson-Ziems

Department of Plant Pathology: Faculty Publications

Agricultural research and development on small unmanned aircraft systems (UAS) has been directed toward UAS enabled sensing to detect features of interest. While compelling, there is an immediate need to increase the breadth and depth of UAS-based research, to move beyond sensing, and explore active intervention in agricultural production systems. This paper is focused on the concept of crop protection through ultra-precise, unmanned aerial application systems, and seeks to initiate research discussion in this important area of opportunity. Toward this end, two different, commercially available, small Unmanned Aerial Application Systems (sUAAS - defined as less than 55 lbs. maximum take-off …

Nutrient Conservation Trait Responses Of Low Resource Adapted Chaparral Shrubs To Increased Resource Availability, Reina Lee Nielsen

Masters Theses

Traits that increase mean nutrient retention times are essential to plant performance in low resource environments, where multiple stressors (low water and nutrients) are present. Although physiological responses to either water or nutrient stress are well understood, fewer studies have investigated the interaction of these stressors from a phylogenetically-controlled, whole-plant perspective. This research focused on three, phylogenetically-controlled pairs of shrubby evergreen species from the California chaparral that either grow on or off serpentine soils, which differ in nutrient availability. Using greenhouse and field studies, the responses of these plants to altered water and nutrient availability were evaluated. The greenhouse study …

Development Of Ifox-Hunting As A Functional Genomic Tool And Demonstration Of Its Use To Identify Early Senescence-Related Genes In The Polyploid Brassica Napus, Juan Ling, Renjie Li, Chinedu Charles Nwafor, Junluo Cheng, Maoteng Li, Qing Xi, Jian Wu, Lu Gan, Qingyong Yang, Chao Liu, Ming Chen, Yongming Zhou, Edgar B. Cahoon, Chunyu Zhang

Center for Plant Science Innovation: Faculty Publications

Functional genomic studies of many polyploid crops, including rapeseed (Brassica napus), are constrained by limited tool sets. Here we report development of a gain-of-function platform, termed ‘iFOX (inducible Full-length cDNA OvereXpressor gene)-Hunting’, for inducible expression of B. napus seed cDNAs in Arabidopsis. A Gateway-compatible plant gene expression vector containing a methoxyfenozide-inducible constitutive promoter for transgene expression was developed. This vector was used for cloning of random cDNAs from developing B. napus seeds and subsequent Agrobacterium-mediated transformation of Arabidopsis. The inducible promoter of this vector enabled identification of genes upon induction that are otherwise lethal when constitutively overexpressed and …

Conventional And Hyperspectral Time-Series Imaging Of Maize Lines Widely Used In Field Trials, Zhikai Liang, Piyush Pandey, Vincent Stoerger, Yuhang Xu, Yumou Qiu, Yufeng Ge, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Background: Maize (Zea mays ssp. mays) is 1 of 3 crops, along with rice and wheat, responsible for more than one-half of all calories consumed around the world. Increasing the yield and stress tolerance of these crops is essential to meet the growing need for food. The cost and speed of plant phenotyping are currently the largest constraints on plant breeding efforts. Datasets linking new types of high-throughput phenotyping data collected from plants to the performance of the same genotypes under agronomic conditions across a wide range of environments are essential for developing new statistical approaches and computer …

Single-Molecule Sequencing And Optical Mapping Yields An Improved Genome Of Woodland Strawberry (Fragaria Vesca) With Chromosome-Scale Contiguity, Patrick P. Edger, Robert Vanburen, Marivi Colle, Thomas J. Poorten, Ching Man Wai, Chad E. Niederhuth, Elizabeth I. Alger, Shujun Ou, Charlotte B. Acharya, Jie Wang, Pete Callow, Michael R. Mckain, Jinghua Shi, Chad Collier, Zhiyong Xiong, Jeffrey P. Mower, Janet P. Slovin, Timo Hytonen, Ning Jiang, Kevin L. Childs, Steven J. Knapp

Center for Plant Science Innovation: Faculty Publications

Background: Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Findings: Here we utilized a robust, cost-effective approach to produce high-quality reference genomes.We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ~7.9 million base pairs (Mb), representing a ~300-fold improvement of the previous version. The vast majority (>99.8%) …

Identification Of Bottlenecks In The Accumulation Of Cyclic Fatty Acids In Camelina Seed Oil, Xiao-Hong Yu, Rebecca E. Cahoon, Patrick J. Horn, Hai Shi, Richa R. Prakash, Yuanheng Cai, Maegan Hearney, Kent D. Chapman, Edgar B. Cahoon, Jorg Schwender, John Shanklin

Center for Plant Science Innovation: Faculty Publications

Modified fatty acids (mFA) have diverse uses; for example, cyclopropane fatty acids (CPA) are feedstocks for producing coatings, lubricants, plastics and cosmetics. The expression of mFA-producing enzymes in crop and model plants generally results in lower levels of mFA accumulation than in their natural-occurring source plants. Thus, to further our understanding of metabolic bottlenecks that limit mFA accumulation, we generated transgenic Camelina sativa lines co-expressing Escherichia coli cyclopropane synthase (EcCPS) and Sterculia foetida lysophosphatidic acid acyltransferase (SfLPAT). In contrast to transgenic CPA-accumulating Arabidopsis, CPA accumulation in camelina caused only minor changes in seed weight, germination rate, oil accumulation and seedling …

Integrating Phylogenetic And Network Approaches To Study Gene Family Evolution: The Case Of The Agamous Family Of Floral Genes, Daniel Santana De Carvalho, James C. Schnable, Ana Maria R. Almeida

Center for Plant Science Innovation: Faculty Publications

The study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes. The results obtained with the two methods largely agreed with one another. In particular, we show how network approaches can provide improved interpretations …

Functional Modeling Of Plant Growth Dynamics, Y. Xu, Y. Qiu, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Recent advances in automated plant phenotyping have enabled the collection of time series measurements from the same plants of a wide range of traits at different developmental time scales. The availability of time series phenotypic datasets has increased interest in statistical approaches for comparing patterns of change among different plant genotypes and different treatment conditions. Two widely used methods of modeling growth with time are pointwise analysis of variance (ANOVA) and parametric sigmoidal curve fitting. Pointwise ANOVA yields discontinuous growth curves, which do not reflect the true dynamics of growth patterns in plants. In contrast, fitting a parametric model to …

Gipc Glcnac Glycosyltransferase, Toshiki Ishikawa, Lin Fang, Emilie A. Rennie, Julien Sechet, Jingwei Yan, Beibei Jing, William Moore, Edgar B. Cahoon, Henrik V. Scheller, Maki Kawai-Yamada, Jenny C. Mortimer

Center for Plant Science Innovation: Faculty Publications

Glycosylinositol phosphorylceramides (GIPCs), which have a ceramide core linked to a glycan headgroup of varying structure, are the major sphingolipids in the plant plasma membrane. Recently, we identified the major biosynthetic genes for GIPC glycosylation in Arabidopsis thaliana, and demonstrated that the glycan headgroup is essential for plant viability. However, the function of GIPCs and the significance of their structural variation are poorly understood. Here, we characterized the Arabidopsis glycosyltransferase GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) and showed that it is responsible for the glycosylation of a subgroup of GIPCs found in seeds and pollen that contain N-acetylglucosamine (GlcNAc) and glucosamine …

Sma1, A Homolog Of The Splicing Factor Prp28, Has A Multifaceted Role In Mirna Biogenesis In Arabidopsis, Shengjun Li, Ran Xu, Aixia Li, Kan Liu, Liqing Gu, Mu Li, Hairui Zhang, Yueying Zhang, Shangshang Zhuang, Quanhui Wang, Gang Gao, Na Li, Chi Zhang, Yunhai Li, Bin Yu

Center for Plant Science Innovation: Faculty Publications

MicroRNAs (miRNAs) are a class of small non-coding RNAs that repress gene expression. In plants, the RNase III enzyme Dicer-like (DCL1) processes primary miRNAs (pri-miRNAs) into miRNAs. Here, we show that SMALL1 (SMA1), a homolog of the DEADbox pre-mRNA splicing factor Prp28, plays essential roles in miRNA biogenesis in Arabidopsis. A hypomorphic sma1-1 mutation causes growth defects and reduces miRNA accumulation correlated with increased target transcript levels. SMA1 interacts with the DCL1 complex and positively influences primiRNA processing. Moreover, SMA1 binds the promoter region of genes encoding pri-miRNAs (MIRs) and is required for MIR transcription. Furthermore, SMA1 also …

Generation And Evaluation Of Modified Opaque-2 Popcorn Suggests A Route To Quality Protein Popcorn, Ying Ren, Abou Yobi, Leandra Marshall, Ruthie Angelovici, Oscar Rodriguez, David R. Holding

Center for Plant Science Innovation: Faculty Publications

Introducing traits from dent corn to popcorn is challenging because it is difficult to recover adequate popping characteristics. QPM (Quality Protein Maize) is a dent corn variety carrying the opaque-2 (o2) mutation, specifying increased amounts of normally limiting essential amino acids, and modifier genes which restore the wild type vitreous kernel phenotype. In this study, we introgressed o2 and selected for endosperm modification using vitreousness and high 27-kD gamma zein content. In this way, we recovered high-lysine, fully poppable Quality Protein Popcorn (QPP). BC₂F₄ individuals with vitreous kernels were confirmed to be o2 mutants by …

Molecular Tools Enabling Pennycress (Thlaspi Arvense) As A Model Plant And Oilseed Cash Cover Crop, Michaela Mcginn, Winthrop B. Phippen, Ratan Chopra, Sunil Bansal, Brice A. Jarvis, Mary E. Phippen, Kevin M. Dorn, Maliheh Esfahanian, Tara J. Nazarenus, Edgar B. Cahoon, Timothy P. Durrett, M. David Marks, John C. Sedbrook

Center for Plant Science Innovation: Faculty Publications

Thlapsi arvense L. (pennycress) is being developed as a profitable oilseed cover crop for the winter fallow period throughout the temperate regions of the world, controlling soil erosion and nutrients run-off on otherwise barren farmland. We demonstrate that pennycress can serve as a user-friendly model system akin to Arabidopsis that is well-suited for both laboratory and field experimentation. We sequenced the diploid genome of the spring-type Spring 32-10 inbred line (1C DNA content of 539 Mb; 2n = 14), identifying variation that may explain phenotypic differences with winter-type pennycress, as well as predominantly a one-to-one correspondence with Arabidopsis genes, …

Lycophyte Plastid Genomics: Extreme Variation In Gc, Gene And Intron Content And Multiple Inversions Between A Direct And Inverted Orientation Of The Rrna Repeat, Jeffrey P. Mower, Peng-Fei Ma, Felix Grewe, Alex Taylor, Todd P. Michael, Robert Vanburen, Yin-Long Qiu

Center for Plant Science Innovation: Faculty Publications

Lycophytes are a key group for understanding vascular plant evolution. Lycophyte plastomes are highly distinct, indicating a dynamic evolutionary history, but detailed evaluation is hindered by the limited availability of sequences. Eight diverse plastomes were sequenced to assess variation in structure and functional content across lycophytes. Lycopodiaceae plastomes have remained largely unchanged compared with the common ancestor of land plants, whereas plastome evolution in Isoetes and especially Selaginella is highly dynamic. Selaginella plastomes have the highest GC content and fewest genes and introns of any photosynthetic land plant. Uniquely, the canonical inverted repeat was converted into a direct repeat (DR) …

The Role Of Type Iii Effectors From Xanthomonas Axonopodis Pv. Manihotis In Virulence And Suppression Of Plant Immunity, Cesar Augusto Medina, Paola Andrea Reyes, Cesar Augusto Trujillo, Juan Luis Gonzalez, David Alejandro Bejarano, Nathaly Andrea Montenegro, Jonathan M. Jacobs, Anna Joe, Silvia Restrepo, James R. Alfano, Adriana Bernal

Center for Plant Science Innovation: Faculty Publications

Xanthomonas axonopodis pv. manihotis (Xam) causes cassava bacterial blight, the most important bacterial disease of cassava. Xam, like other Xanthomonas species, requires type III effectors (T3Es) for maximal virulence. Xam strain CIO151 possesses 17 predicted T3Es belonging to the Xanthomonas outer protein (Xop) class. This work aimed to characterize nine Xop effectors present in Xam CIO151 for their role in virulence and modulation of plant immunity. Our findings demonstrate the importance of XopZ, XopX, XopAO1 and AvrBs2 for full virulence, as well as a redundant function in virulence between XopN and XopQ in susceptible cassava plants. We tested their role …

Xanthomonas Oryzae Pv. Oryzae Tale Proteins Recruit Ostfiiaγ1 To Compensate For The Absence Of Ostfiiaγ5 In Bacterial Blight In Rice, Wenxiu Ma, Lifang Zou, Zhiyuan Ji, Xiameng Xu, Zhengyin Xu, Yangyang Yang, James R. Alfano

Center for Plant Science Innovation: Faculty Publications

Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight (BB) of rice, uses transcription activator-like effectors (TALEs) to interact with the basal transcription factor gamma subunit OsTFIIAγ5 (Xa5) and activates the transcription of host genes. However, how OsTFIIAγ1, the other OsTFIIAγ protein, functions in the presence of TALEs remains unclear. In this study, we show that OsTFIIAγ1 plays a compensatory role in the absence of Xa5. The expression of OsTFIIAγ1, which is activated by TALE PthXo7, increases the expression of host genes targeted by avirulent and virulent TALEs. Defective OsTFIIAγ1 rice lines show reduced expression of the TALE-targeted …

What Drives Species Richness In Colorado's Alpine Tundra, Michael Kintgen

Regis University Student Publications (comprehensive collection)

Despite years of research, drivers of vascular plant species richness in Colorado’s alpine tundra habitats are largely unknown. Factors such as slope aspect, Pleistocene glaciation, nutrient levels, latitude and longitude, snow depth, and disturbance have been studied. Despite this research, few patterns have emerged. Research in Colorado has been conducted on a few well studied mountains. Aridity is one factor that has not been well studied but shows promise in explaining species richness. In Patagonia and the Swiss Alps, increasing aridity correlates with higher species richness. Here, a full species assessment was conducted on nine mountains previously under researched or …