Plant Breeding and Genetics Commons^™

Refernment: An R Package For Annotating Rna Editing In Plastid Genomes, Tanner A. Robison, Paul G. Wolf

Biology Faculty Publications

PREMISE OF THE STUDY: In the absence of cDNA, the annotation of RNA editing in plastomes must be done manually, representing a significant time cost to those studying the organellar genomes of ferns and hornworts.

METHODS AND RESULTS: We developed an R package to automatically annotate apparent nonsense mutations in plastid genomes. The software successfully annotates such sites and results in no false positives for data with no sequencing or assembly errors.

CONCLUSIONS: Compared to manual annotation, ReFernment offers greater speed and accuracy for annotating RNA editing sites. This software should be especially useful for researchers generating large numbers of …

An Albino Mutant In Brassica Rapa Maps To The Pdx2 Locus On Chromosome 10, Cezar L. Sanchez, Beatriz M. Garcia, Edward Himelblau, Nick Diaz

STAR Program Research Presentations

We have identified an albino mutant in the plant Brassica rapa. This recessive mutation could provide insights into the photosynthetic pathways of all plants. Previously the mutation was mapped to chromosome 10 of Brassica rapa. To narrow down the chromosomal region containing the albino mutation, we grew a segregating population of plants. DNA was extracted from albino and wildtype (green) plants and genotyped using PCR markers on chromosome 10. The genotype detected using the INDEL2 marker perfectly predicted whether a plant was albino or WT. This indicates that the INDEL2 marker is tightly linked to the albino mutation. INDEL2 is …

Native Grass And Legume Biology And Establishment, Arvid A. Boe, P. J. Johnson

Oak Lake Field Station 30th Anniversary Retreat Presentations

No abstract provided.

Identification And Characterization Of Mitogen-Activated Protein Kinase (Mapk) Genes In Sunflower (Helianthus Annuus L.), Surendra Neupane, Sarah E. Schweitzer, Achal Neupane, Ethan J. Anderson, Anne Fennell, Ruanbao Zhou, Madhav P. Nepal

Agronomy, Horticulture and Plant Science Faculty Publications

Mitogen-Activated Protein Kinase (MAPK) genes encode proteins that regulate biotic and abiotic stresses in plants through signaling cascades comprised of three major subfamilies: MAP Kinase (MPK), MAPK Kinase (MKK), and MAPKK Kinase (MKKK). The main objectives of this research were to conduct genome-wide identification of MAPK genes in Helianthus annuus and examine functional divergence of these genes in relation to those in nine other plant species (Amborella trichopoda, Aquilegia coerulea, Arabidopsis thaliana, Daucus carota, Glycine max, Oryza sativa, Solanum lycopersicum, Sphagnum fallax, and Vitis vinifera), representing diverse taxonomic groups of …

Identification Of Climate And Genetic Factors That Control Fat Content And Fatty Acid Composition Of Theobroma Cacao L. Beans, Guiliana M. Mustiga, Joe Morrissey, Joseph Conrad Stack, Ashley Duval, Stefan Royaert, Johannes Jansen, Carolina Bizzotto, Cristiano Villela-Dias, Linkai Mei, Edgar B. Cahoon, Ed Seguine, Jean Philippe Marelli, Juan Carlos Motamayor

Center for Plant Science Innovation: Faculty Publications

The main ingredients of chocolate are usually cocoa powder, cocoa butter, and sugar. Both the powder and the butter are extracted from the beans of the cacao tree (Theobroma cacao L.). The cocoa butter represents the fat in the beans and possesses a unique fatty acid profile that results in chocolate’s characteristic texture and mouthfeel. Here, we used a linkage mapping population and phenotypic data of 3,292 samples from 420 progeny which led to the identification of 27 quantitative trait loci (QTLs) for fatty acid composition and six QTLs for fat content. Progeny showed extensive variation in fat levels …

Drought-Responsive Genes, Late Embryogenesis Abundant Group3 (Lea3) And Vicinal Oxygen Chelate, Function In Lipid Accumulation In Brassica Napus And Arabidopsis Mainly Via Enhancing Photosynthetic Efficiency And Reducing Ros, Yu Liang, Kai Kang, Lu Gan, Shaobo Ning, Jinye Xiong, Shuyao Song, Lingzhi Xi, Senying Lai, Yongtai Yin, Jianwei Gu, Jun Xiang, Shisheng Li, Baoshan Wang, Maoteng Li

Center for Plant Science Innovation: Faculty Publications

Drought is an abiotic stress that affects plant growth, and lipids are the main economic factor in the agricultural production of oil crops. However, the molecular mechanisms of drought response function in lipid metabolism remain little known. In this study, overexpression (OE) of different copies of the drought response genes LEA3 and VOC enhanced both drought tolerance and oil content in Brassica napus and Arabidopsis. Meanwhile, seed size, membrane stability and seed weight were also improved in OE lines. In contrast, oil content and drought tolerance were decreased in the AtLEA3 mutant (atlea3) and AtVOC-RNAi of Arabidopsis and in both …

Fad2 Gene Radiation And Positive Selection Contributed To Polyacetylene Metabolism Evolution In Campanulids1[Open], Tao Feng, Ya Yang, Lucas Busta, Edgar B. Cahoon, Hengchang Wang, Shiyou Lü

Center for Plant Science Innovation: Faculty Publications

Polyacetylenes (PAs) are bioactive, specialized plant defense compounds produced by some species in the eudicot clade campanulids. Early steps of PA biosynthesis are catalyzed by Fatty Acid Desaturase 2 (FAD2). Canonical FAD2s catalyze desaturation, but divergent forms can catalyze hydroxylation, conjugation, acetylenation, and epoxygenation. These alternate reactions give rise to valuable unusual fatty acids, including the precursors to PAs. The extreme functional diversity of FAD2 enzymes and the origin of PA biosynthesis are poorly understood from an evolutionary perspective. We focus here on the evolution of the FAD2 gene family. We uncovered a core eudicot-wide gene duplication event giving rise …

Two Distinct Nucleic Acid Binding Surfaces Of Cdc5 Regulate Development, Chao Wang, Mu Li, Guorui Li, Wensheng Zhao, Bin Yu, Junfeng Liu, Jun Yang, You-Liang Peng

Center for Plant Science Innovation: Faculty Publications

Cell division cycle 5 (Cdc5) is a highly conserved nucleic acid binding protein among eukaryotes and plays critical roles in development. Cdc5 can simultaneously bind to DNA and RNA by its N- terminal DNA-binding domain (DBD), but molecular mechanisms describing its nucleic acid recognition and the regulation of development through its nucleic acid binding remain unclear. Herein, we present a crystal structure of the N-terminal DBD of MoCdc5 (MoCdc5-DBD) from the rice blast fungus Magnaporthe oryzae. Residue K100 of MoCdc5 is on the periphery of a positively charged groove that is formed by K42, K45, R47, and N92 and is …

Comprehensive Analysis Of Aspergillus Nidulans Pka Phosphorylome Identifies A Novel Mode Of Crea Regulation, Liliane F. C. Ribeiro, Cynthia Chelius, Karthik R. Boppidi, Nisha S. Naik, Simin Hossain, Jessica J. J. Ramsey, Jyothi Kumar, Lucas F. Ribeiro, Marc Ostermeier, Bao Tran, Young Ah Goo, Leandro J. De Assis, Mevlut Ulas, Ozgur Bayram, Gustavo H. Goldman, Stephen Lincoln, Ranjan Srivastava, Steven D. Harris, Mark R. Marten

Center for Plant Science Innovation: Faculty Publications

In filamentous fungi, an important kinase responsible for adaptation to changes in available nutrients is cyclic AMP (cAMP)-dependent protein kinase (protein kinase A [PKA]). This kinase has been well characterized at a molecular level, but its systemic action and direct/indirect targets are generally not well understood in filamentous fungi. In this work, we used a pkaA deletion strain (ΔpkaA) to identify Aspergillus nidulans proteins for which phosphorylation is dependent (either directly or indirectly) on PKA. A combination of phosphoproteomic and transcriptomic analyses revealed both direct and indirect targets of PKA and provided a global perspective on its function. …

Manipulation Of Β-Carotene Levels In Tomato Fruits Results In Increased Aba Content And Extended Shelf-Life, Gianfranco Diretto, Sarah Frusciante, Claudia Fabbri, Nicolas Schauer, Lucas Busta, Zhonghua Wang, Antonio J. Matas, Alessia Fiore, Jocelyn K. C. Rose, Alisdair R. Fernie, Reinhard Jetter, Benedetta Mattei, Jim Giovannoni, Giovanni Giuliano

Center for Plant Science Innovation: Faculty Publications

Tomato fruit ripening is controlled by the hormone ethylene and by a group of transcription factors, acting upstream of ethylene. During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) resulted in increased β-carotene (provitamin A) content. Unexpectedly, LCYb-overexpressing fruits also exhibited a diverse array of ripening phenotypes, including delayed softening and extended shelf life. These phenotypes were accompanied, at the biochemical level, by an increase of abscisic acid (ABA) content, decreased ethylene production, increased density of cell wall material containing linear pectins with a low degree of …

Identification And Characterization Of Stress Responsive Genes In Soybean And Sunflower, Surendra Neupane

Electronic Theses and Dissertations

Stress responsive genes encode proteins involved in plants’ response to abiotic and biotic stresses. Among such stress responsive proteins, proteins encoded by resistance genes (R genes) or nucleotide binding site-leucine-rich repeats (NBS-LRRs) and mitogen-activated protein kinases (MAPKs) are the major groups of proteins regulating biotic and abiotic stresses, respectively. Previous studies in Nepal’s lab at SDSU identified and characterized coiled coil (CC)-NBS-LRRs (CNLs), resistance to powdery mildew8 (RPW8)-NBS-LRRs (RNLs), NBS-LRR (NLs), and MAPK proteins in soybean. This study focuses on R and MAPK genes in the recently sequenced genome of sunflower as well as the toll-interleukin-1 receptor-like nucleotide-binding site leucine-rich …

Validation Of Candidate Loci For Maize Regrowability And Selection Of Near Isogenic Lines For The Loci, Tajbir Raihan

Electronic Theses and Dissertations

Developing perennial grain crops is an effective way for sustainable agriculture and it can be a tool for the betterment of the overall ecosystem. To understand how perenniality works in perennial species, we made a cross between Zea diploperennis and maize (Z. mays) inbred line B73. F1 hybrids produced from this cross were selfed to get the F2 population and later the F2 population underwent Genotyping-By- Sequencing (GBS) analysis. Based on the candidate loci identified on chromosome 2 and chromosome 7 from GBS, SNP-specific markers were developed from the candidate locus interval and used to genotype the F2 …

Nodule Zone-Specific Gene Expression In Soybean, Sadikshya Aryal

Electronic Theses and Dissertations

Nitrogen is one of the most limiting nutrients for plant growth and yield. Leguminous plants such as soybean (Glycine max) have developed the ability to form a symbiotic association with nitrogen fixing rhizobia. This symbiotic association results in the formation of unique structures called nodules that originate from root cortex via de novo cell differentiation. During soybean nodule development, two major nodule zones, the Nodule primordium (Npr) in the center and the nodule parenchyma (Npa) in the periphery, are clearly distinguishable. Npr gives rise to infection zone (IZ), and the Npa holds vascular bundles. However, it is not clear what …

Development And Characterization Of Wheat-Thinopyrum Junceiforme Chromosome Addition Lines, Dilkaran Singh

Electronic Theses and Dissertations

Production of wheat is challenged by dynamic biotic and abiotic stresses. Genetic improvement via alien gene transfer is an effective approach to tackle such challenges. Alien gene transfer played an important role in the history of wheat crop improvement. Sea wheatgrass (SWG; Thinopyrum junceiforme, 2n = 28, genomes J1J1J2J2) is a wild relative of wheat. In our previous work, we have developed a complete amphiploid between cultivated emmer and SWG and shown that SWG is resistant to wheat streak mosaic virus, Fusarium head blight and wheat stem sawflies (due to the solid stem) and tolerant to waterlogging, salinity, heat, and …

Development Of Computational Techniques For Identification Of Regulatory Dna Motif, Cankun Wang

Electronic Theses and Dissertations

Identifying precise transcription factor binding sites (TFBS) or regulatory DNA motif (motif) plays a fundamental role in researching transcriptional regulatory mechanism in cells and helping construct regulatory networks for biological investigation. Chromatin immunoprecipitation combined with sequencing (ChIP-seq) and lambda exonuclease digestion followed by high-throughput sequencing (ChIP-exo) enables researchers to identify TFBS on a genome-scale with improved resolution. Several algorithms have been developed to perform motif identification, employing widely different methods and often giving divergent results. In addition, these existing methods still suffer from prediction accuracy. Thesis focuses on the development of improved regulatory DNA motif identification techniques. We designed an …

Unraveling The Influence Of Female Flowering Characteristics And Chemical Hybridizing Agent Formulations On Hybrid Wheat (Triticum Aestivum L.) Seed Production, Hannah K. Stoll

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The success of hybrid wheat (Triticum aestivum L.) is largely limited by inefficiencies in seed production. This research aims to address these inefficiencies by examining various Chemical Hybridizing Agent (CHA) formulations using the chemical Croisor®100 on sterility, CHA damage, and female flowering characteristics. In addition, an efficient method of phenotyping female flowering characteristics (contributing factors in hybrid production seed yield) were identified using Stepwise Regression, ANCOVA, and Pearson R-Correlations, and duration of stigma receptivity in the cytoplasmic male sterile (CMS; Triticum timopheevii Zhuk.) background was determined. At an optimally timed spray application, including a moderate rate of CHA with …

Genetic Regulation Of The Elicitation Of Glyceollin Biosynthesis In Soybean, Md. Asraful Jahan

Graduate Theses, Dissertations, and Problem Reports (ETD)

Glyceollin phytoalexins are the pathogen-elicited defense metabolites that belong to the isoflavonoid family of molecules of soybean (Glycine max L. Merr). Phytophthora root and stem rot of soybean caused by Phytophthora sojae is a destructive disease throughout the soybean-growing regions worldwide causing devastating economic damages (globally $1-2 billion and over $250 million in the USA) every year. Engineering soybean plants that produce higher levels of glyceollins could confer resistance against this pathogen. Glyceollins also show anticancer and neuroprotective activities in mammals, therefore they are important for agriculture and medical research. Firstly, we were interested in understanding how biotic and …

Application Of Short Tandem Target Mimic (Sttm) Technique For Functional Analysis Of Micro-Rna396 In Transgenic Poplar Trees, Surattana Boonsai

Dissertations, Master's Theses and Master's Reports

Short Tandem Target Mimic (STTM) is a commonly technique used for functional studies of a number of genes in several plant model systems. However, very little is known about application of STTM technique in tree species. In this study, STTM was applied to knock down microRNA396 (miR396) in transgenic poplar trees for the first time. STTM396 expression resulted in dramatic decrease in miR396 expression levels leading to taller plants with larger leaves and larger leaf cell size. Additionally, an expression analysis of growth regulating factor genes (GRFs) that are members of miR396 target gene family showed up-regulation of GRF07 gene …

Midwest Vegetable Trial Report For 2018, Elizabeth Maynard, Petrus Langenhoven, Wenjing Guan, Brad R. Bergefurd

Purdue Fruit and Vegetable Research Reports

This is a compilation of 15 research trial reports from four land-grant universities in the Midwestern United States. Crops include cantaloupe, pickling cucumber, pepper, potato, pumpkin, summer squash and zucchini, sweet corn, tomato, and watermelon. Somecrops were evaluated in high tunnels or hoophouses. Most trials evaluated different cultivars or varieties. One report addressed plant spacing for sweet corn and one addressed soil block for production of tomato seedlings. A list of vegetable seed sources and a list of other online sources of vegetable trial reports are also included.

Midwest Vegetable Trial Report For 2018, Elizabeth Maynard, Petrus Langenhoven, Wenjing Guan, Brad R. Bergefurd

Midwest Vegetable Trial Reports

This is a compilation of 15 research trial reports from four land-grant universities in the Midwestern United States. Crops include cantaloupe, pickling cucumber, pepper, potato, pumpkin, summer squash and zucchini, sweet corn, tomato, and watermelon. Somecrops were evaluated in high tunnels or hoophouses. Most trials evaluated different cultivars or varieties. One report addressed plant spacing for sweet corn and one addressed soil block for production of tomato seedlings. A list of vegetable seed sources and a list of other online sources of vegetable trial reports are also included.