Plant Biology Commons^™

Evaluation Of Jules-Crop Performance Against Site Observations Of Irrigated Maize From Mead, Nebraska, Karina Williams, Jemma Gornall, Anna Harper, Andy Wiltshire, Debbie Hemming, Tristan Quaife, Tim Arkebauer, David Scoby

Department of Agronomy and Horticulture: Faculty Publications

The JULES-crop model (Osborne et al., 2015) is a parametrisation of crops within the Joint UK Land Environment Simulator (JULES), which aims to simulate both the impact of weather and climate on crop productivity and the impact of croplands on weather and climate. In this evaluation paper, observations of maize at three FLUXNET sites in Nebraska (US-Ne1, US-Ne2 and US-Ne3) are used to test model assumptions and make appropriate input parameter choices. JULES runs are performed for the irrigated sites (US-Ne1 and US-Ne2) both with the crop model switched off (prescribing leaf area index (LAI) and canopy height) and with …

Science In The Supply Chain: Collaboration Opportunities For Advancing Sustainable Agriculture In The United States, Allison M. Thomson, Stewart Ramsey, Ed Barnes, Bruno Basso, Marlen Eve, Sasha Gennet, Patricio Grassini, Brandon Kliethermes, Marty Matlock, Eileen Mcclellen, Ed Spevak, Clifford S. Snyder, Mark D. Tomer, Chris Van Kessel, Tristram West, Grant Wick

Department of Agronomy and Horticulture: Faculty Publications

Consumers and corporations are increasingly interested in understanding the sustainability of agricultural supply chains and reducing the environmental impacts of food, fiber, feed, and fuel production. This emerging need to quantify environmental impacts from agricultural production creates an opportunity for collaboration with the scientific community. Without such collaboration, sustainability efforts risk failure by adopting unrealistic goals or misguided approaches. This commentary explores the role of science in Field to Market, a nonprofit organization developing a sustainability program for US commodity crops, and highlights opportunities to address emerging science challenges. We evaluate changes over the past 35 years in key environmental …

Genetic Characterization Of The Soybean Nested Association Mapping Population, Qijian Song, Long Yan, Charles Quigley, Brandon D. Jordan, Edward Fickus, Steve Schroeder, Bao-Hua Song, Yong-Qiang Charles An, David Hyten, Randall L. Nelson, Katy Rainey, William D. Beavis, Jim Specht, Brian Diers, Perry Cregan

Department of Agronomy and Horticulture: Faculty Publications

A set of nested association mapping (NAM) families was developed by crossing 40 diverse soybean [Glycine max (L.) Merr.] genotypes to the common cultivar. The 41 parents were deeply sequenced for SNP discovery. Based on the polymorphism of the single-nucleotide polymorphisms (SNPs) and other selection criteria, a set of SNPs was selected to be included in the SoyNAM6K BeadChip for genotyping the parents and 5600 RILs from the 40 families. Analysis of the SNP profiles of the RILs showed a low average recombination rate. We constructed genetic linkage maps for each family and a composite linkage map based on …

Editorial: Genomic Approaches For Improvement Of Understudied Grasses, Keenan Amundsen, Gautam Sarath, Teresa Donze-Reiner

Department of Agronomy and Horticulture: Faculty Publications

Grasses are diverse, spanning native prairies to high-yielding grain cropping systems. They are valued for their beauty and useful for soil stabilization, pollution mitigation, biofuel production, nutritional value, and forage quality; grasses encompass the most important grain crops in the world. There are thousands of distinct grass species and many have promiscuous hybridization patterns, blurring species boundaries. Resources for advancing the science and knowledgebase of individual grass species or their unique characteristics varies, often proportional to their perceived value to society. For many grasses, limited genetic information hinders research progress. Presented in this research topic is a brief snapshot of …

Expression Of The Maize Dof1 Transcription Factor In Wheat And Sorghum, Pamela A. Pena, Truyen Quach, Shirley Sato, Zhengxiang Ge, Natalya Nersesian, Taity Changa, Ismail M. Dweikat, Madhavan Soundararajan, Tom E. Clemente

Department of Agronomy and Horticulture: Faculty Publications

Nitrogen is essential for plant growth and development. Improving the ability of plants to acquire and assimilate nitrogen more efficiently is a key agronomic parameter that will augment sustainability in agriculture. A transcription factor approach was pursued to address improvement of nitrogen use efficiency in two major commodity crops. To this end, the Zea mays Dof1 (ZmDof1) transcription factor was expressed in both wheat (Triticum aestivum) and sorghum (Sorghum bicolor) either constitutively, UBI4 promoter from sugarcane, or in a tissue specific fashion via the maize rbcS1 promoter. The primary transcription activation target of ZmDof1 …

Can Sub-Saharan Africa Feed Itself?, Martin K. Van Ittersum, Lenny G. J. Van Bussel, Joost Wolf, Patricio Grassini, Justin Van Wart, Nicolas Guilpart, Lieven Claessens, Hugo De Groot, Keith Wiebe, Daniel Mason-D'Croz, Haishun Yang, Hendrik Boogard, Pepijn A. J. Van Oort, Marloes P. Van Loon, Kazuki Saito, Ochieng Adimo, Samuel Adjei-Nsiah, Alhassane Agali, Abdullahi Bala, Regis Chikowo, Kayuki Kaizzi, Mamoutou Kouressy, Joachim H. J. R. Makoi, Korodjouma Ouattara, Kindie Tesfaye, Kenneth G. Cassman

Department of Agronomy and Horticulture: Faculty Publications

Although global food demand is expected to increase 60% by 2050 compared with 2005/2007, the rise will be much greater in sub- Saharan Africa (SSA). Indeed, SSA is the region at greatest food security risk because by 2050 its population will increase 2.5-fold and demand for cereals approximately triple, whereas current levels of cereal consumption already depend on substantial imports. At issue is whether SSA can meet this vast increase in cereal demand without greater reliance on cereal imports or major expansion of agricultural area and associated biodiversity loss and greenhouse gas emissions. Recent studies indicate that the global increase …

The Coat Protein And Nia Protease Of Two Potyviridae Family Members Independently Confer Superinfection Exclusion, Satyanarayana Tatineni, Roy French

Department of Plant Pathology: Faculty Publications

Superinfection exclusion (SIE) is an antagonistic virus-virus interaction whereby initial infection by one virus prevents subsequent infection by closely related viruses. Although SIE has been described in diverse viruses infecting plants, humans, and animals, its mechanisms, including involvement of specific viral determinants, are just beginning to be elucidated. In this study, SIE determinants encoded by two economically important wheat viruses, Wheat streak mosaic virus (WSMV; genus Tritimovirus, family Potyviridae) and Triticum mosaic virus (TriMV; genus Poacevirus, family Potyviridae), were identified in gain-of-function experiments that used heterologous viruses to express individual virus-encoded proteins in wheat. Wheat plants infected …

Effect Of Smooth Bromegrass Management On Grazing Cattle Dung Decomposition, Co2 Flux, And Soil Nutrient Movement, Bradley D. Schick

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

Rapid nutrient cycling improves forage quality and livestock production in pastures. Interseeding legumes may be a strategy to enhance N cycling, but effects of dung excreted from cattle grazing pastures with legumes on dung decomposition rates and soil N cycling have not been studied. Our objective was to evaluate how dung excreted from cattle grazing legume-interseeded, N-fertilized, and unfertilized smooth bromegrass (Bromus inermis Leyss.) pastures affects dung chemical composition, dry matter decomposition, CO­₂ flux, and N availability in soil. Freshly deposited dung from yearling steers grazing legume-interseeded, N-fertilized, and unfertilized pastures was collected and placed as pats in …

Mechanism Of Resistance, Gene Flow, And Integrated Management Of Ragweeds (Ambrosia) In Nebraska, Zahoor Ahmad Ganie

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

Common ragweed (Ambrosia artemisiifolia L.) and giant ragweed (Ambrosia trifida L.) are native annual broadleaf weeds in the United States found in diverse agroecosystems, roadsides, and wastelands. They are economically important weed species in the Midwest and sources of pollen allergies. Confirmation of glyphosate-resistant (GR) common and giant ragweed in Nebraska justified the need to determine the mechanism of resistance, dispersal of resistance genes via pollen, and to develop an integrated management program. The objectives of this research were to: 1) determine the mechanism of glyphosate resistance in a common ragweed biotype from Nebraska; 2) evaluate the effect …

Modeling Long-Term Corn Yield Response To Nitrogen Rate And Crop Rotation, Laila A. Puntel, John E. Sawyer, Daniel W. Barker, Ranae Dietzel, Hanna Poffenbarger, Michael J. Castellano, Kenneth J. Moore, Peter J. Thorburn, Sotirios V. Archontoulis

Department of Agronomy and Horticulture: Faculty Publications

Improved prediction of optimal N fertilizer rates for corn (Zea mays L.) can reduce N losses and increase profits. We tested the ability of the Agricultural Production Systems sIMulator (APSIM) to simulate corn and soybean (Glycine max L.) yields, the economic optimum N rate (EONR) using a 16-year field-experiment dataset from central Iowa, USA that included two crop sequences (continuous corn and soybean-corn) and five N fertilizer rates (0, 67, 134, 201, and 268 kg N ha^-1) applied to corn. Our objectives were to: (a) quantify model prediction accuracy before and after calibration, and report calibration steps; (b) …

Characterization And Development Mechanism Of Apios Americana Tuber Starch, Hanyu Yangchen, Vikas Belamkar, Steven B. Cannon, Jay-Lin Jane

Department of Agronomy and Horticulture: Faculty Publications

Apios americana is a wild legume-bearing plant with edible tubers. Domestication of Apios is in progress because of the superior nutritional value and health benefits of the tuber. Objectives of this study were to: (1) characterize physicochemical properties of the Apios tuber starch; and (2) understand differences in starch structures and properties between the mother (seed) and child (progeny) tubers and the mechanism of starch development. Granules of the Apios tuber starch displayed ellipsoidal, rod, or kidney shape with diameter ranges of 1–30 m. The mother tuber starches displayed greater percentage crystallinity, larger gelatinization enthalpy-changes, longer branch-chain lengths of amylopectin, …

Genomics-Assisted Characterization Of A Breeding Collection Of Apios Americana, An Edible Tuberous Legume, Vikas Belamkar, Andrew Farmer, Nathan T. Weeks, Scott R. Kalberer, William J. Blackmon, Steven B. Cannon

Department of Agronomy and Horticulture: Faculty Publications

For species with potential as new crops, rapid improvement may be facilitated by new genomic methods. Apios (Apios americana Medik.), once a staple food source of Native American Indians, produces protein-rich tubers, tolerates a wide range of soils, and symbiotically fixes nitrogen. We report the first high-quality de novo transcriptome assembly, an expression atlas, and a set of 58,154 SNP and 39,609 gene expression markers (GEMs) for characterization of a breeding collection. Both SNPs and GEMs identify six genotypic clusters in the collection. Transcripts mapped to the Phaseolus vulgaris genome–another phaseoloid legume with the same chromosome number–provide provisional genetic …

Plants Having Increased Bomass And Methods For Making The Same, Aleel K. Grennan, Donald R. Ort, Stephen Patrick Moose, Damla D. Bilgin, Thomas Clemente, Fredy Altpeter, Stephen P. Long

Department of Agronomy and Horticulture: Faculty Publications

The impact of plastid size change in both monocot and dicot plants has been examined. In both, when plastid size is increased there is an increase in biomass relative to the parental lines. Thus, provided herein are methods for increasing the biomass of a plant, comprising decreasing the expression of at least one plastid division protein in a plant. Optionally, the level of chlorophyll in the plant is also reduced.

Orm Expression Alters Sphingolipid Homeostasis And Differentially Affects Ceramide Synthase Activity, Athen N. Kimberlin, Gongshe Han, Kyle D. Luttgeharm, Ming Chen, Rebecca E. Cahoon, Julie M. Stone, Jennifer E. Markham, Teresa M. Dunn, Edgar B. Cahoon

Center for Plant Science Innovation: Faculty Publications

Sphingolipid synthesis is tightly regulated in eukaryotes. This regulation in plants ensures sufficient sphingolipids to support growth while limiting the accumulation of sphingolipid metabolites that induce programmed cell death. Serine palmitoyltransferase (SPT) catalyzes the first step in sphingolipid biosynthesis and is considered the primary sphingolipid homeostatic regulatory point. In this report, Arabidopsis (Arabidopsis thaliana) putative SPT regulatory proteins, orosomucoidlike proteins AtORM1 and AtORM2, were found to interact physically with Arabidopsis SPT and to suppress SPT activity when coexpressed with Arabidopsis SPT subunits long-chain base1 (LCB1) and LCB2 and the small subunit of SPT in a yeast ( …

Mapping Quantitative Trait Loci For Resistance To Goss’S Bacterial Wilt And Leaf Blight In North American Maize By Joint Linkage Analysis, Amritpal Singh, Aaron P. Andersen, Tamra A. Jackson-Ziems, Aaron J. Lorenz

Department of Plant Pathology: Faculty Publications

Goss’s wilt and leaf blight is a bacterial disease of maize (Zea mays L.) caused by the Gram-positive bacterium Clavibacter michiganensis subsp. nebraskensis. Goss’s wilt has reemerged as an important disease in the western United States and is spreading to other areas. Although the reasons for this reemergence are not completely known, it is important to understand the genetic basis of resistance to Goss’s wilt. The objective of this study was to map the quantitative trait loci (QTL) underlying resistance to Goss’s wilt. To achieve this objective, joint linkage and linkage mapping in 3 of the 25 nested …

Corn Yield Loss Estimates Due To Diseases In The United States And Ontario, Canada From 2012 To 2015, Daren S. Mueller, Kiersten A. Wise, Adam J. Sisson, Tom W. Allen, Gary C. Bergstrom, D. Bruce Bosley, Carl A. Bradley, Kirk D. Broders, Emmanuel Byamukama, Martin I. Chilvers, Alyssa Collins, Travis R. Faske, Andrew J. Friskop, Ron W. Heiniger, Clayton A. Hollier, David C. Hooker, Tom Isakeit, Tamra A. Jackson-Ziems, Douglas J. Jardine, Heather M. Kelly, Kasia Kinzer, Steve R. Koenning, Dean K. Malvick, Marcia Mcmullen, Ron F. Meyer, Pierce A. Paul, Alison E. Robertson, Gregory W. Roth, Damon L. Smith, Connie A. Tande, Albert U. Tenuta, Paul Vincelli, Fred Warner

Department of Plant Pathology: Faculty Publications

Annual decreases in corn yield caused by diseases were estimated by surveying members of the Corn Disease Working Group in 22 corn-producing states in the United States and in Ontario, Canada, from 2012 through 2015. Estimated loss from each disease varied greatly by state and year. In general, foliar diseases such as northern corn leaf blight, gray leaf spot, and Goss’s wilt commonly caused the largest estimated yield loss in the northern United States and Ontario during nondrought years. Fusarium stalk rot and plant-parasitic nematodes caused the most estimated loss in the southern-most United States. The estimated mean economic loss …

Bacterial Leaf Streak Of Corn Confirmed In Nebraska, Other Corn Belt States August 26, 2016, Tamra Jackson-Ziems, Kevin A. Korus, Tony Adesemoye, Julie Van Meter

Department of Plant Pathology: Faculty Publications

Bacterial leaf streak disease of corn, caused by Xanthomonas vasicola pv. vasculorum, has now been confirmed in Nebraska, as well as in Colorado, Illinois, Iowa, and Kansas. The disease had not been previously identified in the U.S., but had been reported on corn in South Africa. Surveys are currently underway across the Corn Belt to identify the disease distribution. Initial observations and survey results suggest that it may be widely distributed throughout the Corn Belt. Unusual symptoms were first reported on corn samples received by the University of Nebraska Plant and Pest Diagnostic Clinic. Over the last two years, the …

Transcriptome Response Of Cassava Leaves Under Natural Shade, Zehong Ding, Yang Zhang, Yi Xiao, Fangfang Liu, Minghui Wang, Xinguang Zhu, Peng Liu, Qi Sun, Wenquan Wang, Ming Peng, Tom Brutnell, Pinghua Li

Center for Plant Science Innovation: Faculty Publications

Cassava is an important staple crop in tropical and sub-tropical areas. As a common farming practice, cassava is usually cultivated intercropping with other crops and subjected to various degrees of shading, which causes reduced productivity. Herein, a comparative transcriptomic analysis was performed on a series of developmental cassava leaves under both full sunlight and natural shade conditions. Gene expression profiles of these two conditions exhibited similar developmental transitions, e.g. genes related to cell wall and basic cellular metabolism were highly expressed in immature leaves, genes involved in lipid metabolism and tetrapyrrole synthesis were highly expressed during the transition stages, and …

Validation Of Reference Genes For Robust Qrt-Pcr Gene Expression Analysis In The Rice Blast Fungus Magnaporthe Oryzae, Sarena Che Omar, Michael A. Bentley, Giulia Morieri, Gail M. Preston, Sarah J. Gurr, Richard Wilson (Editor)

Department of Plant Pathology: Faculty Publications

The rice blast fungus causes significant annual harvest losses. It also serves as a genetically- tractable model to study fungal ingress. Whilst pathogenicity determinants have been unmasked and changes in global gene expression described, we know little about Magnaporthe oryzae cell wall remodelling. Our interests, in wall remodelling genes expressed during infection, vegetative growth and under exogenous wall stress, demand robust choice of reference genes for quantitative Real Time-PCR (qRT-PCR) data normalisation. We describe the expression stability of nine candidate reference genes profiled by qRT-PCR with cDNAs derived during asexual germling development, from sexual stage perithecia and from vegetative mycelium …

Cross Species Selection Scans Identify Components Of C4 Photosynthesis In The Grasses, Pu Huang, Anthony J. Studer, James C. Schnable, Elizabeth A. Kellogg, Thomas P. Brutnell

Department of Agronomy and Horticulture: Faculty Publications

C₄ photosynthesis is perhaps one of the best examples of convergent adaptive evolution with over 25 independent origins in the grasses (Poaceae) alone. The availability of high quality grass genome sequences presents new opportunities to explore the mechanisms underlying this complex trait using evolutionary biology-based approaches. In this study, we performed genome-wide cross-species selection scans in C₄ lineages to facilitate discovery of C₄ genes. The study was enabled by the well conserved collinearity of grass genomes and the recently sequenced genome of a C₃ panicoid grass, Dichanthelium oligosanthes. This method, in contrast to previous studies, …

Rna-Seq Based Analysis Of Population Structure Within The Maize Inbred B73, Zhikai Liang, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Recent reports have shown than many identically named genetic lines used in research around the world actually contain large amounts of uncharacterized genetic variation as a result of cross contamination of stocks, unintentional crossing, residual heterozygosity within original stocks, or de novo mutation. 27 public, large scale, RNA-seq datasets from 20 independent research groups around the world were used to assess variation within the maize (Zea mays ssp. mays) inbred B73, a four decade old variety which served as the reference genotype for the original maize genome sequencing project and is widely used in genetic, genomic, and phenotypic research. Several …

Antiviral Rna Silencing Suppression Activity Of Tomato Spotted Wilt Virus Nss Protein, Tania Ocampo Ocampo, Sergio M. Gabriel Peralta, Nicole Bacheller, Stella Uiterwaal, Aaron Knapp, Alanna Hennen, Daniel Leobardo Ochoa-Martínez, Hernan Garcia-Ruiz

Department of Plant Pathology: Faculty Publications

In addition to regulating gene expression, RNA silencing is an essential antiviral defense system in plants. Triggered by double-stranded RNA, silencing results in degradation or translational repression of target transcripts. Viruses are inducers and targets of RNA silencing. To condition susceptibility, most plant viruses encode silencing suppressors that interfere with this process, such as the Tomato spotted wilt virus (TSWV) NSs protein. The mechanism by which NSs suppresses RNA silencing and its role in viral infection and movement remain to be determined. We cloned NSs from the Hawaii isolate of TSWV and using two independent assays show for the first …

Description Of Mesocriconema Ericaceum N. Sp. (Nematoda: Criconematidae) And Notes On Other Nematode Species Discovered In An Ericaceous Heath Bald Community In Great Smoky Mountains National Park, Usa, Thomas O. Powers, Peter Mullin, Rebecca Higgins, Timothy Harris, Kirsten S. Powers

Department of Plant Pathology: Faculty Publications

A new species of Mesocriconema and a unique assemblage of plant-parasitic nematodes was discovered in a heath bald atop Brushy Mountain in Great Smoky Mountains National Park. Mesocriconema ericaceum n. sp., a species with males, superficially resembles M. xenoplax. DNA barcoding with the mitochondrial COI gene provided evidence of the new species as a distinct lineage. SEM revealed significant variability in arrangement of labial submedian lobes, plates, and anterior and posterior annuli. Three other nematodes in the family Criconematidae were characterized from the heath bald. Ogma seymouri, when analyzed by statistical parsimony, established connections with isolates from north-eastern Atlantic …

Herbicide Resistantsorghum Mutants, Ismail M. Dweikat

Department of Agronomy and Horticulture: Faculty Publications

This disclosure provides for four different sorghum mutants that exhibit resistance to ALS-inhibiting herbicides. This dis closure also provides for methods of using such Sorghum mutants that exhibit resistance to ALS-inhibiting herbicides in breeding methods to make Sorghum hybrids, varieties, or lines. The Sorghum hybrids, varieties, and lines provided in this disclosure can be used in methods of controlling weeds.

Long-Term Sandhills Prairie Responses To Precipitation, Temperature, And Cattle Stocking Rate, John A. Guretzky, Cheryl Dunn, Heidi L. Hillhouse

Department of Agronomy and Horticulture: Faculty Publications

Understanding of Sandhills prairie, the most expansive sand dune region stabilized by perennial grasses in the Western Hemisphere, is limited by lack of long-term vegetation data. We used a 26-year dataset to evaluate Sandhills prairie responses to yearto- year variation in precipitation, temperature, and cattle stocking rate. Basal cover, a measurement that is constant seasonally and used to detect long-term changes in bunchgrass vegetation, was measured in 38–40 permanent plots positioned along four transects spanning 769 ha from 1979 to 2007. Across this period, total basal cover averaged 2.4 % and was dominated by warm-season grasses (81.1 %). Schizachyrium scoparium …

A Brief History Of Corn: Looking Back To Move Forward, Jon Derek Pruitt

Doctor of Plant Health Program: Dissertations and Student Research

Maize was domesticated from teosinte in Mexico some 7,000 to 10,000 years ago and quickly spread through the Americas. It has become one of the most important crops at a local and global level. Two types, Northern Flint corn and Southern Dent corns provided the basis of the genetic background of modern maize hybrids. The development of hybrids, first double-cross and later single-cross hybrids, along with a transition to high input farming provided huge yield increases, which have continued to improve with improving technology.

Increase in maize production also caused a rise in Western corn Rootworm (Diabrotica virgifera virgifera …

Microbe-Id: An Open Source Toolbox For Microbial Genotyping And Species Identification, Javier F. Tabima, Sydney E. Everhart, Meredith M. Larsen, Alexaandra J. Weisberg, Zhian N. Kamvar, Mathew A. Tancos, Christine D. Smart, Jeff H. Chang, Niklaus J. Grünwald

Department of Plant Pathology: Faculty Publications

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by …

Managing Drought Stress In California Agricultural Systems, Gregory D. Brittain Jr.

Doctor of Plant Health Program: Dissertations and Student Research

California is currently facing a historic drought, and this has led many farmers in the state to severely cut back on irrigation. Optimal use of water for irrigation requires a comprehensive understanding of how plants respond physiologically to water stress (Chapter 1). By monitoring water requirements in crops and managing irrigation to meet those requirements, growers can significantly reduce water use (Chapter 2). This can be done through improving application efficiency of irrigation technology as well as increasing the water use efficiency of the crops themselves. Deficit irrigation practices can be used to manipulate the physiology of water use in …

Is A Mitochondrial Plasmid Really A Virus?, Mackenzie Strehle

UCARE: Research Products

In addition to containing a large and complex mitochondrial genome, the mitochondria of several species of plants have been shown to contain an independent, self-replicating DNA molecule in the form of a plasmid. Plants in the Brassica genus contain a linear plasmid that is approximately 11.6 kilobases in length. The plasmid is characterized by the presence of terminal inverted repeats and covalently bonded proteins at its termini (Handa 2008). The plasmid also contains six ORFs that encode DNA and RNA polymerases and a number of unknown proteins (Figure 1). Currently, both the function of this plasmid and the mechanisms by …

Information Thermodynamics Of Cytosine Dna Methylation, Robersy Sanchez Rodriguez, Sally Ann Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Cytosine DNA methylation (CDM) is a stable epigenetic modification to the genome and a widespread regulatory process in living organisms that involves multicomponent molecular machines. Genome-wide cytosine methylation patterning participates in the epigenetic reprogramming of a cell, suggesting that the biological information contained within methylation positions may be amenable to decoding. Adaptation to a new cellular or organismal environment also implies the potential for genome-wide redistribution of CDM changes that will ensure the stability of DNA molecules. This raises the question of whether or not we would be able to sort out the regulatory methylation signals from the CDM background …