Plant Biology Commons^™

A First Insight Into Population Structure And Linkage Disequilibrium In The U.S. Peanut Minicore Collection, Vikas Belamkar, Michael Gomez Selvaraj, Jamie L. Ayers, Paxton R. Payton, Naveen Puppala, Mark D. Burow

Department of Agronomy and Horticulture: Faculty Publications

Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipaënsis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance- and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions …

Genes Identified By Visible Mutant Phenotypes Show Increased Bias Toward One Of Two Subgenomes Of Maize, James C. Schnable, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (Zea mays L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these ‘‘classical’’ maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that …

Dose–Sensitivity, Conserved Non-Coding Sequences, And Duplicate Gene Retention Through Multiple Tetraploidies In The Grasses, James C. Schnable, Brent S. Pedersen, Sabarinath Subramaniam, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Whole genome duplications, or tetraploidies, are an important source of increased gene content. Following whole genome duplication, duplicate copies of many genes are lost from the genome. This loss of genes is biased both in the classes of genes deleted and the subgenome from which they are lost. Many or all classes are genes preferentially retained as duplicate copies are engaged in dose sensitive protein–protein interactions, such that deletion of any one duplicate upsets the status quo of subunit concentrations, and presumably lowers fitness as a result. Transcription factors are also preferentially retained following every whole genome duplications studied. This …

Hybrid Oaks: Full Of Vexation And Wonder, W. John Hayden

Biology Faculty Publications

Distinguishing different species of oak in the forests of eastern North America can be challenging. For one thing, there are simply a lot of different species to sort out. A recent reference (Stein et al. 2003), describes 50 species in the genus Quercusoccurring naturally east of the 100th meridian, and 90 species are distinguished for all of North America north of Mexico (Nixon 1997). With so many species to parse, confident identification requires careful study of leaves, stem and leaf hairiness, and fully mature acorns with their caps. But care is not always enough, because in addition to the …

Sphingolipids In The Root Play An Important Role In Regulating The Leaf Ionome In Arabidopsis Thaliana, Dai-Yin Chao, Kenneth Gable, Ming Chen, Ivan Baxter, Charles R. Dietrich, Edgar B. Cahoon, Mary Lou Guerinot, Brett Lahner, Shiyu Lu, Jennifer E. Markham, Joe Morrissey, Gongshe Han, Sita Gupta, Jeffrey M. Harmon, Jan G. Jaworski, Teresa M. Dunn, David E. Salt

Department of Biochemistry: Faculty Publications

Sphingolipid synthesis is initiated by condensation of Ser with palmitoyl-CoA producing 3-ketodihydrosphinganine (3-KDS), which is reduced by a 3-KDS reductase to dihydrosphinganine. Ser palmitoyltransferase is essential for plant viability. Arabidopsis thaliana contains two genes (At3g06060/TSC10A and At5g19200/TSC10B) encoding proteins with significant similarity to the yeast 3-KDS reductase, Tsc10p. Heterologous expression in yeast of either Arabidopsis gene restored 3-KDS reductase activity to the yeast tsc10D mutant, confirming both as bona fide 3-KDS reductase genes. Consistent with sphingolipids having essential functions in plants, double mutant progeny lacking both genes were not recovered from crosses of single tsc10A and tsc10B …

Crop Updates 2011 - Nutrition, Precision Agriculture & Climate And Forecasting, Deb Archdeacon, Andrew Gulliver, David Cullen, Qifu Ma, Richard Bell, Ross Brennan, Craig Scanlan, Wen Chen, Geoff Anderson, Mike Bolland, Peter Rees, Sandy Alexander, Frank D'Emden, Stephen Davies, Breanne Best, Louise Barton, Klaus Butterbach-Bahl, Ralph Kiese, Daniel Murphy, Peter Newman, Roger Mandel, Roger Lawes, Michael Robertson, Derk Bakker, Jeremy Lemon, Alison Lacey, John Paul Collins, Glen Riethmuller, Fiona H. Evans, David Stephens, Caroline Peek, Tim Scanlon

Crop Updates

This session covers sixteen papers from different authors:

Nutrition

1. Balance® used in conventional cropping practice with half of the upfront fertiliser rate can sustain crop yield and build soil biological fertility, Deb Archdeacon1, Andrew Gulliver2 and David Cullen2, 1Agronomica, Wellington Mill, WA, 2Custom Composts, Nambeelup, WA

2. Effects of potassium (K) supply on plant growth, potassium uptake and grain Yield in wheat grown in grey sand, Qifu Ma1, Richard Bell1, Ross Brennan2 and Craig Scanlan2, 1School of Environmental Science, Murdoch University, 2Department of Agriculture and Food

3. Improving fertiliser management: redefining the …

Crop Updates 2011 - Farming Systems, Janette Drew, Rob Grima, Bob French, Raj Malik, Mark Seymour, Christine Zaicou-Kunesch, Glenn Mcdonald, Brendon Nicholas, Dennis Van Gool, James Fisher, Peter Tozer, Doug Abrecht, Michael Robertson, Cameron Weeks, Michael O'Conner, Peter Newman, Mike Clarke, Andrew Blake, Gordon Macaulay, Vijay Jayasena, Syed M. Nasar-Abbas, Larisa Cato, Robert Loughman, Ken Quail

Crop Updates

This session covers twelve papers from different authors:

1. Fallowing 50% of the farm each year – does it pay? Janette Drew and Rob Grima

Department of Agriculture and Food

2. How crop sequences affect the productivity and resilience of cropping systems in two Western Australian environments, Bob French, Raj Malik, Mark Seymour, Department of Agriculture and Food

3. When is continuous wheat or barley sustainable? Christine Zaicou-Kunesch and Rob Grima Department of Agriculture and Food

4. Identifying constraints to bridging the yield gap, Glenn McDonald, Department of Agriculture and Food

5. Land constraints limiting wheat yields in …

Crop Updates 2011 - Cereals, David Bowran, Bill Crabtree, Peter Carberry, Peter Burges, Bevan Buirchell, Ben Curtis, Sarah Ellis, Brenda Shackley, Christine Zaicou, Siva Sivapalan, Penny Goldsmith, Gae Plunkett, Darshan Sharma, Mario D'Antuono, Art Diggle, Peter Mangano, Sally Peltzer, Michael Renton, Bill Macleod, Fumie Horiuchi, George Wyatt, Geoff Anderson, Richard Bell, Ross Brennan, Wen Chen, Penny Riffkin

Crop Updates

This session covers eleven papers from different authors:

OPENING, NEW CROP VARIETIES & DECISION SUPPORT

Opening

1. Overview of the 2010 season, David Bowran, Director, Practice and Systems Innovation, Department of Agriculture and Food,

2. My experience in a drought as a farmer and consultant, Bill Crabtree, Morawa, Western Australia

3. Meeting the productivity and sustainability challenges to Australian agriculture until 2030, Peter Carberry, CSIRO Sustainable Agriculture Flagship

New Crop Varieties

4. National Variety Trials (NTV) wheat variety performance – captivity vs broadacre, Peter Burgess, Kalyx Agriculture

5. WALAN2289 – a new lupin variety to replace …

Delivery Of Prolamins To The Protein Storage Vacuole In Maize Aleurone Cells, Francisca C. Reyes, Taijoon Chung, David Holding, Rudolf Jung, Richard Vierstra, Marisa S. Otegui

Center for Plant Science Innovation: Faculty Publications

Zeins, the prolamin storage proteins found in maize (Zea mays), accumulate in accretions called protein bodies inside the endoplasmic reticulum (ER) of starchy endosperm cells. We found that genes encoding zeins, a-globulin, and legumin-1 are transcribed not only in the starchy endosperm but also in aleurone cells. Unlike the starchy endosperm, aleurone cells accumulate these storage proteins inside protein storage vacuoles (PSVs) instead of the ER. Aleurone PSVs contain zeinrich protein inclusions, a matrix, and a large system of intravacuolar membranes. After being assembled in the ER, zeins are delivered to the aleurone PSVs in atypical prevacuolar compartments …

Plant Targets For Pseudomonas Syringae Type Iii Effectors: Virulence Targets Or Guarded Decoys?, Anna Block, James R. Alfano

Center for Plant Science Innovation: Faculty Publications

The phytopathogenic bacterium Pseudomonas syringae can suppress both pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) by the injection of type III effector (T3E) proteins into host cells. T3Es achieve immune suppression using a variety of strategies including interference with immune receptor signaling, blocking RNA pathways and vesicle trafficking, and altering organelle function. T3Es can be recognized directly or indirectly by resistance proteins monitoring specific T3E targets resulting in ETI. It is presently unclear whether the monitored targets represent bona fide virulence targets or guarded decoys. Extensive overlap between PTI and ETI signaling suggests that T3Es may suppress …

The N-Terminal Region Of Wheat Streak Mosaic Virus Coat Protein Is A Host- And Strain-Specific Long-Distance Transport Factor, Satyanarayana Tatineni, David H. Van Winkle, Roy French

Department of Plant Pathology: Faculty Publications

Understanding the genetics underlying host range differences among plant virus strains can provide valuable insights into viral gene functions and virus-host interactions. In this study, we examined viral determinants and mechanisms of differential infection of Zea mays inbred line SDp2 by Wheat streak mosaic virus (WSMV) isolates. WSMV isolates Sidney 81 (WSMV-S81) and Type (WSMV-T) share 98.7% polyprotein sequence identity but differentially infect SDp2: WSMV-S81 induces a systemic infection, but WSMV-T does not. Coinoculation and sequential inoculation of SDp2 with WSMV-T and/or WSMV-S81 did not affect systemic infection by WSMV-S81, suggesting that WSMV-T does not induce a restrictive defense response …

Systematics And Biogeography Of The Clusioid Clade (Malpighiales), Brad R. Ruhfel

Biological Sciences Faculty and Staff Research

The clusioids are a clade of flowering plants in the diverse rosid order Malpighiales. It includes five families (i.e., Bonnetiaceae, Calophyllaceae, Clusiaceae sensu stricto, Hypericaceae, and Podostemaceae) that form a conspicuous element of tropical forests worldwide and are economically important. Their phylogenetic and biogeographical history has remained uncertain, however, which has hindered our understanding of their evolution. I conducted the first taxon-rich multigene analysis of this important clade to clarify their phylogenetic relationships (Chapter 1). Plastid (cp:matK, ndhF, and rbcL) and mitochondrial (mt: matR) nucleotide sequence data from nearly 200 taxa produced a well-resolved clusioid phylogeny and indicate that several …

Co-Culture Of Yeast Antagonists Of Fusarium Head Blight And Their Effect On Disease Development In Wheat, D. A. Schisler, P. J. Slininger, Michael J. Boehm, P. A. Paul

Department of Plant Pathology: Faculty Publications

Multistrain mixtures of biocontrol agents which can reduce plant disease to a greater extent than the individual strains of the mixture, commonly, are prepared by blending separately produced fermentation products. Co-cultivation of strains to equivalent biomass yields would provide mixture advantages without incurring the cost disadvantages of multiple fermentation and processing protocols. Fusariwn Head Blight (FHB) antagonists Cryptococcus flavescens OR 182.9 (NRRL Y-302l6), C. aureus OH 181.1 (NRRL Y-302l5) and C. aureus OR 181.1 (NRRL Y -30215), were grown in two- and three-strain co-cultures to assess the quality and efficacy of the fermentation end products produced. Final cell counts of …

The Gc-Rich Mitochondrial And Plastid Genomes Of The Green Alga Coccomyxa Give Insight Into The Evolution Of Organelle Dna Nucleotide Landscape, David Roy Smith, Fabien Burki, Takashi Burki, Jane Grimwood, Igor V, Grigoriev, James L. Van Etten, Patrick J. Keeling

Department of Plant Pathology: Faculty Publications

Most of the available mitochondrial and plastid genome sequences are biased towards adenine and thymine (AT) over guanine and cytosine (GC). Examples of GC-rich organelle DNAs are limited to a small but eclectic list of species, including certain green algae. Here, to gain insight in the evolution of organelle nucleotide landscape, we present the GC-rich mitochondrial and plastid DNAs from the trebouxiophyte green alga Coccomyxa sp. C-169. We compare these sequences with other GC-rich organelle DNAs and argue that the forces biasing them towards G and C are nonadaptive and linked to the metabolic and/or life history features of this …

Seedlings 2011, Sean M. Goins, Joseph Braner, Amy L. Myers, Charlie Jackson, Julia I. Chapman, Ryan W. Mcewan

Data Files: Drew Woods Permanent Plots

Seedling data (woody species up to 50 centimeters in height) collected in 2011 at Drew Woods State Nature Preserve in Darke County, OH. Data key is provided in a supplemental file.

A Preliminary Study Of The Vegetation Of Vernal Pools Of Acadia National Park, Mount Desert Island, B Ciccotelli, T B. Harris, B Connery, N Rajakaruna

Faculty Publications, Biological Sciences

We conducted a preliminary floristic study of six vernal pools in Acadia National Park on Mount Desert Island, Maine. Plant species were recorded on three sampling dates from April to October, 2008. Sixty-five vascular plant species from 26 families were recorded. Of these, 27 are considered occasional or uncommon in Acadia National Park. Thirteen species are new reports for vernal pools in the northeastern United States. This represents the first published study of the vernal pool flora of Acadia National Park

Is There A Relationship Between Water Potential And The Mechanical Strength Of Salix Lasiolepis?, William Cohen, Gina Fitzgerald, Joseph Liao

Featured Research



Structural And Functional Analysis Of The Type Iii Secretion System From Pseudomonas Fluorescens Q8r1-96, Dmitri V. Mavrodi, Anna Joe, Olga V. Mavrodi, Karl A. Hassan, David M. Weller, Ian T. Paulsen, Joyce E. Loper, James R. Alfano, Linda S. Thomashow

Center for Plant Science Innovation: Faculty Publications

Pseudomonas fluorescens Q8r1-96 represents a group of rhizosphere strains responsible for the suppressiveness of agricultural soils to take-all disease of wheat. It produces the antibiotic 2,4-diacetylphloroglucinol and aggressively colonizes the roots of cereal crops. In this study, we analyzed the genome of Q8r1-96 and identified a type III protein secretion system (T3SS) gene cluster that has overall organization similar to that of the T3SS gene cluster of the plant pathogen Pseudomonas syringae. We also screened a collection of 30 closely related P. fluorescens strains and detected the T3SS genes in all but one of them. The Q8r1-96 genome contained …

Mpk6, Sphinganine And The Lcb2a Gene From Serine Palmitoyltransferase Are Required In The Signaling Pathway That Mediates Cell Death Induced By Long Chain Bases In Arabidopsis, Mariana Saucedo-García, Arturo Guevara-Garcia, Ariadna González-Solís, Felipe Cruz-García, Sonia Vázquez-Santana, Jennifer E. Markham, M. Guadalupe Lozano-Rosas, Charles R. Dietrich, Maricela Ramos-Vega, Edgar B. Cahoon, Marina Gavilanes-Ruíz

Center for Plant Science Innovation: Faculty Publications

• Long chain bases (LCBs) are sphingolipid intermediates acting as second messengers in programmed cell death (PCD) in plants. Most of the molecular and cellular features of this signaling function remain unknown.

• We induced PCD conditions in Arabidopsis thaliana seedlings and analyzed LCB accumulation kinetics, cell ultrastructure and phenotypes in serine palmitoyltransferase (spt), mitogen-activated protein kinase (mpk), mitogenactivated protein phosphatase (mkp1) and lcb-hydroxylase (sbh) mutants.

• The lcb2a-1 mutant was unable to mount an effective PCD in response to fumonisin B1 (FB1), revealing that the LCB2a gene is essential for the …

A Plant Dj-1 Homolog Is Essential For Arabidopsis Thaliana Chloroplast Development, Jiusheng Lin, Tara J. Nazarenus, Jeanine L. Frey, Xinwen Liang, Mark A. Wilson, Julie M. Stone

Center for Plant Science Innovation: Faculty Publications

Protein superfamilies can exhibit considerable diversification of function among their members in various organisms. The DJ-1 superfamily is composed of proteins that are principally involved in stress response and are widely distributed in all kingdoms of life. The model flowering plant Arabidopsis thaliana contains three close homologs of animal DJ-1, all of which are tandem duplications of the DJ-1 domain. Consequently, the plant DJ-1 homologs are likely pseudo-dimeric proteins composed of a single polypeptide chain. We report that one A. thaliana DJ-1 homolog (AtDJ1C) is the first DJ-1 homolog in any organism that is required for viability. Homozygous disruption of …

Two Distinct Roles Of Arabidopsis Homolog Of Trithorax1 (Atx1) At Promoters And Within Transcribed Regions Of Atx1-Regulated Genes, Yong Ding, Zoya Avramova, Michael E. Fromm

Center for Plant Science Innovation: Faculty Publications

The Arabidopsis thaliana trithorax-like protein, ATX1, shares common structural domains, has similar histone methyltransferase (HMT) activity, and belongs in the same phylogenetic subgroup as its animal counterparts. Most of our knowledge of the role of HMTs in trimethylating lysine 4 of histone H3 (H3K4me3) in transcriptional regulation comes from studies of yeast and mammalian homologs. Little is known about the mechanism by which ATX1, or any other HMT of plant origin, affects transcription. Here, we provide insights into how ATX1 influences transcription at regulated genes, playing two distinct roles. At promoters, ATX1 is required for TATA binding protein (TBP) and …

Structure Function Analysis Of An Adp-Ribosyltransferase Type Iii Effector And Its Rna-Binding Target In Plant Immunity, Byeong-Ryool Jeong, Yan Lin, Anna Joe, Ming Guo, Christin Korneli, Huirong Yang, Ping Wang, Min Yu, Ronald Cerny, Dorothee Staiger, James R. Alfano, Yanhui Xu

Center for Plant Science Innovation: Faculty Publications

Background: HopU1 ADP-ribosylates GRP7, suppressing plant immunity.

Results: The HopU1 structure has two novel loops required for GRP7 recognition, and HopU1 ribosylates GRP7 at an arginine in position 49 disrupting its function.

Conclusion: HopU1 targets a conserved arginine in GRP7, disabling its ability to bind immunity-related RNA.

Significance: The mechanistic details of how HopU1 recognizes its substrate reveal how HopU1 contributes to pathogenesis.

Effects Of 2, 4-D On Zea Maize Physiology, Caitlin Thompson, Lori Patrick, Acacia Osbourne, Katrina Brock

Featured Research

Growth rate, fluorescence and stomatal conductance, in zea was examined to determine the effects of artificial auxin, 2-4-d, on common crop plants. We measured florescence, growth rate, and stomatal conductance. Low concentrations of 2,4-D increased light-adapted fluorescence, anthocyanin levels and height of zea maize. A high concentration of 2,4-D increased anthocyanin levels, but also caused decreased fluorescence and height and spindliness to occur. It appears 2,4-D is only beneficial to monocot crop plants in low quantities. We cannot accurately comment on the accuracy of our data, however, due to several potential sources of error.

Effects Of Soil Moisture On Photosynthesis And Fluorescence In Heteromeles Arbutifolia, Ali Alyami, Colin Byrne, Katherine Currie

Featured Research

Some plants have evolved to increase their chances of survival by being drought-adapted. Among those plant species is Heteromeles arbutifolia, native to California. Logically, the fact that Heteromeles arbutifolia tolerates the low supply of water makes this plant more likely to be within environments where the level of sun exposure is high. Thus, we hypothesized that lowering soil moisture will cause an increase in xylem pressure, causing an increase in photo-protection and florescence, and a decrease in photosynthetic rate. This has not been tested before on a native chaparral plant such as Heteromeles arbutifolia. The experiment was held …

The Effect Of Nitrogen Soil Concentration On Leaf Fluorescence In Zea Mays, Ashton Garbutt, Daniel Rossie, Anup Solsi

Featured Research

Macronutrients in the soil are essential to the growth and development of a plant. One of the most important nutrients to a plants growth is nitrogen. Nitrogen has been directly correlated to photosynthetic output in various studies and this relationship is the subject of this experiment. Since nitrogen has an effect on photosynthetic rate, there should be a correlation between nitrogen and fluorescence – a form of energy dissipation. This study attempted to show that nitrogen concentration in the soil is inversely proportional to fluorescence of the plant because the more nitrogen in the soil, the more energy should be …

The Effect Of Proximity To A Highway On The Health Of Malosma Laurina Leaves, Jessica Bermea, Haley Clayton, Jack Klobas

Featured Research

Due to an increase in air pollutants, heavy metal contaminates, and other adverse ecological conditions that plants near a road endure, it was hypothesized that plant species situated near a road would have a detectable decrease in photosynthetic performance when compared to plants away from the road. This investigation evaluated the in vivo photosynthetic status of two Malasma Laurina pairs with differing microhabitats, adjacent to the Pacific Coast Highway and 100 meters away from a Pacific Coast Highway. Maximum quantum yield and stomatal conductance measurements were recorded for each group. On average, the maximum quantum yield was greater on plants …

The Effect Of Hydration Status On Tensile Strength Of The Leaves Of Elymus Glaucus, Chelsie Corbett, Uri Hong, Scott Davis

Featured Research

Tensile strength and water potential are both factors that are essential to the life and survival of a plant. Tensile strength is a measure of the amount of force that a plant can undergo before tissue damage and breakage occur. The primary objective of this study was to examine the correlation between tensile strength and leaf hydration status, or water potential. The water potential of leaves of a monocot grass native to North America, Elymus Glaucus, commonly known as blue wildrye, was measured using the Scholander-Hammel Pressure Chamber. The tensile strength of hydrated and of dehydrated leaves was measured …

The Effects Of Agitation Upon Plant Anatomy In Phaseolus Vulgaris, Craig Sutter, Nicholas Huron

Featured Research

The earthquake that struck Japan’s coast a month ago gained national attention for the damage caused by the tsunami that was caused by the earthquake. Japan’s coast is subject to multiple earthquakes each year with tremors and aftershocks following. The quakes are bound to have an effect on the growth and development of Camellia sinensis, the tea plant, which is one of the most important exports of Japan. Due to the time restraints of this project, C. sinensis were not tested, instead two week old Phaseolus vulgaris were used to show the effects of constant agitation which might mimic …

Effects Of Dehydration Stress On The Dark Adapted Fluorescence (Fv/Fm) Of Giant Bladder Kelp (Macrocystis Pyrifera), J. Avery Powell, Leah Smith

Featured Research

The unique semi-diurnal tide system of Southern California suspends beach wrack along the beaches for approximately six hour periods before being washed back into the ocean. It has been noted in prior research that beach wrack is an essential part of Southern California's costal ecology but not much research has been done to learn about the viability of beach wrack as it dehydrates on the beach. To better understand the viability of wrack as it travels through these hydration changes, this study tested the effect of dehydration and rehydration on the fronds of Macrocystis pyrifera as they have been partially …

Exploring The Open-Close Mechanism Of Dimorphotheca Aurantiaca: Day Versus Night And Cold Versus Hot Temperatures, Tommy Chung, Kathleen Aguilar, Sunny Kim

Featured Research

In the spring of every year on Pepperdine University’s campus, patches of hills are covered with the South African native flower Dimorphotheca aurantiaca or more commonly known as the African Daisy. An observation of the opening and closing mechanism of the flower triggered an important question: does the flower change its shape based on temperature or the presence of light? At night, the African Daisy closes and then opens up again in the daytime. Because temperature has such strong effects on different species of ectodermic animals and temperature-sensitive plants, we hypothesized that the change in temperature initiates the flower’s morphological …