Genetics and Genomics Commons^™

The Trehalose Pathway In Maize: Conservation And Gene Regulation In Response To The Diurnal Cycle And Extended Darkness, Clémence Henry, Samuel W. Bledsoe, Allison Siekman, Alec Kollman, Brian M. Waters, Regina Feil, Mark Stitt, L. Mark Lagrimini

Department of Agronomy and Horticulture: Faculty Publications

Energy resources in plants are managed in continuously changing environments, such as changes occurring during the day/night cycle. Shading is an environmental disruption that decreases photosynthesis, compromises energy status, and impacts on crop productivity. The trehalose pathway plays a central but not well-defined role in maintaining energy balance. Here, we characterized the maize trehalose pathway genes and deciphered the impacts of the diurnal cycle and disruption of the day/night cycle on trehalose pathway gene expression and sugar metabolism. The maize genome encodes 14 trehalose-6-phosphate synthase (TPS) genes, 11 trehalose-6-phosphate phosphatase (TPP) genes, and one trehalase gene. Transcript abundance of most …

Sheep Updates 2014, James Kynge, David Lindsay, Johan Greeff, John Young, Luke Stephen, Graham Gardner, Stephen Lee, Bindi Murray, James Rowe

Sheep Updates

This session covers nine papers from different authors:

Genetic Research: A brave new world of opportunities

1. "China's Appetite" - The implications for WA, James Kynge, Chairman, FT Confidential Research, Emerging Markets Editor, Financial Times, London.

2. The genetics warm-up - the secret language of genetic research and its impacts on WA's sheep flock, Professor David Lindsay, University of Western Australia, Perth WA

The strength of genetic data: is it really valuable?

3. Genetic research in Western Australia - What have the compromises in production been? Johan Greeff, Senior Geneticist, Department of Agriculture and Food Western Australia

4. Show …

Functional Genomics Of Maize Endosperm Maturation And Protein Quality, Lingling Yuan

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

Maize is one of the most important cereal crops and widely cultivated throughout the world. The study on maize kernel development including protein quality improvement is essential for removing dietary protein deficiency because of the lack of essential amino acids, especially lysine and tryptophan, in maize kernel. Quality Protein Maize (QPM) is a hard kernel variant of the high-lysine mutant, opaque-2. We created opaque QPM variants to identify opaque-2 modifier genes and to investigate deletion mutagenesis combined with Illumina sequencing as a maize functional genomics tool. A K0326Y-QPM deletion mutant, line 107, was null for the 27- and 50-kD …

Heterogeneity, Not Randomness, Sets Challenges For Quantitative Genetics And Epidemiology: A Response To Davey Smith’S “Gloomy Prospect”, Peter J. Taylor

Working Papers on Science in a Changing World

Social epidemiologist Davey Smith (2011) argues that epidemiologists should accept a gloomy prospect: considerable randomness at the individual level means that they should keep their focus on modifiable causes of disease at the population level. The difficulty epidemiology has had in moving from significant population-level risk factors to improved prediction of cases at an individual level is analogous to the lack of success in the search for systematic aspects of the non-shared environmental influences that human quantitative genetics claims overshadow common environmental influences (e.g., the family’s socioeconomic status which siblings have in common). This article responds to the argument and …

Draft Genome Sequence Of Xylella Fastidiosa Pear Leaf Scorch Strain In Taiwan, C.-C. Su, W.-L. Deng, F.-J. Jan, C.-J. Chang, Hong Huang, J. Chen

School of Information Faculty Publications

The draft genome sequence of Xylella fastidiosa pear leaf scorch strain PLS229, isolated from the pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan, is reported here. The bacterium has a genome size of 2,733,013 bp, with a G+C content of 53.1%. The PLS229 genome was annotated and has 3,259 open reading frames and 50 RNA genes.

Phylogeny And Population Genetics Of The Endangered Dwarf Bear-Poppy, Arctomecon Humilis Coville (Papaveraceae) Using Microsatellite Markers, Joshua Simpson

Dissertations, Theses, and Capstone Projects

The genus Arctomecon (Papaveraceae) is comprised of three narrowly endemic rare species that are largely restricted to gypsum soils of the eastern Mojave Desert. The small, remaining populations of these species have become increasingly isolated by urban development and habitat fragmentation. Arctomecon humilis is federally listed as endangered due to its limited distribution within a ~15 km radius of an actively expanding city. Organizations involved with land management and conservation have called for greater insight into the genetic variation and population structure of the remaining subpopulations as they make important decisions regarding where to focus their efforts and resources.

The …

Fate Of Antimicrobials And Antimicrobial Resistance Genes In Simulated Swine Manure Storage, Stacey R. Joy, Xu Li, Daniel D. Snow, John Gilley, Bryan L. Woodbury, Shannon L. Bartelt-Hunt

School of Natural Resources: Faculty Publications

The behavior of three antibiotics (bacitracin, chlortetracycline, and tylosin) and two classes of antibiotic resistance genes (ARGs), tet and erm, were monitored in swine manure slurry under anaerobic conditions. First-order decay rates were determined for each antibiotic with half-lives ranging from1 day (chlortetracycline) to 10 days (tylosin). ARGs were monitored in the swine manure slurry, and losses of approximately 1 to 3 orders of magnitude in relative abundance were observed during the 40 day storage period. First-order degradation profiles were observed for chlortetracycline and its corresponding resistance genes, tet(X) and tet(Q). Tylosin was degraded to approximately 10% …

Sudden Aspen Decline Report For Spruce Beetle Epidemic And Aspen Decline Management Response Eis, Jim Worrall, Suzanne Marchetti, Gerald E. Rehfeldt

Aspen Bibliography

Aspen is an important component of GMUG’s forests. Over 288,000 ha (712,000 acres) of aspendominated forest type (TAA) occur across the GMUG (Table 1). Just over half (55%) of the aspen forest type is outside wilderness and roadless areas.

Origins Of The Classical Gene Concept, 1900–1950: Genetics, Mechanistic, Philosophy, And The Capitalization Of Agriculture, Garland E. Allen

Biology Faculty Research

In the period of “classical genetics” (roughly 1915–1950), the common view of the gene was mechanistic—that is, genes were seen as individual, atomistic units, as material components of the chromosomes. Although it was recognized early on that genes could interact and influence each other’s expression, they were still regarded as individually functioning units, much like the chemists’ atoms or molecules. Although geneticists in particular knew the story was more complex, the atomistic gene remained the central view for a variety of reasons. It fit the growing philosophy of mechanistic materialism in the life sciences, as biologists tried to make their …

Soil Microbial Community Distributions And Disease Suppressiveness In The Coastal Plain Of Georgia, Michael J. Sabula

College of Graduate Studies: Theses & Dissertations

This study compared the soil microbial communities of three vegetation types in the coastal plain of Georgia: 1. crop land actively in use for agricultural production, 2. transitional grassland in early stages of secondary succession, and 3. pristine unmanaged forest land. Microbial species diversity and quantities of microbial DNA were determined from each of these vegetation types at three separate locations near Statesboro, Georgia. Length heterogeneity PCR(LH-PCR) methods and subsequent analysis of fungal, bacterial, and metazoan communities by analysis of similarity (ANOSIM) revealed high within-group similarity by vegetation type, indicating land management intensity and vegetation cover is a strong determining …

Global Changes In Mineral Transporters In Tetraploid Switchgrasses (Panicum Virgatum L.), Nathan A. Palmer, Aaron J. Saathoff, Brian M. Waters, Teresa Donze, Tiffany M. Heng-Moss, Paul Twigg, Christian M. Tobias, Gautam Sarath

Department of Agronomy and Horticulture: Faculty Publications

Switchgrass (Panicum virgatum L) is a perennial, C4 grass with great potential as a biofuel crop. An in-depth understanding of the mechanisms that control mineral uptake, distribution, and remobilization will benefit sustainable production. Nutrients are mobilized from aerial portions to below-ground crowns and rhizomes as a natural accompaniment to above-ground senescence post seed-set. Mineral uptake and remobilization is dependent on transporters, however, little if any information is available about the specific transporters that are needed and how their relative expression changes over a growing season.Using well-defined classes of mineral transporters, we identified 520 genes belonging to 40 different transporter …

Switchgrass (Panicum Virgatum L) Flag Leaf Transcriptomes Reveal Molecular Signatures Of Leaf Development, Senescence, And Mineral Dynamics, Nathan A. Palmer, Teresa Donze-Reiner, David Horvath, Tiffany Heng-Moss, Brian M. Waters, Christian M. Tobias, Gautam Sarath

Department of Agronomy and Horticulture: Faculty Publications

Switchgrass flag leaves can be expected to be a source of carbon to the plant, and its senescence is likely to impact the remobilization of nutrients from the shoots to the rhizomes. However, many genes have not been assigned a function in specific stages of leaf development. Here, we characterized gene expression in flag leaves over their development. By merging changes in leaf chlorophyll and the expression of genes for chlorophyll biosynthesis and degradation, a four-phase molecular roadmap for switchgrass flag leaf ontogeny was developed. Genes associated with early leaf development were up-regulated in phase 1. Phase 2 leaves had …

Fusarium Head Blight Resistance And Agronomic Performance In Soft Red Winter Wheat Populations, Daniela Sarti Dvorjak

Theses and Dissertations--Plant and Soil Sciences

Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe [telomorph: Gibberella zeae Schwein.(Petch)], is recognized as one of the most destructive diseases of wheat (Triticum aestivum L. and T. durum L.) and barley (Hordeum vulgare L.) worldwide. Breeding for FHB resistance must be accompanied by selection for desirable agronomic traits. Donor parents with two FHB resistance quantitative trait loci (QTL) Fhb1 (chromosome 3BS) and QFhs.nau-2DL (chromosome 2DL) were crossed to four adapted SRW wheat lines to generate backcross and forward cross progeny. F₂ individuals were genotyped and assigned to 4 different groups according to presence/ absence of …

An Intergenic Region Shared By At4g35985 And At4g35987 In Arabidopsis Thaliana Is A Tissue Specific And Stress Inducible Bidirectional Promoter Analyzed In Transgenic Arabidopsis And Tobacco Plants, Joydeep Banerjee, Dipak K. Sahoo, Nrisingha Dey, Robert Houtz, Indu B. Maiti

Kentucky Tobacco Research and Development Center Faculty Publications

On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985) are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS) in both orientations in transient tobacco protoplast and …

Draft Genome Sequence Of Xylella Fastidiosa Subsp. Multiplex Strain Griffin-1 From Quercus Rubra In Georgia, Jianchi Chen, Hong Huang, Chung-Jan Chang, Drake C. Stenger

School of Information Faculty Publications

The draft genome sequence of Xylella fastidiosa subsp. multiplex strain Griffin-1, isolated from a red oak tree (Quercus rubra) in Georgia, is reported here. The bacterium has a genome size of 2,387,314 bp, with a G+C content of 51.7%. The Griffin-1 strain genome contains 2,903 predicted open reading frames and 50 RNA genes.

Elk (Cervus Elaphus) Seasonal Habitat Selection In A Heterogeneous Forest Structure, Jesse N. Popp, David N.C. Mcgeachy, Josef Hamr

Aspen Bibliography

Seasonal habitat selection by the reintroduced Burwash elk population, approximately 30 km south of Sudbury, Ontario, has been analysed in order to assist in the development of future management. Twenty-five adult females were radio-collared and tracked 1–3 times a week for 3 years. The most prominent patterns included selection of intolerant hardwood forests (trembling aspen, white birch, and balsam poplar) during all seasons, while Great Lakes-St. Lawrence pines (white and red pine dominated stands) were used less than expected based on availability for all seasons. The selection patterns are likely associated with seasonal climatic conditions and forage preferences. Because the …

Characterization Of Resistance To The Cry1f Toxin From Bacillus Thuringiensis In Resistant Fall Armyworm, Spodoptera Frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) From Puerto Rico, Ana Maria Velez

Department of Entomology: Dissertations, Theses, and Student Research

Transgenic corn expressing Cry1F protein from Bacillus thuringiensis Berliner has been registered for Spodoptera frugiperda control since 2003. Unexpected damage to Cry1F corn was reported in 2006 in Puerto Rico and Cry1F resistance in S. frugiperda was documented. The inheritance of Cry1F resistance was characterized in a S. frugiperda resistant strain from Puerto Rico which displayed >387-fold resistance to Cry1F. Concentration-response bioassays of reciprocal crosses of resistant and susceptible parental populations indicated that resistance is recessive and autosomal. Bioassays of the backcross of the F₁ generation crossed with the resistant parental strain suggest that a single locus is responsible …

Characterization And Distribution Of Novel Non-Ltr Retroelements Driving High Telomere Rflp Diversity In Clonal Lines Of Magnaporthe Oryzae, John H. Starnes

Theses and Dissertations--Plant Pathology

The filamentous ascomycete fungus Magnaporthe oryzae is a pathogen of over 50 genera of grasses. Two important diseases it can cause are gray leaf spot in Lolium perenne (perennial ryegrass) and blast in Oryza sativa (rice). The telomeres of M. oryzae isolates causing gray leaf spot are highly variable, and can spontaneously change during fungal culture. In this dissertation, it is shown that a rice-infecting isolate is much more stable at the telomeres than an isolate from gray leaf spot. To determine the molecular basis of telomere instability several gray leaf spot isolates telomeres were cloned, which revealed two non-LTR …

Transcriptome Characterization And Detection Of Gene Expression Differences In Aspen (Populus Tremuloides), Hardeep S. Rai, Karen E. Mock, Bryce A. Richardson, Richard C. Cronn, Katherine J. Hayden, Jessica W. Wright, Brian J. Knaus, Paul G. Wolf

Aspen Bibliography

No abstract provided.

Wolf Creek Ranch Aspen Monitoring Report, Paul C. Rogers, Allison Jones, James Catlin, James Shuler, Arthur Morris, Michael Kuhns

Aspen Bibliography

In the summer of 2012 we undertook a landscape assessment of aspen forest conditions at Wolf Creek Ranch (WCR) near Kamas, Utah. Using a geographic information system (GIS) coverage of predicted aspen coverage, fifty systematically selected field "plots" were located and mapped with aspen stands around WCR. Seven plots were eventually discarded from our survey due to lack of aspen cover. Volunteer field crews, mostly WCR homeowners, collected aspen data documenting tree sizes, height/age groups, diameters, reproduction, mortality, browse levels, and browse animal use levels.

Aspen Status Report And Recommendation For The Book Cliffs, Paul C. Rogers, Cody M. Mittanck, Ronald J. Ryel

Aspen Bibliography

Regionally quaking aspen (Populus tremuloides Michx.) forests are experiencing numerous impediments to resilience. In the West, recent drought, fire suppression, insects, diseases, climate trends, inappropriate management, and ungulate herbivory are impacting these high biodiversity forests. We conducted a landscape assessment of aspen communities in the Book Cliffs region, Vernal Field Office of the Bureau of Land Management, for the purposes of determining landscape-level status of aspen and making recommendations for future management of these forests. The study area consists of 268 distinct aspen polygons totaling approximately 70 ha (174 acres) of aspen forest surrounded by much larger tracts of …

Book Cliffs Roadless Area Aspen Study 2013 : Grand & Uintah Counties, Utah, Cody M. Mittanck

Aspen Bibliography

No abstract provided.

The Effect Of Temperature On Seed Quality And Quantity In Crosses Between European (Populus Tremula) And Hybrid Aspens (P. Tremula X P. Tremuloides), L. Koviuranta, T. Latva-Karjanmaa, P. Pulkkinen

Aspen Bibliography

Hybrid aspen (Populus tremula L. Populus tremuloides Michx.) plantations are expanding in Fennoscandia and the Baltic countries; however, the possible effects of plantations on the native European aspen (P. tremula) and the level of gene flow between European and hybrid aspen have not been investigated. We studied seed quantity and quality in intraspecific and interspecific crosses of the European and hybrid aspens over a two year period. In order to study whether elevated temperatures due to climate change would benefit the species differently, we performed the crosses in different temperatures. In both years, interspecific crosses produced more seeds with higher …

Effects Of Slash Pile Burning After Restoring Conifer- Encroached Aspen, Christa M. Dagley, John-Pascal Berrill, Stephanie Coppeto, Kyle Jacobson

Aspen Bibliography

Removal of conifers encroaching aspen stands has been advocated and is being practiced in the Lake Tahoe Basin (EIP Project #10080: Aspen Community Restoration Projects). In remote and roadless areas, thinning of conifers is generating large volumes of wood and pile burning is currently being implemented to handle this biomass on site. However, the effects of pile burning on aspen are unknown, and there is an urgent need for guidelines to support design of thinning treatment prescriptions; specifically burn pile size and safe distances from live aspen trees of any size to prevent injury.

Survey Of Endosymbionts In The Diaphorina Citri Metagenome And Assembly Of A Wolbachia Wdi Draft Genome, Surya Saha, Wayne B. Hunter, Justin Reese, J. Kent Morgan, Mizuri Marutani-Hert, Hong Huang, Magdalen Lindeberg

School of Information Faculty Publications

Diaphorina citri (Hemiptera: Psyllidae), the Asian citrus psyllid, is the insect vector of Ca. Liberibacter asiaticus, the causal agent of citrus greening disease. Sequencing of the D. citrimetagenome has been initiated to gain better understanding of the biology of this organism and the potential roles of its bacterial endosymbionts. To corroborate candidate endosymbionts previously identified by rDNA amplification, raw reads from the D. citri metagenome sequence were mapped to reference genome sequences. Results of the read mapping provided the most support for Wolbachia and an enteric bacterium most similar to Salmonella. Wolbachia-derived reads were extracted using …

Organellar Signaling Expands Plant Phenotypic Variation And Increases The Potential For Breeding The Epigenome, Roberto De La Rosa Santamaria

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

MUTS HOMOLOGUE 1 (MSH1) is a nuclear gene unique to plants that functions in mitochondria and plastids, where it confers genome stability. Phenotypic effects of MSH1 down- regulation were studied in sorghum inbreed line Tx430 and Arabidopsis ecotype Columbia-0, with the hypothesis that RNAi suppression of MSH1 triggers retrograde signaling from organelles to the nucleus, alters the epigenome, and derives heritable phenotypic variation suitable for artificial selection. An array of morphological traits and metabolic pathways was detected, including leaf variegation, male sterility and dwarfism, associated with altered gibberellic acid metabolism, higher levels of reactive oxygen species (ROS), and decreased synthesis …

Facilitation Drives Mortality Patterns Along Succession Gradients Of Aspen-Conifer Forests, W. John Calder, Samuel B. St. Clair

Aspen Bibliography

While it is well established that facilitation and competition are important structuring forces in plant communities, a clear understanding of the interactions between them and how they change through the life stages of plants and affect long-term plant community development is lacking. We have observed that conifer seedlings are rarely found growing in meadows but readily establish under adjacent aspen stands, particularly at the base of aspen trees, creating the potential for antagonistic interactions in later life stages. To examine these relationships and their potential consequences on forest community development, we characterized patterns of establishment, regeneration, and overstory mortality of …

Escape From Preferential Retention Following Repeated Whole Genome Duplications In Plants, James C. Schnable, Xiaowu Wang, J. Chris Pires, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

The well supported gene dosage hypothesis predicts that genes encoding proteins engaged in dose–sensitive interactions cannot be reduced back to single copies once all interacting partners are simultaneously duplicated in a whole genome duplication. The genomes of extant flowering plants are the result of many sequential rounds of whole genome duplication, yet the fraction of genomes devoted to encoding complex molecular machines does not increase as fast as expected through multiple rounds of whole genome duplications. Using parallel interspecies genomic comparisons in the grasses and crucifers, we demonstrate that genes retained as duplicates following a whole genome duplication have only …

Genome-Wide Analysis Of Syntenic Gene Deletion In The Grasses, James C. Schnable, Michael Freeling, Eric Lyons

Department of Agronomy and Horticulture: Faculty Publications

The grasses, Poaceae, are one of the largest and most successful angiosperm families. Like many radiations of flowering plants, the divergence of the major grass lineages was preceded by a whole-genome duplication (WGD), although these events are not rare for flowering plants. By combining identification of syntenic gene blocks with measures of gene pair divergence and different frequencies of ancient gene loss, we have separated the two subgenomes present in modern grasses. Reciprocal loss of duplicated genes or genomic regions has been hypothesized to reproductively isolate populations and, thus, speciation. However, in contrast to previous studies in yeast and teleost …

Index Selection In Terminal Sires Improves Early Lamb Growth, G. C. Márquez, W. Haresign, M. H. Davies, G. C. Emmans, Rainer Roehe, L Bünger, G. Simm, Ronald M. Lewis

Department of Animal Science: Faculty Publications

The use of terminal sires (TS) for crossbreeding is integral to the UK sheep industry where approximately 71% of market lambs are sired by TS rams. Early growth of these crossbred lambs affects profitability. The objectives of this study were i) to evaluate the effectiveness of index selection among TS on BW and ADG of their crossbred offspring; and ii) to compare the efficacy of that selection within TS breeds. The most widely used TS breeds in the United Kingdom are Charollais, Suffolk, and Texel. These participated in sire referencing schemes in which they were evaluated on a lean growth …