Life Sciences Commons^™

Chromomap: An R Package For Interactive Visualization Of Multi-Omics Data And Annotation Of Chromosomes, Lakshay Anand, Carlos M. Rodriguez Lopez

Horticulture Faculty Publications

BACKGROUND: The recent advancements in high-throughput sequencing have resulted in the availability of annotated genomes, as well as of multi-omics data for many living organisms. This has increased the need for graphic tools that allow the concurrent visualization of genomes and feature-associated multi-omics data on single publication-ready plots.

RESULTS: We present chromoMap, an R package, developed for the construction of interactive visualizations of chromosomes/chromosomal regions, mapping of any chromosomal feature with known coordinates (i.e., protein coding genes, transposable elements, non-coding RNAs, microsatellites, etc.), and chromosomal regional characteristics (i.e. genomic feature density, gene expression, DNA methylation, chromatin modifications, etc.) of organisms …

Feature Papers In Horticulturae, Douglas D. Archbold

Horticulture Faculty Publications

No abstract provided.

Effect Of Biofertilizer In Organic And Conventional Systems On Growth, Yield And Baking Quality Of Hard Red Winter Wheat, Ammar Al-Zubade, Timothy D. Phillips, Mark A. Williams, Krista L. Jacobsen, David Van Sanford

Horticulture Faculty Publications

A two-year study (harvest years 2019 and 2020) was conducted to investigate the effect of a commercially available biofertilizer, in combination with variable nitrogen (N) rate, on bread baking quality and agronomic traits in hard winter wheat grown in conventional (CONV) and organic (ORG) farming systems in Kentucky, USA. The hard red winter wheat cultivar ‘Vision 45’ was used with three N rates (44, 89.6 and 134.5 kg/ha as Low, Med and High, respectively) and three biofertilizer spray regimes (no spray, one spray and two sprays). All traits measured were significantly affected by the agricultural production system (CONV or ORG) …

Farmer Perceptions Of Adopting Novel Legumes In Traditional Maize-Based Farming Systems In The Yucatan Peninsula, Jacques Fils Pierre, Luis Latournerie-Moreno, René Garruña-Hernández, Krista L. Jacobsen, Carrie A. M. Laboski, Lucila De Lourdes Salazar-Barrientos, Esaú Ruiz-Sánchez

Horticulture Faculty Publications

Intercropping constitutes the traditional farming system practice used in various forms for maize production in the Yucatan peninsula. Although practiced for centuries, problems persist with competition for water, nutrients and light between crop species in traditional farming systems. Furthermore, little is known about farmers’ perceptions regarding changes to traditional maize-legume intercropping systems and their interest in novel crop adoption to increase yields in the system while maintaining the practice. The objective of this study was to investigate the maize-based traditional cropping system by assessing the underlying motives and concepts of farmers to practice intercropping in the Yucatan Peninsula and to …

The Regulation Of Plant Vegetative Phase Transition And Rejuvenation: Mirnas, A Key Regulator, Tajbir Raihan, Robert L. Geneve, Sharyn E. Perry, Carlos M. Rodriguez Lopez

Horticulture Faculty Publications

In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase transitions need to be tightly regulated and coordinated to ensure they occur under optimal seasonal, environmental conditions. Polycarpic perennials transition through vegetative stages and the mature, reproductive stage many times during their lifecycles and, in both perennial and annual species, environmental factors and culturing methods can reverse the otherwise unidirectional vector of plant development. Epigenetic factors regulating …

Against The Odds: Hybrid Zones Between Mangrove Killifish Species With Different Mating Systems, Waldir M. Berbel-Filho, Andrey Tatarenkov, George Pacheco, Helder M. V. Espírito-Santo, Mateus G. Lira, Carlos Garcia De Leaniz, John C. Avise, Sergio M. Q. Lima, Carlos M. Rodriguez Lopez, Sofia Consuegra

Horticulture Faculty Publications

Different mating systems are expected to affect the extent and direction of hybridization. Due to the different levels of sexual conflict, the weak inbreeder/strong outbreeder (WISO) hypothesis predicts that gametes from self-incompatible (SI) species should outcompete gametes from self-compatible (SC) ones. However, other factors such as timing of selfing and unilateral incompatibilities may also play a role on the direction of hybridization. In addition, differential mating opportunities provided by different mating systems are also expected to affect the direction of introgression in hybrid zones involving outcrossers and selfers. Here, we explored these hypotheses with a unique case of recent hybridization …

Best Papers Introduction, Douglas D. Archbold

Horticulture Faculty Publications

No abstract provided.

Special Issue: Feature Papers 2020, Douglas D. Archbold

Horticulture Faculty Publications

No abstract provided.

Wine Terroir And The Soil Bacteria: An Amplicon Sequencing-Based Assessment Of The Barossa Valley And Its Sub-Regions, Jia Zhou, Timothy R. Cavagnaro, Roberta De Bei, Tiffanie M. Nelson, John R. Stephen, Andrew Metcalfe, Matthew Gilliham, James Breen, Cassandra Collins, Carlos M. Rodríguez López

Horticulture Faculty Publications

A wines’ terroir, represented as wine traits with regional distinctiveness, is a reflection of both the biophysical and human-driven conditions in which the grapes were grown and wine made. Soil is an important factor contributing to the uniqueness of a wine produced by vines grown in specific conditions. Here, we evaluated the impact of environmental variables on the soil bacteria of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that both dispersal isolation by geographic distance and environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row …

Rhizobacterial Species Richness Improves Sorghum Growth And Soil Nutrient Synergism In A Nutrient-Poor Greenhouse Soil, Mohammad Radhi Sahib, Zahida H. Pervaiz, Mark A. Williams, Muhammad Saleem, Seth Debolt

Horticulture Faculty Publications

Although microbes influence plant growth, little is known about the impact of microbial diversity on plant fitness trade-offs, intraspecific-interactions, and soil nutrient dynamics in the context of biodiversity-ecosystem functioning (BEF) research. The BEF theory states that higher species richness can enhance ecosystem functioning. Thus, we hypothesize that rhizobacterial species richness will alter sorghum (Sorghum bicolor L.) growth, soil nutrient dynamics and interactions (antagonism or synergism) in a nutrient-poor greenhouse soil. Using six rhizobacterial species in a BEF experiment, we tested the impact of a species richness gradient (0, 1, 3, 5 or 6 species per community) on plant growth, …

Greenhouse Spatial Effects Detected In The Barley (Hordeum Vulgare L.) Epigenome Underlie Stochasticity Of Dna Methylation, Moumouni Konate, Michael J. Wilkinson, Julian Taylor, Eileen S. Scott, Bettina Berger, Carlos M. Rodriguez Lopez

Horticulture Faculty Publications

Environmental cues are known to alter the methylation profile of genomic DNA, and thereby change the expression of some genes. A proportion of such modifications may become adaptive by adjusting expression of stress response genes but others have been shown to be highly stochastic, even under controlled conditions. The influence of environmental flux on plants adds an additional layer of complexity that has potential to confound attempts to interpret interactions between environment, methylome, and plant form. We therefore adopt a positional and longitudinal approach to study progressive changes to barley DNA methylation patterns in response to salt exposure during development …

Rapid In Vitro Multiplication Of Non-Runnering Fragaria Vesca Genotypes From Seedling Shoot Axillary Bud Explants, Babul C. Sarker, Douglas D. Archbold, Robert L. Geneve, Sharon T. Kester

Horticulture Faculty Publications

Fragaria vesca L. has become a model species for genomic studies relevant to important crop plant species in the Rosaceae family, but generating large numbers of plants from non-runner-producing genotypes is slow. To develop a protocol for the rapid generation of plants, leaf explants were compared to single axillary bud shoot explants, both from in vitro-grown Fragaria vesca seedlings, as sources of shoots for new plant production in response to benzyladenine (BA) or thidiazuron (TDZ) combined with indolebutyric acid (IBA) on Murashige and Skoog’s Basal Salt (MS) medium. BA at 2.0 and 4.0 mg L⁻¹ and TDZ at 1.5 …

Shotgun Metagenomic Sequencing Data Of Sunflower Rhizosphere Microbial Community In South Africa, Olubukola Oluranti Babalola, Temitayo Tosin Alawiye, Carlos M. Rodriguez Lopez, Ayansina Segun Ayangbenro

Horticulture Faculty Publications

This dataset presents shotgun metagenomic sequencing of sunflower rhizosphere microbiome in Bloemhof, South Africa. Data were collected to decipher the structure and function in the sunflower microbial community. Illumina HiSeq platform using next generation sequencing of the DNA was carried out. The metagenome comprised 8,991,566 sequences totaling 1,607,022,279 bp size and 66% GC content. The metagenome was deposited into the NCBI database and can be accessed with the SRA accession number SRR10418054. An online metagenome server (MG RAST) using the subsystem database revealed bacteria had the highest taxonomical representation with 98.47%, eukaryote at 1.23%, and archaea at 0.20%. The most …

Common Garden Experiment Reveals Altered Nutritional Values And Dna Methylation Profiles In Micropropagated Three Elite Ghanaian Sweet Potato Genotypes, Belinda Akomeah, Marian D. Quain, Sunita A. Ramesh, Lakshay Anand, Carlos M. Rodríguez López

Horticulture Faculty Publications

Micronutrient deficiency is the cause of multiple diseases in developing countries. Staple crop biofortification is an efficient means to combat such deficiencies in the diets of local consumers. Biofortified lines of sweet potato (Ipomoea batata L. Lam) with enhanced beta-carotene content have been developed in Ghana to alleviate Vitamin A Deficiency. These genotypes are propagated using meristem micropropagation to ensure the generation of virus-free propagules. In vitro culture exposes micropropagated plants to conditions that can lead to the accumulation of somaclonal variation with the potential to generate unwanted aberrant phenotypes. However, the effect of micropropagation induced somaclonal variation on …

Improved Draft Genome Sequence Of Bacillus Sp. Strain Yf23, Which Has Plant Growth-Promoting Activity, Ye Xia, Seth Debolt, Qin Ma, Adam Mcdermaid, Cankun Wang, Nicole Shapiro, Tanja Woyke, Nikos C. Kyrpides

Horticulture Faculty Publications

We report here the improved draft genome sequence of Bacillus sp. strain YF23, a bacterium originally isolated from switchgrass (Panicum virgatum) plants and shown to exhibit plant growth-promoting activity. The genome comprised 5.82 Mbp, containing 5,933 genes, with 193 as RNA genes, and a GC content of 35.10%.

Liberation Of Recalcitrant Cell Wall Sugars From Oak Barrels Into Bourbon Whiskey During Aging, Jarrad Wade Gollihue, Mitchell D. Richmond, Harlen Wheatley, Victoria G. Pook, Meera Nair, Isabelle A. Kagan, Seth Debolt

Horticulture Faculty Publications

Oak barrels have been used by humans for thousands of years to store and transport valuable materials. Early settlers of the United States in Kentucky began charring the interior of new white oak barrels prior to aging distillate to create the distinctively flavored spirit we know as bourbon whiskey. Despite the unique flavor and cultural significance of "America's Spirit", little is known about the wood-distillate interaction that shapes bourbon whiskey. Here, we employed an inverse method to measure the loss of specific wood polysaccharides in the oak cask during aging for up to ten years. We found that the structural …

Developmental Variation In Fruit Polyphenol Content And Related Gene Expression Of A Red-Fruited Versus A White-Fruited Fragraria Vesca Genotype, Sutapa Roy, Sanjay Singh, Douglas D. Archbold

Horticulture Faculty Publications

Two cultivars of F. vesca, red-fruited Baron Solemacher (BS) and white-fruited Pineapple Crush (PC), were studied to compare and contrast the quantitative accumulation of major polyphenols and related biosynthetic pathway gene expression patterns during fruit development and ripening. Developing PC fruit showed higher levels of hydroxycinnamic acids in green stages and a greater accumulation of ellagitannins in ripe fruit in comparison to BS. In addition to anthocyanin, red BS fruit had greater levels of flavan-3-ols when ripe than PC. Expression patterns of key structural genes and transcription factors of the phenylpropanoid/flavonoid biosynthetic pathway, an abscisic acid (ABA) biosynthetic gene, …

Near-Infrared Spectroscopy Used To Predict Soybean Seed Germination And Vigour, Maythem Al-Amery, Robert L. Geneve, Mauricio F. Sanches, Paul R. Armstrong, Elizabeth B. Maghirang, Chad Lee, Roberval D. Vieira, David F. Hildebrand

Horticulture Faculty Publications

Rapid, non-destructive methods for measuring seed germination and vigour are valuable. Standard germination and seed vigour were determined using 81 soybean seed lots. From these data, seed lots were separated into high and low germinating seed lots as well as high, medium and low vigour seed lots. Near-infrared spectra (950–1650 nm) were collected for training and validation samples for each seed category and used to create partial least squares (PLS) prediction models. For both germination and vigour, qualitative models provided better discrimination of high and low performing seed lots compared with quantitative models. The qualitative germination prediction models correctly identified …

Salt Stress Induces Non-Cg Methylation In Coding Regions Of Barley Seedlings (Hordeum Vulgare), Moumouni Konate, Michael J. Wilkinson, Benjamin T. Mayne, Stephen M. Pederson, Eileen S. Scott, Bettina Berger, Carlos M. Rodriguez Lopez

Horticulture Faculty Publications

Salinity can negatively impact crop growth and yield. Changes in DNA methylation are known to occur when plants are challenged by stress and have been associated with the regulation of stress-response genes. However, the role of DNA-methylation in moderating gene expression in response to salt stress has been relatively poorly studied among crops such as barley. Here, we assessed the extent of salt-induced alterations of DNA methylation in barley and their putative role in perturbed gene expression. Using Next Generation Sequencing, we screened the leaf and root methylomes of five divergent barley varieties grown under control and three salt concentrations, …

Optimizing The Use Of A Liquid Handling Robot To Conduct A High Throughput Forward Chemical Genetics Screen Of Arabidopsis Thaliana, B. Kirtley Amos, Victoria G. Pook, Seth Debolt

Horticulture Faculty Publications

Chemical genetics is increasingly being employed to decode traits in plants that may be recalcitrant to traditional genetics due to gene redundancy or lethality. However, the probability of a synthetic small molecule being bioactive is low; therefore, thousands of molecules must be tested in order to find those of interest. Liquid handling robotics systems are designed to handle large numbers of samples, increasing the speed with which a chemical library can be screened in addition to minimizing/standardizing error. To achieve a high-throughput forward chemical genetics screen of a library of 50,000 small molecules on Arabidopsis thaliana (Arabidopsis), protocols using a …

Kelch F-Box Protein Positively Influences Arabidopsis Seed Germination By Targeting Phytochrome-Interacting Factor1, Manoj Majee, Santosh Kumar, Praveen Kumar Kathare, Shuiqin Wu, Derek Gingerich, Nihar R. Nayak, Louai Salaita, Randy Dinkins, Kathleen Martin, Michael M. Goodin, Lynnette M. A. Dirk, Taylor D. Lloyd, Ling Zhu, Joseph Chappell, Arthur G. Hunt, Richard Vierstra, Enamul Huq, A. Bruce Downie

Horticulture Faculty Publications

Seeds employ sensory systems that assess various environmental cues over time to maximize the successful transition from embryo to seedling. Here we show that the Arabidopsis F-BOX protein COLD TEMPERATURE-GERMINATING (CTG)-10, identified by activation tagging, is a positive regulator of this process. When overexpressed (OE), CTG10 hastens aspects of seed germination. CTG10 is expressed predominantly in the hypocotyl, and the protein is localized to the nucleus. CTG10 interacts with PHYTOCHROME-INTERACTING FACTOR 1 (PIF1) and helps regulate its abundance in planta. CTG10-OE accelerates the loss of PIF1 in light, increasing germination efficiency, while PIF1-OE lines fail to complete germination in …

Genome-Wide Analyses Of The Nac Transcription Factor Gene Family In Pepper (Capsicum Annuum L.): Chromosome Location, Phylogeny, Structure, Expression Patterns, Cis-Elements In The Promoter, And Interaction Network, Weiping Diao, John C. Snyder, Shubin Wang, Jinbing Liu, Baogui Pan, Guangjun Guo, Wei Ge, Mohammad Hasan Salman Ali Dawood

Horticulture Faculty Publications

The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family, which is involved in the regulation of tissue development in response to biotic and abiotic stress. To date, there have been no comprehensive studies investigating chromosomal location, gene structure, gene phylogeny, conserved motifs, or gene expression of NAC in pepper (Capsicum annuum L.). The recent release of the complete genome sequence of pepper allowed us to perform a genome-wide investigation of Capsicum annuum L. NAC (CaNAC) proteins. In the present study, a comprehensive analysis of the CaNAC gene family in pepper was performed, …

Cover Crops And Fertilization Alter Nitrogen Loss In Organic And Conventional Conservation Agriculture Systems, Rebecca E. Shelton, Krista L. Jacobsen, Rebecca L. Mcculley

Horticulture Faculty Publications

Agroecosystem nitrogen (N) loss produces greenhouse gases, induces eutrophication, and is costly for farmers; therefore, conservation agricultural management practices aimed at reducing N loss are increasingly adopted. However, the ecosystem consequences of these practices have not been well-studied. We quantified N loss via leaching, NH₃ volatilization, N₂O emissions, and N retention in plant and soil pools of corn conservation agroecosystems in Kentucky, USA. Three systems were evaluated: (1) an unfertilized, organic system with cover crops hairy vetch (Vicia villosa), winter wheat (Triticum aestivum), or a mix of the two (bi-culture); (2) an organic …

Reciprocal Effect Of Parental Lines On The Physiological Potential And Seed Composition Of Corn Hybrid Seeds, Juliana F. Santos, Lynnette M. A. Dirk, A. Bruce Downie, Mauricio F. G. Sanches, Roberval D. Vieira

Horticulture Faculty Publications

Obtaining corn hybrid seeds (Zea mays L.) with high vigour depends on the parental lines and the direction of the cross, and this relates to seed desiccation tolerance and composition. This research studied reciprocal crosses between pairs of proprietary, elite parent lines (L1 and L5; L2 and L4) producing hybrid seeds with different qualities attempting to correlate vigour with seed composition, focusing on storage proteins, starch and soluble sugar amounts. Four corn hybrid seed lots produced from reciprocal crosses were compared (HS 15 with HS 51, and HS 24 with HS 42) by assessing germination, vigour, and seedling emergence …

Positioning Of The Scrambled Receptor Requires Udp-Glc:Sterol Glucosyltransferase 80b1 In Arabidopsis Roots, Victoria G. Pook, Meera Nair, Kookhui Ryu, James C. Arpin, John Schiefelbein, Kathrin Schrick, Seth Debolt

Horticulture Faculty Publications

The biological function of sterol glucosides (SGs), the most abundant sterol derivatives in higher plants, remains uncertain. In an effort to improve our understanding of these membrane lipids we examined phenotypes exhibited by the roots of Arabidopsis (Arabidopsis thaliana) lines carrying insertions in the UDP-Glc:sterol glucosyltransferase genes, UGT80A2 and UGT80B1. We show that although ugt80A2 mutants exhibit significantly lower levels of total SGs they are morphologically indistinguishable from wild-type plants. In contrast, the roots of ugt80B1 mutants are only deficient in stigmasteryl glucosides but exhibit a significant reduction in root hairs. Sub-cellular investigations reveal that the plasma membrane …

Apple Tree Responses To Deficit Irrigation Combined With Periodic Applications Of Particle Film Or Abscisic Acid, Khalid M. Al-Absi, Douglas D. Archbold

Horticulture Faculty Publications

The objective of this study was to determine if the application of two antitranspirant compounds would moderate water deficit stress effects on physiological responses of “Granny Smith”, “Royal Gala” and “Golden Delicious” apple (Malus domestica Borkh.) trees on MM106 rootstock that occur during deficit irrigation. Uniform trees were grown in pots under water supply regimes of 30%, 60%, and 80% depletion of available water (DAW) before irrigation to runoff and received applications of kaolin particle film (PF) or abscisic acid (ABA) at 0, 30 and 60 days. At 120 days, genotype and deficit irrigation affected nearly all leaf traits, …

Combined Effects Of Fertilizer, Irrigation, And Paclobutrazol On Yield And Fruit Quality Of Mango, Babul C. Sarker, Mohammad A. Rahim, Douglas D. Archbold

Horticulture Faculty Publications

Combinations of fertilizer rates, foliar N sprays, irrigation practices, and paclobutrazol were studied to determine how much they could alter and/or improve mango (Mangifera indica L.) growth, flowering, and yield. Two treatment combinations derived from several years of prior studies of individual practices were compared: one combination was comprised of the best (BT) individual practices from the prior studies and included three applications of fertilizer, a 4% KNO₃ spray application before flowering, paclobutrazol at 7.5 g/L, and weekly irrigation, and the other combination was comprised of the next best (NB) individual practices including two applications of the same …

The Hiv-1 Tat Protein Is Monomethylated At Lysine 71 By The Lysine Methyltransferase Kmt7, Ibraheem Ali, Holly Ramage, Daniela Boehm, Lynnette M. A. Dirk, Naoki Sakane, Kazuki Hanada, Sara Pagans, Katrin Kaehlcke, Katherine Aull, Leor Weinberger, Raymond Trievel, Martina Schnoelzer, Masafumi Kamada, Robert L. Houtz, Melanie Ott

Horticulture Faculty Publications

The HIV-1 transactivator protein Tat is a critical regulator of HIV transcription primarily enabling efficient elongation of viral transcripts. Its interactions with RNA and various host factors are regulated by ordered, transient post-translational modifications. Here, we report a novel Tat modification, monomethylation at lysine 71 (K71). We found that Lys-71 monomethylation (K71me) is catalyzed by KMT7, a methyltransferase that also targets lysine 51 (K51) in Tat. Using mass spectrometry, in vitro enzymology, and modification-specific antibodies, we found that KMT7 monomethylates both Lys-71 and Lys-51 in Tat. K71me is important for full Tat transactivation, as KMT7 knockdown impaired the transcriptional activity …

[14C] Glucose Cell Wall Incorporation Assay For The Estimation Of Cellulose Biosynthesis, Chad Brabham, Jozsef Stork, Seth Debolt

Horticulture Faculty Publications

Cellulose is synthesized by Cellulose Synthase A proteins at the plasma membrane using the substrate UDP glucose. Herein, we provide a detailed method for measuring the incorporation of radiolabeled glucose into the cellulose fraction of the cell wall. In this method Arabidopsis seedlings are treated for 2 h with a cellulose biosynthesis inhibitor in the presence of radiolabeled glucose, and are subsequently boiled in acetic-nitric acid to solubilize non-cellulosic material. The radiolabeled glucose detected in the insoluble fraction indicates the amount of cellulose synthesized during the experimental timeframe. The short-term nature of this method is a useful tool in determining …

Prospecting For Energy-Rich Renewable Raw Materials: Agave Leaf Case Study, Kendall R. Corbin, Caitlin S. Byrt, Stefan Bauer, Seth Debolt, Don Chambers, Joseph A. M. Holtum, Ghazwan Karem, Marilyn Henderson, Jelle Lahnstein, Cherie T. Beahan, Antony Bacic, Geoffrey B. Fincher, Natalie S. Betts, Rachel A. Burton

Horticulture Faculty Publications

Plant biomass from different species is heterogeneous, and this diversity in composition can be mined to identify materials of value to fuel and chemical industries. Agave produces high yields of energy-rich biomass, and the sugar-rich stem tissue has traditionally been used to make alcoholic beverages. Here, the compositions of Agave americana and Agave tequilana leaves are determined, particularly in the context of bioethanol production. Agave leaf cell wall polysaccharide content was characterized by linkage analysis, non-cellulosic polysaccharides such as pectins were observed by immuno-microscopy, and leaf juice composition was determined by liquid chromatography. Agave leaves are fruit-like--rich in moisture, …