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Plant natural variation

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https://www.readbyqxmd.com/read/30310969/various-phyllosphere-and-soil-bacterial-communities-of-natural-grasses-and-the-impact-factors-in-a-copper-tailings-dam
#1
Tong Jia, Rui-Hong Wang, Bao-Feng Chai
Copper mining caused severe damage to the ecological environment of mining areas. The combination of microbe and plant remediation has an application potential in improving the absorption and transformation efficiency of heavy metals. The phyllosphere is the largest biointerface on the planet, and bacteria are the dominant microbial inhabitants of the phyllosphere, believed to be critical to plant growth and health. This study investigated the phyllospheric and soil bacteria communities using high-throughput sequencing, and endophyte infection statuses of four natural grasses by toluidine blue heparin assay...
October 11, 2018: Current Microbiology
https://www.readbyqxmd.com/read/30308821/antibiotics-in-a-typical-karst-river-system-in-china-spatiotemporal-variation-and-environmental-risks
#2
Fuyang Huang, Shengzhang Zou, Dongdong Deng, Hang Lang, Fei Liu
Karst aquifers are highly susceptible to contamination because compounds in water from the land surface are able to enter aquifers directly through sinkholes and travel rapidly through conduits. To investigate the occurrence and profiles of antibiotics in the typical karst river system in Kaiyang, southwest China, 34 aqueous samples were collected periodically to delineate seasonal trends in antibiotic levels. Thirty-five antibiotics, including nine sulfonamides, four tetracyclines, five macrolides, 16 quinolones and chloramphenicol, were analysed via solid phase extraction combined with ultra-performance liquid chromatography-tandem mass spectrometry...
February 10, 2019: Science of the Total Environment
https://www.readbyqxmd.com/read/30302260/the-usda-cucumber-cucumis-sativus-l-collection-genetic-diversity-population-structure-genome-wide-association-studies-and-core-collection-development
#3
Xin Wang, Kan Bao, Umesh K Reddy, Yang Bai, Sue A Hammar, Chen Jiao, Todd C Wehner, Axel O Ramírez-Madera, Yiqun Weng, Rebecca Grumet, Zhangjun Fei
Germplasm collections are a crucial resource to conserve natural genetic diversity and provide a source of novel traits essential for sustained crop improvement. Optimal collection, preservation and utilization of these materials depends upon knowledge of the genetic variation present within the collection. Here we use the high-throughput genotyping-by-sequencing (GBS) technology to characterize the United States National Plant Germplasm System (NPGS) collection of cucumber ( Cucumis sativus L.). The GBS data, derived from 1234 cucumber accessions, provided more than 23 K high-quality single-nucleotide polymorphisms (SNPs) that are well distributed at high density in the genome (~1 SNP/10...
2018: Horticulture Research
https://www.readbyqxmd.com/read/30302259/multiple-haploids-triploids-and-tetraploids-found-in-modern-day-living-fossil-ginkgo-biloba
#4
Petr Šmarda, Lucie Horová, Ondřej Knápek, Heidi Dieck, Martin Dieck, Katarína Ražná, Pavel Hrubík, Laszlo Orlóci, Laszlo Papp, Kristýna Veselá, Pavel Veselý, Petr Bureš
Ginkgo biloba , the last extant representative of a lineage of Mesozoic gymnosperms, is one of the few seed plants with an exceptionally long (~300 Myr) evolutionary history free of genome-wide duplications (polyploidy). Despite this genome conservatism, we have recently found a viable spontaneous tetraploid Ginkgo sapling during routine screening of several plants, demonstrating that natural polyploidy is possible in Ginkgo . Here we provide a much wider flow cytometry survey of ploidy in some European Ginkgo collections, and own seedlings (>2200 individuals and ~200 cultivars)...
2018: Horticulture Research
https://www.readbyqxmd.com/read/30291759/whole-genome-sequencing-reveals-rare-off-target-mutations-and-considerable-inherent-genetic-or-and-somaclonal-variations-in-crispr-cas9-edited-cotton-plants
#5
Jianying Li, Hakim Manghwar, Lin Sun, Pengcheng Wang, Guanying Wang, Hanyan Sheng, Jie Zhang, Hao Liu, Lei Qin, Hangping Rui, Bo Li, Keith Lindsey, Henry Daniell, Shuangxia Jin, Xianlong Zhang
The CRISPR/Cas9 system has been extensively applied for crop improvement. However, our understanding of Cas9 specificity is very limited in Cas9-edited plants. To identify on- and off-target mutation in an edited crop, we described whole genome sequencing (WGS) of 14 Cas9-edited cotton plants targeted to three genes, and 3 negative (Ne) control and 3 wild-type (WT) plants. In total, 4,188 - 6,404 unique single nucleotide polymorphisms (SNPs) and 312 - 745 insertions/deletions (indels) were detected in 14 Cas9-edited plants compared with WT, negative and cotton reference genome sequences...
October 6, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30290396/infraspecific-variation-of-huperzine-a-and-b-in-icelandic-huperzia-selago-complex
#6
Maonian Xu, Starri Heidmarsson, Margret Thorsteinsdottir, Pawel Wasowicz, Hang Sun, Tao Deng, Sesselja Omarsdottir, Elin Soffia Olafsdottir
The alkaloids huperzine A and huperzine B were originally isolated from the Chinese club moss Huperzia serrata . They are known inhibitors of acetylcholinesterase, and especially huperzine A shows pharmaceutical potential for the treatment of Alzheimer's disease. Its supply heavily relies on natural plant sources belonging to the genus Huperzia , which shows considerable interspecific huperzine A variations. Furthermore, taxonomic controversy remains in this genus, particularly in the Huperzia selago group...
October 5, 2018: Planta Medica
https://www.readbyqxmd.com/read/30289567/manipulating-host-resistance-structure-reveals-impact-of-pathogen-dispersal-and-environmental-heterogeneity-on-epidemics
#7
Rachel M Penczykowski, Steven R Parratt, Benoit Barrès, Suvi K Sallinen, Anna-Liisa Laine
Understanding how variation in hosts, parasites, and the environment shapes patterns of disease is key to predicting ecological and evolutionary outcomes of epidemics. Yet in spatially structured populations, variation in host resistance may be spatially confounded with variation in parasite dispersal and environmental factors that affect disease processes. To tease apart these disease drivers, we paired surveys of natural epidemics with experiments manipulating spatial variation in host susceptibility to infection...
October 5, 2018: Ecology
https://www.readbyqxmd.com/read/30289553/ethylene-signaling-regulates-natural-variation-in-the-abundance-of-antifungal-acetylated-diferuloylsucroses-and-fusarium-graminearum-resistance-in-maize-seedling-roots
#8
Shaoqun Zhou, Ying K Zhang, Karl A Kremling, Yezhang Ding, John S Bennett, Justin S Bae, Dean K Kim, Hayley H Ackerman, Michael V Kolomiets, Eric A Schmelz, Frank C Schroeder, Edward S Buckler, Georg Jander
The production and regulation of defensive specialized metabolites play a central role in pathogen resistance in maize (Zea mays) and other plants. Therefore, identification of genes involved in plant specialized metabolism can contribute to improved disease resistance. We used comparative metabolomics to identify previously unknown antifungal metabolites in maize seedling roots, and investigated the genetic and physiological mechanisms underlying their natural variation using quantitative trait locus (QTL) mapping and comparative transcriptomics approaches...
October 5, 2018: New Phytologist
https://www.readbyqxmd.com/read/30288820/transcriptional-effects-of-cadmium-on-iron-homeostasis-differ-in-calamine-accessions-of-noccaea-caerulescens
#9
Pauliina Halimaa, Daniel Blande, Erol Baltzi, Mark G M Aarts, Lars Granlund, Markku Keinänen, Sirpa Orvokki Kärenlampi, Anna D Kozhevnikova, Sirpa Peräniemi, Henk Schat, Ilya V Seregin, Marjo Tuomainen, Arja Irmeli Tervahauta
Calamine accessions of the zinc/cadmium/nickel hyperaccumulator, Noccaea caerulescens, exhibit striking variation in foliar cadmium accumulation in nature. The accession Ganges (GA) from Southern France displays foliar cadmium hyperaccumulation (> 1000 μg g-1 DW), whereas the accession La Calamine (LC) from Belgium, with similar local soil metal composition, does not (< 100 μg g-1 DW). All calamine accessions are cadmium-hypertolerant. To find out differences between LC and GA in their basic adaptation mechanisms, we bypassed the cadmium excluding phenotype of LC by exposing the plants to 50 μM cadmium in hydroponics, achieving equal cadmium accumulation in the shoots...
October 4, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30288705/natural-variation-in-freezing-tolerance-and-cold-acclimation-response-in-arabidopsis-thaliana-and-related-species
#10
Ellen Zuther, Yang Ping Lee, Alexander Erban, Joachim Kopka, Dirk K Hincha
During low-temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. The molecular mechanisms involved in cold acclimation have been mostly investigated in Arabidopsis thaliana. In addition, other Brassicaceae species related to A. thaliana have been employed in recent years to study plant stress responses on a phylogenetically broader basis and in some cases with extremophile species with a much higher stress tolerance. In this paper, we briefly summarize cold acclimation responses in A...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/30288701/gene-regulatory-networks-mediating-cold-acclimation-the-cbf-pathway
#11
Javier Barrero-Gil, Julio Salinas
Under low nonfreezing temperature conditions, plants from temperate climates undergo physiological and biochemical adjustments that increase their tolerance to freezing temperatures. This response, termed cold acclimation, is largely regulated by changes in gene expression. Molecular and genetic studies have identified a small family of transcription factors, called C-repeat binding factors (CBFs), as key regulators of the transcriptomic rearrangement that leads to cold acclimation. The function of these proteins is tightly controlled, and an inadequate supply of CBF activity may be detrimental to the plant...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/30287788/time-dependent-degradation-of-polyphenols-from-thermally-processed-berries-and-their-in-vitro-antiproliferative-effects-against-melanoma
#12
Zorița Diaconeasa
Polyphenols are natural occurring micronutrients that can protect plants from natural weathering and are also helpful to humans. These compounds are abundantly found in fruits or berries. Because of berry seasonal availability and also due to their rapid degradation, people have found multiple ways to preserve them. The most common options are freezing or making jams. Polyphenol stability, during processing is a continuous challenge for the food industry. There are also multiple published data providing that they are sensitive to light, pH or high temperature, vectors which are all present during jam preparation...
October 4, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/30282123/genome-wide-association-study-reveals-new-loci-involved-in-arabidopsis-thaliana-and-turnip-mosaic-virus-tumv-interactions-in-the-field
#13
Bernadette Rubio, Patrick Cosson, Mélodie Caballero, Frédéric Revers, Joy Bergelson, Fabrice Roux, Valérie Schurdi-Levraud
The genetic architecture of plant response to viruses has often been studied in model non-natural pathosystems under controlled conditions. There is an urgent need to elucidate the genetic architecture of the response to viruses in a natural setting. A field experiment was performed in each of two years. In total, 318 Arabidopsis thaliana accessions were inoculated with its natural Turnip mosaic virus (TuMV). The accessions were phenotyped for viral accumulation, frequency of infected plants, stem length and symptoms...
October 3, 2018: New Phytologist
https://www.readbyqxmd.com/read/30278089/trace-metals-organic-carbon-and-nutrients-in-the-beidagang-wetland-nature-reserve-northern-china
#14
Yueqin Chen, Qiuyang Song, Ling Pan, Meiqing Jia, Congwei Li, Beibei Hu, Guanghong Wu
This study aimed to determine sediment contamination in the Beidagang Wetland Nature Reserve to describe atmospheric deposition of trace metals. We analyzed Hg, Cd, Pb, TOC, TN, TP, δ13C, and δ15N, and studied their variations in surface sediments and in the vertical profiles of sediment cores collected from the reserve. Evaluation of environmental trace metal contamination using sediment quality guidelines and geochemical background values indicated that the risk of metal pollution in the reserve sediments was relatively low...
2018: PloS One
https://www.readbyqxmd.com/read/30270914/promoting-scientific-transparency-to-facilitate-the-safe-and-open-international-exchange-of-biological-materials-and-electronic-data
#15
Kenneth B Yeh, Corina Monagin, Jacqueline Fletcher
Scientific communication, collaboration and progress are enhanced through the exchange of data, materials and ideas. Recent advances in technology, commercial proprietary discovery and current local and global events (e.g., emerging human, animal and plant disease outbreaks) have increased the demand, and shortened optimal timelines for material and data exchange, both domestically and internationally. Specific circumstances in each case, such as the type of material being transferred (i.e., select agent, disease-causing agent and assessed biosafety risk level) and current events, dictate the level of agreements and requirements...
October 31, 2017: Tropical Medicine and Infectious Disease
https://www.readbyqxmd.com/read/30267789/modeling-reproduction-of-whitetail-deer-and-its-applications
#16
Dinesh B Ekanayake, Amy J Ekanayake, Jason Hunt, Catherine L Miller-Hunt
Many environmental factors, such as annual precipitation, temperature variations, and the embedded stochasticity of natural systems, affect resource availability from one region to the next, such that animal survival and reproduction rates differ by region. For species exhibiting phenotypic plasticity, embedding phenotypes in a model of population dynamics becomes important, as region-driven plastic responses play a significant role when estimating parameters values. In this paper, we discuss how to include observable characteristics and climate patterns in estimates of reproduction rates of whitetail deer (Odocoileus virginianus)...
September 26, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30266040/natural-allelic-variation-of-gvs1-confers-diversity-in-the-regulation-of-leaf-senescence-in-arabidopsis
#17
Jae Il Lyu, Jin Hee Kim, Hyosub Chu, Mark A Taylor, Sukjoon Jung, Seung Hee Baek, Hye Ryun Woo, Pyung Ok Lim, Jeongsik Kim
• Leaf senescence affects plant fitness. Plants that evolve in different environments are expected to acquire distinct regulations of leaf senescence. However, the adaptive and evolutionary roles of leaf senescence are largely unknown. • We investigated leaf senescence in 259 natural accessions of Arabidopsis by quantitatively assaying dark-induced senescence responses using a high-throughput chlorophyll fluorescence imaging system. A meta-analysis of our data with phenotypic and climatic information demonstrated biological and environmental links with leaf senescence...
September 28, 2018: New Phytologist
https://www.readbyqxmd.com/read/30265666/the-genetic-architecture-of-colonization-resistance-in-brachypodium-distachyon-to-non-adapted-stripe-rust-puccinia-striiformis-isolates
#18
Jan Bettgenhaeuser, Matthew Gardiner, Rebecca Spanner, Phon Green, Inmaculada Hernández-Pinzón, Amelia Hubbard, Michael Ayliffe, Matthew J Moscou
Multilayered defense responses ensure that plants are hosts to only a few adapted pathogens in the environment. The host range of a plant pathogen depends on its ability to fully overcome plant defense barriers, with failure at any single step sufficient to prevent life cycle completion of the pathogen. Puccinia striiformis, the causal agent of stripe rust (=yellow rust), is an agronomically important obligate biotrophic fungal pathogen of wheat and barley. It is generally unable to complete its life cycle on the non-adapted wild grass species Brachypodium distachyon, but natural variation exists for the degree of hyphal colonization by Puccinia striiformis...
September 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30258717/plant-dominance-in-a-subalpine-montane-meadow-biotic-vs-abiotic-controls-of-subordinate-diversity-within-and-across-sites
#19
Erika LaPlante, Lara Souza
Background: Understanding the underlying factors that determine the relative abundance of plant species is critical to predict both biodiversity and ecosystem function. Biotic and abiotic factors can shape the distribution and the relative abundance of species across natural communities, greatly influencing local biodiversity. Methods: Using a combination of an observational study and a five-year plant removal experiment we: (1) documented how plant diversity and composition of montane meadow assemblages vary along a plant dominance gradient using an observational study; (2) tracked above- and belowground functional traits of co-dominant plant species Potentilla and Festuca along a plant dominance gradient in an observational study; (3) determined whether plant species diversity and composition was directly influenced by commonly occurring species Potentilla and Festuca with the use of a randomized plot design, 5-year plant removal experiment (no removal control, Potentilla removed, Festuca removed, n  = 10)...
2018: PeerJ
https://www.readbyqxmd.com/read/30258092/evolution-and-functional-analysis-of-natural-resistance-associated-macrophage-proteins-nramps-from-theobroma-cacao-and-their-role-in-cadmium-accumulation
#20
Ihsan Ullah, Yirong Wang, David J Eide, Jim M Dunwell
The presence of the toxic metal cadmium (Cd2+ ) in certain foodstuffs is recognised as a global problem, and there is increasing legislative pressure to reduce the content of Cd in food. The present study was conducted on cacao (Theobroma cacao), the source of chocolate, and one of the crops known to accumulate Cd in certain conditions. There are a range of possible genetic and agronomic methods being tested as a route to such reduction. As part of a gene-based approach, we focused on the Natural Resistance-Associated Macrophage Proteins (NRAMPS), a family of proton/metal transporter proteins that are evolutionarily conserved across all species from bacteria to humans...
September 26, 2018: Scientific Reports
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