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Plant association mapping

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https://www.readbyqxmd.com/read/29792207/metagenomic-analysis-of-viruses-associated-with-maize-lethal-necrosis-in-kenya
#1
Mwathi Jane Wamaitha, Deepti Nigam, Solomon Maina, Francesca Stomeo, Anne Wangai, Joyce Njoki Njuguna, Timothy A Holton, Bramwel W Wanjala, Mark Wamalwa, Tanui Lucas, Appolinaire Djikeng, Hernan Garcia-Ruiz
BACKGROUND: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA...
May 23, 2018: Virology Journal
https://www.readbyqxmd.com/read/29789386/antagonistic-interactions-between-two-map-kinase-cascades-in-plant-development-and-immune-signaling
#2
Tongjun Sun, Yukino Nitta, Qian Zhang, Di Wu, Hainan Tian, Jin Suk Lee, Yuelin Zhang
Mitogen-activated protein kinase (MAPK) signaling plays important roles in diverse biological processes. In Arabidopsis , MPK3/MPK6, MKK4/MKK5, and the MAPKKK YODA (YDA) form a MAPK pathway that negatively regulates stomatal development. Brassinosteroid (BR) stimulates this pathway to inhibit stomata production. In addition, MPK3/MPK6 and MKK4/MKK5 also serve as critical signaling components in plant immunity. Here, we report that MAPKKK3/MAPKKK5 form a kinase cascade with MKK4/MKK5 and MPK3/MPK6 to transduce defense signals downstream of multiple plant receptor kinases...
May 22, 2018: EMBO Reports
https://www.readbyqxmd.com/read/29788417/poor-feed-efficiency-in-sheep-is-associated-with-several-structural-abnormalities-in-the-community-metabolic-network-of-their-ruminal-microbes
#3
Rocky D Patil, Melinda J Ellison, Sara M Wolff, Courtney Shearer, Anna M Wright, Rebecca R Cockrum, Kathy J Austin, William R Lamberson, Kristi M Cammack, Gavin C Conant
Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not...
May 18, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29783940/small-rna-based-prediction-of-hybrid-performance-in-maize
#4
Felix Seifert, Alexander Thiemann, Tobias A Schrag, Dominika Rybka, Albrecht E Melchinger, Matthias Frisch, Stefan Scholten
BACKGROUND: Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analyze the relation of parental sRNA expression with the performance of their hybrids, to develop a sRNA-based prediction approach, and to compare it to more common SNP and mRNA transcript based predictions using a factorial mating scheme of a maize hybrid breeding program...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29775784/genome-wide-association-mapping-of-virulence-gene-in-rice-blast-fungus-magnaporthe-oryzae-using-a-genotyping-by-sequencing-approach
#5
Siripar Korinsak, Sithichoke Tangphatsornruang, Wirulda Pootakham, Samart Wanchana, Anucha Plabpla, Chatchawan Jantasuriyarat, Sujin Patarapuwadol, Apichart Vanavichit, Theerayut Toojinda
Magnaporthe oryzae is a fungal pathogen causing blast disease in many plant species. In this study, Seventy three isolates of M. oryzae collected from rice (Oryza sativa) in 1996-2014 were genotyped using a genotyping-by-sequencing approach to detect genetic variation. Association study was performed to identify single nucleotide polymorphism (SNP) associated with virulence genes using 831 selected SNP and infection phenotypes on local and improved rice varieties. Population structure analysis revealed eight subpopulations...
May 15, 2018: Genomics
https://www.readbyqxmd.com/read/29771278/a-pelota-like-gene-regulates-root-development-and-defence-responses-in-rice
#6
Wona Ding, Jing Wu, Jin Ye, Wenjuan Zheng, Shanshan Wang, Xinni Zhu, Jiaqin Zhou, Zhichong Pan, Botao Zhang, Shihua Zhu
Background and Aims: Pelota (Pelo) are evolutionarily conserved genes reported to be involved in ribosome rescue, cell cycle control and meiotic cell division. However, there is little known about their function in plants. The aim of this study was to elucidate the function of an ethylmethane sulphonate (EMS)-derived mutation of a Pelo-like gene in rice (named Ospelo). Methods: A dysfunctional mutant was used to characterize the function of OsPelo. Analyses of its expression and sub-cellular localization were performed...
May 16, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29767279/identification-and-validation-of-qtl-for-grain-yield-and-plant-water-status-under-contrasting-water-treatments-in-fall-sown-spring-wheats
#7
Junli Zhang, Shiferaw Abate Gizaw, Eligio Bossolini, Joshua Hegarty, Tyson Howell, Arron H Carter, Eduard Akhunov, Jorge Dubcovsky
Chromosome regions affecting grain yield, grain yield components and plant water status were identified and validated in fall-sown spring wheats grown under full and limited irrigation. Increases in wheat production are required to feed a growing human population. To understand the genetic basis of grain yield in fall-sown spring wheats, we performed a genome-wide association study (GWAS) including 262 photoperiod-insensitive spring wheat accessions grown under full and limited irrigation treatments. Analysis of molecular variance showed that 4...
May 16, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29761498/storage-lipid-accumulation-is-controlled-by-photoperiodic-signal-acting-via-regulators-of-growth-cessation-and-dormancy-in-hybrid-aspen
#8
Åsa Grimberg, Ida Lager, Nathaniel R Street, Kathryn M Robinson, Salla Marttila, Niklas Mähler, Pär K Ingvarsson, Rishikesh P Bhalerao
The signalling pathways that control seasonal modulation of carbon metabolism in perennial plants are poorly understood. Using genetic, metabolic and natural variation approaches, we identify factors mediating photoperiodic control of storage lipid accumulation in the model tree hybrid aspen (Populus tremula × tremuloides). We characterized lipid accumulation in transgenic hybrid aspen with impaired photoperiodic and hormonal responses. Genome-wide association mapping was performed in Swedish aspen (P. tremula) genotypes to determine genetic loci associated with genotype variation in lipid content...
May 15, 2018: New Phytologist
https://www.readbyqxmd.com/read/29754326/acid-phosphatase-gene-gmhad1-linked-to-low-phosphorus-tolerance-in-soybean-through-fine-mapping
#9
Zhandong Cai, Yanbo Cheng, Peiqi Xian, Qibin Ma, Ke Wen, Qiuju Xia, Gengyun Zhang, Hai Nian
Map-based cloning identified GmHAD1, a gene which encodes a HAD-like acid phosphatase, associated with soybean tolerance to low phosphorus stress. Phosphorus (P) deficiency in soils is a major limiting factor for crop growth worldwide. Plants may adapt to low phosphorus (LP) conditions via changes to root morphology, including the number, length, orientation, and branching of the principal root classes. To elucidate the genetic mechanisms for LP tolerance in soybean, quantitative trait loci (QTL) related to root morphology responses to LP were identified via hydroponic experiments...
May 12, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29754093/evaluation-of-vehicular-pollution-using-the-trad-mcn-mutagenic-bioassay-with-tradescantia-pallida-commelinaceae
#10
Aline do Nascimento Rocha, Liliam Silvia Candido, Joelson Gonçalves Pereira, Caio Augusto Mussury Silva, Sandra Verza da Silva, Rosilda Mara Mussury
Biomonitoring is one of the tools used to assess the mutagenic potential of the atmosphere. In this study, the mutagenicity of Tradescantia pallida, a species of plant largely present in urban environments, was investigated. The objectives of this study was to estimate the mutagenic potential of vehicular flow through the TRAD-MCN bioassay in cities located at different altitudes in the southwest mesoregion of Mato Grosso do Sul, Brazil, to infer possible abiotic agents that may contribute to the effects of atmospheric pollutants, and finally to map the cities with greater risks to the health of the local population...
May 9, 2018: Environmental Pollution
https://www.readbyqxmd.com/read/29751173/a-systemic-ecological-risk-assessment-based-on-spatial-distribution-and-source-apportionment-in-the-abandoned-lead-acid-battery-plant-zone-china
#11
Yimei Zhang, Shuai Li, Zhuang Chen, Fei Wang, Jie Chen, Liqun Wang
In China, potential heavy metal hazard around abandoned lead-acid battery plant (ALBP) area has been a great concern but without detailed report. The distribution and sources of heavy metals in soils and so by risk assessment associated with ALBP are conducted in this contribution, based on geographies and statistics. Pb and Zn are quantitively identified to be still emitted from ALBP soil, and Cd as well As are from agricultural activity. We investigate vertical metal distribution, and fortunately find that metals migrate within limit of 40 cm below topsoil, which is higher than groundwater table...
April 23, 2018: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/29750477/apple-fruit-acidity-is-genetically-diversified-by-natural-variations-in-three-hierarchical-epistatic-genes-mdsaur37-mdpp2ch-and-mdalmtii
#12
Dongjie Jia, Fei Shen, Yi Wang, Ting Wu, Xuefeng Xu, Xinzhong Zhang, Zhenhai Han
Many efforts have been made to map quantitative trait loci (QTLs) to facilitate practical marker-assisted selection (MAS) in plants. In the present study, we identified four genome-wide major QTLs responsible for apple fruit acidity by MapQTL and BSA-seq analyses using two independent pedigree-based populations. Candidate genes were screened in major QTL regions, and three functional gene markers, including a non-synonymous A/G single nucleotide polymorphism (SNP) in the coding region of MdPP2CH, a 36-bp insertion in the promoter of MdSAUR37, and a previously reported SNP in MdALMTII, were validated to influence the malate content of apple fruits...
May 11, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29747401/the-dna-methylome-and-association-of-differentially-methylated-regions-with-differential-gene-expression-during-heat-stress-in-brassica-rapa
#13
Gaofeng Liu, Yudong Xia, Tongkun Liu, Shaojun Dai, Xilin Hou
Cytosine DNA methylation is a critical epigenetic mechanism in the silencing of transposable elements, imprinting and regulating gene expression. However, little is known about the potential role of mC in response to heat stress. To determine and explore the functions of the dynamic DNA methylome during heat stress, we characterized single-base resolution methylome maps of Brassica rapa and assessed the dynamic changes of mC under heat stress using whole genome bisulfite sequencing. On average, the DNA methylation levels of CG, CHG and CHH are 39...
May 9, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29744525/mapping-of-a-dominant-rust-resistance-gene-revealed-two-r-genes-around-the-major-rust_qtl-in-cultivated-peanut-arachis-hypogaea-l
#14
Suvendu Mondal, Anand M Badigannavar
A consensus rust QTL was identified within a 1.25 cM map interval of A03 chromosome in cultivated peanut. This map interval contains a TIR-NB-LRR R gene and four pathogenesis-related genes. Disease resistance in plants is manifested due to the specific interaction between the R gene product and its cognate avirulence gene product (AVR) in the pathogen. Puccinia arachidis Speg. causes rust disease and inflicts economic damages to peanut. Till now, no experimental evidence is known for the action of R gene in peanut for rust resistance...
May 9, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29740461/genome-wide-association-mapping-of-seedling-and-adult-plant-resistance-to-barley-stripe-rust-puccinia-striiformis-f-sp-hordei-in-india
#15
Andrea Visioni, Sanjaya Gyawali, Rajan Selvakumar, Om P Gangwar, Pradeep S Shekhawat, Subhash C Bhardwaj, Ayed M Al-Abdallat, Zakaria Kehel, Ramesh P S Verma
Barley stripe rust is caused by Puccinia striiformis f.sp. hordei , (Psh), occurs worldwide, and is a major disease in South Asia. The aim of this work was to identify and estimate effects of loci underlying quantitative resistance to rust at seedling and adult plant stages. HI-AM panel of 261 barley genotypes consisting of released cultivars from North and South America, Europe, Australia, advanced breeding lines, and local landraces from ICARDA barley program were screened at seedling and adult plant stages for resistance to Psh...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29736624/leaf-lipidome-and-transcriptome-profiling-of-portulaca-oleracea-characterization-of-lysophosphatidylcholine-acyltransferase
#16
Varadarajan Venkateshwari, Anitha Vijayakumar, Arun Kumar Vijayakumar, L Prasanna Anjaneya Reddy, Malathi Srinivasan, Ram Rajasekharan
Portulaca leaves serve as an alternative bioresource for edible PUFAs. Transcriptome data provide information to explore Portulaca as a model system for galactolipids, leaf lipid metabolism, and PUFA-rich designer lipids. Poly-unsaturated fatty acids (PUFAs) are gaining importance due to their innumerable health benefits, and hence, understanding their biosynthesis in plants has attained prominence in recent years. The most common source of PUFAs is of marine origin. Although reports have identified Portulaca oleracea (purslane) as a leaf source of omega-3 fatty acids in the form of alpha-linolenic acid (ALA), the mechanism of ALA accumulation and its distribution into various lipids has not been elucidated...
May 7, 2018: Planta
https://www.readbyqxmd.com/read/29729397/seuss-and-pif4-coordinately-regulate-light-and-temperature-signaling-pathways-to-control-plant-growth
#17
Junling Huai, Xinyu Zhang, Jialong Li, Tingting Ma, Ping Zha, Yanjun Jing, Rongcheng Lin
Plants continuously monitor environmental conditions (such as light and temperature) and adjust their growth and development accordingly. The transcription factor PHYTOCHROME-INTERACTING FACTOR4 (PIF4) regulates both light and temperature signaling pathways. Here, we identified ENHANCED PHOTOMORPHOGENIC2 (EPP2) as a new repressor of photomorphogenesis in red, far-red, and blue light. Map-based cloning revealed that EPP2 encodes the SEUSS (SEU) transcription regulator. The C-terminus of SEU has transcriptional activation activity and SEU physically interacts with PIF4...
May 2, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29729219/finding-invisible-quantitative-trait-loci-with-missing-data
#18
Iulian Gabur, Harmeet Singh Chawla, Xiwei Liu, Vinod Kumar, Sébastien Faure, Andreas von Tiedemann, Christophe Jestin, Emmanuelle Dryzska, Susann Volkmann, Frank Breuer, Régine Delourme, Rod Snowdon, Christian Obermeier
Evolutionary processes during plant polyploidisation and speciation have led to extensive presence-absence variation (PAV) in crop genomes, and there is increasing evidence that PAV associates with important traits. Today, high-resolution genetic analysis in major crops frequently implements simple, cost-effective, high-throughput genotyping from single nucleotide polymorphism (SNP) hybridization arrays, however these are normally not designed to distinguish PAV from failed SNP calls caused by hybridization artefacts...
May 5, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29728606/structure-and-mechanism-of-the-two-component-%C3%AE-helical-pore-forming-toxin-yaxab
#19
Bastian Bräuning, Eva Bertosin, Florian Praetorius, Christian Ihling, Alexandra Schatt, Agnes Adler, Klaus Richter, Andrea Sinz, Hendrik Dietz, Michael Groll
Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures. YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the molecular basis for its two-component lytic mechanism remains elusive. Here, we present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy map of the YaxAB complex...
May 4, 2018: Nature Communications
https://www.readbyqxmd.com/read/29723916/genome-wide-association-analyses-of-plant-growth-traits-during-the-stem-elongation-phase-in-wheat
#20
Zifeng Guo, Guozheng Liu, Marion S Röder, Jochen C Reif, Martin W Ganal, Thorsten Schnurbusch
One of the primary objectives of wheat breeding is to increase grain yield. Floral abortion during the stem elongation phase (SEP) leads to a loss of more than 50% of the grain number potential. In this study, we quantified 75 plant growth-associated traits at seven stages during the SEP, and mapped 15,696 single nucleotide polymorphism (SNP) markers in 210 accessions of wheat (Triticum aestivum). Our genome-wide association study identified trait-associated SNPs that are shared among various stages of the SEP, as well as SNPs that are shared between plant growth traits and grain yield in the field...
May 3, 2018: Plant Biotechnology Journal
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