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Plant association mapping

Chaoyun Hao, Zhiqiang Xia, Rui Fan, Lehe Tan, Lisong Hu, Baoduo Wu, Huasong Wu
BACKGROUND: Piper nigrum L., or "black pepper", is an economically important spice crop in tropical regions. Black pepper production is markedly affected by foot rot disease caused by Phytophthora capsici, and genetic improvement of black pepper is essential for combating foot rot diseases. However, little is known about the mechanism of anti- P. capsici in black pepper. The molecular mechanisms underlying foot rot susceptibility were studied by comparing transcriptome analysis between resistant (Piper flaviflorum) and susceptible (Piper nigrum cv...
October 21, 2016: BMC Genomics
Stacy L DeBlasio, Richard S Johnson, Michael J MacCoss, Stewart M Gray, Michelle Cilia
Phloem localization of plant viruses is advantageous for acquisition by sap-sucking vectors but hampers host-virus protein interaction studies. In this study, Potato leafroll virus (PLRV)-host protein complexes were isolated from systemically infected potato, a natural host of the virus. Comparing two different co-immunoprecipitation support matrices coupled to mass spectrometry, we identified 44 potato proteins and one viral protein (P1) specifically associated with virus isolated from infected phloem. An additional 142 proteins interact in complex with virus at varying degrees of confidence...
October 20, 2016: Journal of Proteome Research
Nashmiah Aid Alrashedy, Jeanmaire Molina
Psychoactive plants contain chemicals that presumably evolved as allelochemicals but target certain neuronal receptors when consumed by humans, altering perception, emotion and cognition. These plants have been used since ancient times as medicines and in the context of religious rituals for their various psychoactive effects (e.g., as hallucinogens, stimulants, sedatives). The ubiquity of psychoactive plants in various cultures motivates investigation of the commonalities among these plants, in which a phylogenetic framework may be insightful...
2016: PeerJ
Si Wu, Saleh Alseekh, Álvaro Cuadros-Inostroza, Corina M Fusari, Marek Mutwil, Rik Kooke, Joost B Keurentjes, Alisdair R Fernie, Lothar Willmitzer, Yariv Brotman
Plant primary metabolism is a highly coordinated, central, and complex network of biochemical processes regulated at both the genetic and post-translational levels. The genetic basis of this network can be explored by analyzing the metabolic composition of genetically diverse genotypes in a given plant species. Here, we report an integrative strategy combining quantitative genetic mapping and metabolite‒transcript correlation networks to identify functional associations between genes and primary metabolites in Arabidopsis thaliana...
October 2016: PLoS Genetics
Jin S Xiong, Steven E McKeand, Fikret Isik, Jill Wegrzyn, David B Neale, Zhao-Bang Zeng, Luciano da Costa E Silva, Ross W Whetten
BACKGROUND: The use of wood as an industrial raw material has led to development of plantation forestry, in which trees are planted, managed, and harvested as crops. The productivity of such plantations often exceeds that of less-intensively-managed forests, and land managers have the option of choosing specific planting stock to produce specific types of wood for industrial use. Stem forking, or division of the stem into two or more stems of roughly equal size, is a character trait important in determining the quality of the stem for production of solid wood products...
October 18, 2016: BMC Genetics
V Paunovic, M Kosic, S Djordjevic, A Zugic, N Djalinac, U Gasic, V Trajkovic, J Harhaji-Trajkovic
Marrubium vulgare is a European medicinal plant with numerous beneficial effects on human health. The aim of the study was to isolate the plant ethanolic extract (MVE) and to investigate its anti-melanoma and anti-glioma effects. MVE was prepared by the modified pharmacopoeial percolation method and characterized by UHPLC-LTQ OrbiTrap MS. MVE dose-dependently reduced viability of melanoma (B16) and glioma (U251) cells, but not peripheral blood mononuclear cells. It arrested cell cycle in S+G2/M phase, which was associated with the activation of MAP kinase p38 and up-regulation of antiproliferative genes p53, p21 and p27...
September 30, 2016: Cellular and Molecular Biology
Maria J Santos, Shruti Khanna, Erin L Hestir, Jonathan A Greenberg, Susan L Ustin
Processes of spread and patterns of persistence of invasive species affect species and communities in the new environment. Predicting future rates of spread is of great interest for timely management decisions, but this depends on models that rely on understanding the processes of invasion and historic observations of spread and persistence. Unfortunately, the rates of spread and patterns of persistence are difficult to model or directly observe, especially when multiple rates of spread and diverse persistence patterns may be co-occurring over the geographic distribution of the invaded ecosystem...
September 2016: Ecological Applications: a Publication of the Ecological Society of America
Bastian Minkenberg, Kabin Xie, Yinong Yang
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 nuclease (Cas9) system depends on a guide RNA (gRNA) to specify its target. By efficiently co-expressing multiple gRNAs that target different genomic sites, the polycistronic tRNA-gRNA gene (PTG) strategy enables multiplex gene editing in the family of closely related rice mitogen-activated protein kinase (MPK) genes. In this study, we identified MPK1 and MPK6 (Arabidopsis AtMPK6 and AtMPK4 orthologues, respectively) as essential genes for rice development by finding the preservation of MPK functional alleles and normal phenotypes in CRISPR-edited mutants...
October 16, 2016: Plant Journal: for Cell and Molecular Biology
Christiane Gebhardt
This article evaluates the main contributions of tomato, tobacco, petunia, potato, pepper and eggplant to classical and molecular plant genetics and genomics since the beginning of the twentieth century. Species from the Solanaceae family form integral parts of human civilizations as food sources and drugs since thousands of years, and, more recently, as ornamentals. Some Solanaceous species were subjects of classical and molecular genetic research over the last 100 years. The tomato was one of the principal models in twentieth century classical genetics and a pacemaker of genome analysis in plants including molecular linkage maps, positional cloning of disease resistance genes and quantitative trait loci (QTL)...
October 15, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Max E Kraner, Katrin Link, Michael Melzer, Arif B Ekici, Steffen Uebe, Pablo Tarazona, Ivo Feussner, Jörg Hofmann, Uwe Sonnewald
Plasmodesmata (PD) are microscopic pores connecting plant cells and enable cell-to-cell transport. Currently, little is known about the molecular mechanisms regulating PD formation and development. To uncover components of PD development we made use of the 17 kDa movement protein (MP17) encoded by the Potato leafroll virus (PLRV). The protein is required for cell-to-cell movement of the virus and localises to complex PD. Forward genetic screening for Arabidopsis mutants with altered PD-binding of MP17 revealed several mutant lines, while molecular genetics, biochemical and microscopic studies allowed further characterisation...
October 15, 2016: Plant Journal: for Cell and Molecular Biology
Cheng-Yu Hou, Wen-Chi Lee, Hsiao-Chun Chou, Ai-Ping Chen, Shu-Jen Chou, Ho-Ming Chen
High-throughput approaches for profiling the 5' ends of RNA degradation intermediates on a genome-wide scale are frequently applied to analyze and validate cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome other than miRNA targets is currently largely uncharacterized, and this limits the application of RNA degradome studies. We conducted a global analysis of 5'-truncated mRNA ends that mapped to coding sequences (CDSs) of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and soybean (Glycine max)...
October 14, 2016: Plant Cell
Jiafa Chen, Rosemary Shrestha, Junqiang Ding, Hongjian Zheng, Chunhua Mu, Jianyu Wu, George Mahuku
Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance...
October 14, 2016: G3: Genes—Genomes—Genetics
Jingyin Yu, Komivi Dossa, Linhai Wang, Yanxin Zhang, Xin Wei, Boshou Liao, Xiurong Zhang
Microsatellite DNAs (or SSRs) are important genomic components involved in many important biological functions. SSRs have been extensively exploited as molecular markers for diverse applications including genetic diversity, linkage/association mapping of gene/QTL, marker-assisted selection, variety identification and evolution analysis. However, a comprehensive database or web service for studying microsatellite DNAs and marker development in plants is lacking. Here, we developed a database, PMDBase, which integrates large amounts of microsatellite DNAs from genome sequenced plant species and includes a web service for microsatellite DNAs identification...
October 12, 2016: Nucleic Acids Research
Weiwei Li, Ming Chen, Erhui Wang, Liqin Hu, Malcolm J Hawkesford, Li Zhong, Zhu Chen, Zhaoshi Xu, Liancheng Li, Yongbin Zhou, Changhong Guo, Youzhi Ma
BACKGROUND: Autophagy is a cellular degradation process that is highly evolutionarily-conserved in yeast, plants, and animals. In plants, autophagy plays important roles in regulating intracellular degradation and recycling of amino acids in response to nutrient starvation, senescence, and other environmental stresses. Foxtail millet (Setaria italica) has strong resistance to stresses and has been proposed as an ideal material for use in the study of the physiological mechanisms of abiotic stress tolerance in plants...
October 12, 2016: BMC Genomics
Takahiro Hamada, Seiji Sonobe
Microtubules are essential cellular structures in plant cells. They are polymerized from tubulin dimers and are regulated by microtubule-associated proteins (MAPs). Here, we describe a protocol for purifying tubulin dimers and MAPs from plant cells. The protocol involves preparing vacuole-free mini-protoplasts, a high quality cytoplasmic extract, cycles of microtubule polymerization and depolymerization to increase tubulin and MAP concentration, separation of tubulin and MAPs by column chromatography. We also present tubulin purification methods for biochemical assays...
2017: Methods in Molecular Biology
Pieter Clauw, Frederik Coppens, Arthur Korte, Dorota Herman, Bram Slabbinck, Stijn Dhondt, Twiggy Van Daele, Liesbeth De Milde, Mattias Vermeersch, Katrien Maleux, Steven Maere, Nathalie Gonzalez, Dirk Inzé
Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under non-lethal drought conditions is lacking. Recent advances in genomics, phenomics and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of Arabidopsis thaliana accessions. The genetic architecture of the growth responses upon mild drought was investigated by subjecting the different leaf growth phenotypes to genome-wide association mapping and by characterizing the transcriptome of young developing leaves...
October 11, 2016: Plant Cell
Longxin Wang, Bowen Wang, Qingzhang Du, Jinhui Chen, Jiaxing Tian, Xiaohui Yang, Deqiang Zhang
Photosynthesis is one of the most important reactions on earth. PsbW, a nuclear-encoded subunit of photosystem II (PSII), stabilizes PSII structure and plays an important role in photosynthesis. Here, we used candidate gene-based linkage disequilibrium (LD) mapping to detect significant associations between allelic variations of PtoPsbW and traits related to photosynthesis, growth, and wood properties in Populus tomentosa. PtoPsbW showed the highest expression in leaves and it increased during the development of these leaves, suggesting that PtoPsbW may play an important role in plant growth and development...
October 8, 2016: Molecular Genetics and Genomics: MGG
Vikas Belamkar, Andrew D Farmer, Nathan T Weeks, Scott R Kalberer, William J Blackmon, Steven B Cannon
For species with potential as new crops, rapid improvement may be facilitated by new genomic methods. Apios (Apios americana Medik.), once a staple food source of Native American Indians, produces protein-rich tubers, tolerates a wide range of soils, and symbiotically fixes nitrogen. We report the first high-quality de novo transcriptome assembly, an expression atlas, and a set of 58,154 SNP and 39,609 gene expression markers (GEMs) for characterization of a breeding collection. Both SNPs and GEMs identify six genotypic clusters in the collection...
October 10, 2016: Scientific Reports
Hafiz Mamoon Rehman, Muhammad Amjad Nawaz, Le Bao, Zahid Hussain Shah, Jae-Min Lee, Muhammad Qadir Ahmad, Gyuhwa Chung, Seung Hwan Yang
Family-1 UDP-glycosyltransferases (EC 2.4.1.x; UGTs) are enzymes that glycosylate aglycones into glycoside-associated compounds with improved transport and water solubility. This glycosylation mechanism is vital to plant functions, such as regulation of hormonal homeostasis, growth and development, xenobiotic detoxification, stress response, and biosynthesis of secondary metabolites. Here, we report a genome-wide analysis of soybean that identified 149 putative UGTs based on 44 conserved plant secondary product glycosyl-transferase (PSPG) motif amino acid sequences...
September 22, 2016: Journal of Plant Physiology
Petr Smýkal, Rajeev K Varshney, Vikas K Singh, Clarice J Coyne, Claire Domoney, Eduard Kejnovský, Thomas Warkentin
This work discusses several selected topics of plant genetics and breeding in relation to the 150th anniversary of the seminal work of Gregor Johann Mendel. In 2015, we celebrated the 150th anniversary of the presentation of the seminal work of Gregor Johann Mendel. While Darwin's theory of evolution was based on differential survival and differential reproductive success, Mendel's theory of heredity relies on equality and stability throughout all stages of the life cycle. Darwin's concepts were continuous variation and "soft" heredity; Mendel espoused discontinuous variation and "hard" heredity...
October 7, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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