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https://www.readbyqxmd.com/read/28647896/omics-based-hybrid-prediction-in-maize
#1
Matthias Westhues, Tobias A Schrag, Claas Heuer, Georg Thaller, H Friedrich Utz, Wolfgang Schipprack, Alexander Thiemann, Felix Seifert, Anita Ehret, Armin Schlereth, Mark Stitt, Zoran Nikoloski, Lothar Willmitzer, Chris C Schön, Stefan Scholten, Albrecht E Melchinger
Complementing genomic data with other "omics" predictors can increase the probability of success for predicting the best hybrid combinations using complex agronomic traits. Accurate prediction of traits with complex genetic architecture is crucial for selecting superior candidates in animal and plant breeding and for guiding decisions in personalized medicine. Whole-genome prediction has revolutionized these areas but has inherent limitations in incorporating intricate epistatic interactions. Downstream "omics" data are expected to integrate interactions within and between different biological strata and provide the opportunity to improve trait prediction...
June 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28645873/generation-of-nitric-oxide-by-olive-olea-europaea-l-pollen-during-in-vitro-germination-and-assessment-of-the-s-nitroso-and-nitro-pollen-proteomes-by-computational-predictive-methods
#2
María José Jimenez-Quesada, Rosario Carmona, Elena Lima-Cabello, José Ángel Traverso, Antonio Jesús Castro, M Gonzalo Claros, Juan de Dios Alché
Nitric oxide is recognized as a signaling molecule involved in a broad range of physiological processes in plants including sexual reproduction. NO has been detected in the pollen grain at high levels and regulates pollen tube growth. Previous studies demonstrated that NO as well as ROS are produced in the olive reproductive tissues in a stage- and tissue-specific manner. The aim of this study was to assess the production of NO throughout the germination of olive (Olea europaea L.) pollen in vitro. The NO fluorescent probe DAF-2DA was used to image NO production in situ, which was correlated to pollen viability...
June 20, 2017: Nitric Oxide: Biology and Chemistry
https://www.readbyqxmd.com/read/28645245/transcriptomic-dynamics-in-soybean-near-isogenic-lines-differing-in-alleles-for-an-aphid-resistance-gene-following-infestation-by-soybean-aphid-biotype-2
#3
Sungwoo Lee, Bryan J Cassone, Asela Wijeratne, Tae-Hwan Jun, Andrew P Michel, M A Rouf Mian
BACKGROUND: Genetic resistance of soybean [Glycine max (L.) Merr] against Aphis glycines provides effective management of this invasive pest, though the underlying molecular mechanisms are largely unknown. This study aimed to investigate genome-wide changes in gene expressions of soybean near-isogenic lines (NILs) either with the Rag5 allele for resistance or the rag5 allele for susceptibility to the aphid following infestation with soybean aphid biotype 2. RESULTS: The resistant (R)-NIL responded more rapidly to aphid infestation than the susceptible (S)-NIL, with differential expressions of 2496 genes during first 12 h of infestation (hai), compared to the aphid-free control...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28645179/system-wide-analysis-of-short-term-response-to-high-temperature-in-pinus-radiata
#4
Mónica Escandón, Luis Valledor, Jesús Pascual, Gloria Pinto, María Jesús Cañal, Mónica Meijón
Pinus radiata seedlings, the most widely planted pine species in the world, were exposed to temperatures within a range mimicking future scenarios based on current models of heat increase. The short-term heat response in P. radiata was studied in detail by exploring the metabolome, proteome and targeted transcriptome. The use of complementary mass spectrometry techniques, GC-MS and LC-Orbitrap-MS, together with novel bioinformatics tools allowed the reliable quantification of 2,075 metabolites and 901 protein groups...
June 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28644561/the-redox-sensitive-module-of-cyclophilin-20-3-2-cysteine-peroxiredoxin-and-cysteine-synthase-integrates-sulfur-metabolism-and-oxylipin-signaling-in-the-high-light-acclimation-response
#5
Sara M Müller, Shanshan Wang, Wilena Telman, Michael Liebthal, Helena Schnitzer, Andrea Viehhauser, Carsten Sticht, Carolina Delatorre, Markus Wirtz, Rüdiger Hell, Karl-Josef Dietz
The integration of redox- and reactive oxygen species-dependent signaling and metabolic activities are fundamental to plant acclimation to biotic and abiotic stresses. Previous data suggest the existence of a dynamically interacting module in the chloroplast stroma consisting of cyclophilin 20-3 (Cyp20-3), O-acetylserine(thiol)lyase B (OASTL-B), 2-cysteine peroxiredoxins A/B (2-CysPrx) and serine acetyltransferase 2;1 (SERAT2;1). The functionality of this COPS module is influenced by redox stimuli and oxophytodienoic acid (OPDA) which is the precursor for jasmonic acid...
June 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28642777/transcriptome-analysis-of-genes-associated-with-the-artemisinin-biosynthesis-by-jasmonic-acid-treatment-under-the-light-in-artemisia-annua
#6
Xiaolong Hao, Yijun Zhong, Xueqing Fu, Zongyou Lv, Qian Shen, Tingxiang Yan, Pu Shi, Yanan Ma, Minghui Chen, Xueying Lv, Zhangkuanyu Wu, Jingya Zhao, Xiaofen Sun, Ling Li, Kexuan Tang
Artemisinin is a sesquiterpene lactone endoperoxide extracted from a traditional Chinese medicinal plant Artemisia annua. Artemisinin-based combination therapies (ACTs) are recommended as the best treatment of malaria by the World Health Organization (WHO). Both the phytohormone jasmonic acid (JA) and light promote artemisinin biosynthesis in A. annua. Interestingly, we found that the increase of artemisinin biosynthesis by JA was dependent on light. However, the relationship between the two signal pathways mediated by JA and light remains unclear...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642771/transcriptomic-analysis-of-avocado-hass-persea-americana-mill-in-the-interaction-system-fruit-chitosan-colletotrichum
#7
Luis-Ángel Xoca-Orozco, Esther Angélica Cuellar-Torres, Sandra González-Morales, Porfirio Gutiérrez-Martínez, Ulises López-García, Luis Herrera-Estrella, Julio Vega-Arreguín, Alejandra Chacón-López
Avocado (Persea americana) is one of the most important crops in Mexico as it is the main producer, consumer, and exporter of avocado fruit in the world. However, successful avocado commercialization is often reduced by large postharvest losses due to Colletotrichum sp., the causal agent of anthracnose. Chitosan is known to have a direct antifungal effect and acts also as an elicitor capable of stimulating a defense response in plants. However, there is little information regarding the genes that are either activated or repressed in fruits treated with chitosan...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642770/interplay-between-carotenoids-abscisic-acid-and-jasmonate-guides-the-compatible-rice-meloidogyne-graminicola-interaction
#8
Tina Kyndt, Kamrun Nahar, Ashley Haeck, Ruben Verbeek, Kristof Demeestere, Godelieve Gheysen
In this study, we have characterized the role of carotenoids and chlorophyll in the compatible interaction between the sedentary root knot nematode (RKN) Meloidogyne graminicola and the monocot model plant rice (Oryza sativa). Previous transcriptome data showed a differential expression of carotenoid and chlorophyll biosynthesis genes in nematode-induced giant cells and gall tissue. Metabolite measurement showed that galls indeed accumulate chlorophyll a, b and carotenoids, as well as the hormone abscisic acid (ABA)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642763/rootstock-sub-optimal-temperature-tolerance-determines-transcriptomic-responses-after-long-term-root-cooling-in-rootstocks-and-scions-of-grafted-tomato-plants
#9
Georgia Ntatsi, Dimitrios Savvas, Vassilis Papasotiropoulos, Anastasios Katsileros, Rita M Zrenner, Dirk K Hincha, Ellen Zuther, Dietmar Schwarz
Grafting of elite cultivars onto tolerant rootstocks is an advanced strategy to increase tomato tolerance to sub-optimal temperature. However, a detailed understanding of adaptive mechanisms to sub-optimal temperature in rootstocks and scions of grafting combinations on a physiological and molecular level is lacking. Here, the commercial cultivar Kommeet was grafted either onto 'Moneymaker' (sensitive) or onto the line accession LA 1777 of Solanum habrochaites (tolerant). Grafted plants were grown in NFT-system at either optimal (25°C) or sub-optimal (15°C) temperatures in the root environment with optimal air temperature (25°C) for 22 days...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28640974/resistance-to-powdery-mildew8-1-boosts-pattern-triggered-immunity-against-multiple-pathogens-in-arabidopsis-and-rice
#10
Yan Li, Yong Zhang, Qing-Xia Wang, Ting-Ting Wang, Xiao-Long Cao, Zhi-Xue Zhao, Sheng-Li Zhao, Yong-Ju Xu, Zhi-Yuan Xiao, Jin-Lu Li, Jing Fan, Hui Yang, Fu Huang, Shunyuan Xiao, Wen-Ming Wang
The Arabidopsis gene RESISTANCE TO POWDERY MILDEW8.1 (RPW8.1) confers resistance to virulent fungal and oomycete pathogens that cause powdery mildew and downy mildew, respectively. However, the underlying mechanism remains unclear. Here, we show that ectopic expression of RPW8.1 boosts pattern-triggered immunity (PTI) resulting in enhanced resistance against different pathogens in both Arabidopsis and rice. In Arabidopsis, transcriptome analysis revealed that ectopic expression of RPW8.1-YFP constitutively up-regulates expression of many pathogen-associated molecular pattern-(PAMP-) inducible genes...
June 22, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28640973/production-of-red-flowered-oilseed-rape-via-the-ectopic-expression-of-orychophragmus-violaceus-ovpap2
#11
Wenqin Fu, Daozong Chen, Qi Pan, Fengfeng Li, Zhigang Zhao, Xianhong Ge, Zaiyun Li
Oilseed rape (Brassica napus L.), which has yellow flowers, is both an important oil crop and a traditional tourism resource in China, whereas the Orychophragmus violaceus, which has purple flowers, likely possesses a candidate gene or genes to alter the flower color of oilseed rape. A previously established B. napus line has a particular pair of O. violaceus chromosomes (M4) and exhibits slightly red petals. In this study, the transcriptomic analysis of M4, B. napus (H3), and O. violaceus with purple petals (OvP) and with white petals (OvW) revealed that most anthocyanin biosynthesis genes were up-regulated in both M4 and OvP...
June 22, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28640868/functional-metabolomics-as-a-tool-to-analyze-mediator-function-and-structure-in-plants
#12
Celine Davoine, Ilka N Abreu, Khalil Khajeh, Jeanette Blomberg, Brendan N Kidd, Kemal Kazan, Peer M Schenk, Lorenz Gerber, Ove Nilsson, Thomas Moritz, Stefan Björklund
Mediator is a multiprotein transcriptional co-regulator complex composed of four modules; Head, Middle, Tail, and Kinase. It conveys signals from promoter-bound transcriptional regulators to RNA polymerase II and thus plays an essential role in eukaryotic gene regulation. We describe subunit localization and activities of Mediator in Arabidopsis through metabolome and transcriptome analyses from a set of Mediator mutants. Functional metabolomic analysis based on the metabolite profiles of Mediator mutants using multivariate statistical analysis and heat-map visualization shows that different subunit mutants display distinct metabolite profiles, which cluster according to the reported localization of the corresponding subunits in yeast...
2017: PloS One
https://www.readbyqxmd.com/read/28639116/integration-of-transcriptomic-and-metabolic-data-reveals-hub-transcription-factors-involved-in-drought-stress-response-in-sunflower-helianthus-annuus-l
#13
Sebastián Moschen, Julio A Di Rienzo, Janet Higgins, Takayuki Tohge, Mutsumi Watanabe, Sergio González, Máximo Rivarola, Francisco García-García, Joaquin Dopazo, H Esteban Hopp, Rainer Hoefgen, Alisdair R Fernie, Norma Paniego, Paula Fernández, Ruth A Heinz
By integration of transcriptional and metabolic profiles we identified pathways and hubs transcription factors regulated during drought conditions in sunflower, useful for applications in molecular and/or biotechnological breeding. Drought is one of the most important environmental stresses that effects crop productivity in many agricultural regions. Sunflower is tolerant to drought conditions but the mechanisms involved in this tolerance remain unclear at the molecular level. The aim of this study was to characterize and integrate transcriptional and metabolic pathways related to drought stress in sunflower plants, by using a system biology approach...
June 21, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28638836/detecting-the-candidate-gender-determinants-by-bioinformatic-prediction-of-mirnas-and-their-targets-from-transcriptome-sequences-of-the-male-and-female-flowers-in-salix-suchowensis
#14
Suyun Wei, Ning Ye, Tongming Yin
MicroRNAs (miRNAs) belong to a class of small, noncoding, and endogenous single-stranded RNAs that negatively regulate gene expression at the posttranscriptional level. Potential miRNAs can be identified based on sequence homology since miRNAs are highly conserved in plants. In this study, we aligned the expressed sequence tags derived from flower buds of male and female S. suchowensis to miRNAs in the miRBase, which enable us to identify 34 potential miRNAs from flower buds of the alternate sexes. Among them, 11 were from the female and 23 were from the male...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28638386/weighted-gene-co-expression-network-analysis-of-the-dioscin-rich-medicinal-plant-dioscorea-nipponica
#15
Wei Sun, Bo Wang, Jun Yang, Weihao Wang, An Liu, Liang Leng, Li Xiang, Chi Song, Shilin Chen
Dioscorea contains critically important species which can be used as staple foods or sources of bioactive substances, including Dioscorea nipponica, which has been used to develop highly successful drugs to treat cardiovascular disease. Its major active ingredients are thought to be sterol compounds such as diosgenin, which has been called "medicinal gold" because of its valuable properties. However, reliance on naturally growing plants as a production system limits the potential use of D. nipponica, raising interest in engineering metabolic pathways to enhance the production of secondary metabolites...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28638079/transcriptome-changes-between-compatible-and-incompatible-graft-combination-of-litchi-chinensis-by-digital-gene-expression-profile
#16
Zhe Chen, Jietang Zhao, Fuchu Hu, Yonghua Qin, Xianghe Wang, Guibing Hu
Plant grafting has been practiced widely in horticulture and proved as a useful tool in science. However, the mechanisms of graft healing or graft incompatibility remain poorly understood. In this study, Litchi chinensis cv. 'Jingganghongnuo' homograft ('J/J') and 'Jingganghongnuo'/'zhuangyuanhong' heterograft ('J/Z') as compatible and incompatible combination, respectively, was used to study transcriptional changes between incompatible and compatible graft during graft union formation. Anatomical observation indicated that three stages (2 h, 14 d and 21 d after grafting) were critical for graft union formation and selected for high-throughput sequencing...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28638069/global-profiling-of-phytohormone-dynamics-during-combined-drought-and-pathogen-stress-in-arabidopsis-thaliana-reveals-aba-and-ja-as-major-regulators
#17
Aarti Gupta, Hiroshi Hisano, Yuko Hojo, Takakazu Matsuura, Yoko Ikeda, Izumi C Mori, Muthappa Senthil-Kumar
Global transcriptome studies demonstrated the existence of unique plant responses under combined stress which are otherwise not seen during individual stresses. In order to combat combined stress plants use signaling pathways and 'cross talk' mediated by hormones involved in stress and growth related processes. However, interactions among hormones' pathways in combined stressed plants are not yet known. Here we studied dynamics of different hormones under individual and combined drought and pathogen infection in Arabidopsis thaliana by liquid chromatography-mass spectrometry (LC-MS) based profiling...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637269/announcing-the-genome-atlas-of-bamboo-and-rattan-gabr-project-promoting-research-in-evolution-and-in-economically-and-ecologically-beneficial-plants
#18
Hansheng Zhao, Shancen Zhao, Benhua Fei, Huan Liu, Huanming Yang, Honghai Dai, Dan Wang, Wei Jin, Feng Tang, Qiang Gao, Hang Xun, Yuwei Wang, Lianghua Qi, Xianghua Yue, Shuyan Lin, Lianfeng Gu, Lubin Li, Tiansheng Zhu, Qiang Wei, Zhen Su, Tarmeze Bin Wan Ariffin Wan, Daniel A Ofori, George Mbeva Muthike, Yigardu Mulatu Mengesha, Roberto Magno de Castro E Silva, Antonio Ludovico Beraldo, Zhimin Gao, Xin Liu, Zehui Jiang
Bamboo and rattan are widely grown for manufacturing, horticulture, and agroforestry. Bamboo and rattan production might help reduce poverty, boost economic growth, mitigate climate change, and protect the natural environment. Despite progress in research, sufficient molecular and genomic resources to study these species are lacking. We launched the Genome Atlas of Bamboo and Rattan (GABR) project, a comprehensive, coordinated international effort to accelerate understanding of BR genetics through genome analysis...
June 16, 2017: GigaScience
https://www.readbyqxmd.com/read/28637218/genome-wide-characterization-and-expression-analysis-enables-identification-of-abiotic-stress-responsive-myb-transcription-factors-in-cassava-manihot-esculenta
#19
Meng-Bin Ruan, Xin Guo, Bin Wang, Yi-Ling Yang, Wen-Qi Li, Xiao-Ling Yu, Peng Zhang, Ming Peng
The myeloblastosis (MYB) transcription factor superfamily is the largest transcription factor family in plants, playing different roles during stress response. However, abiotic stress-responsive MYB transcription factors have not been systematically studied in cassava (Manihot esculenta), an important tropical tuber root crop. In this study, we used a genome-wide transcriptome analysis to predict 299 putative MeMYB genes in the cassava genome. Under drought and cold stresses, many MeMYB genes exhibited different expression patterns in cassava leaves, indicating that these genes might play a role in abiotic stress responses...
June 20, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28635135/the-gene-expression-landscape-of-pine-seedling-tissues
#20
Rafael A Cañas, Zhen Li, M Belén Pascual, Vanessa Castro-Rodríguez, Concepción Ávila, Lieven Sterck, Yves Van de Peer, Francisco M Cánovas
Conifers dominate vast regions of the Northern hemisphere. They are the main source of raw materials for timber industry as well as a wide range of biomaterials. Despite their inherent difficulties as experimental models for classical plant biology research, the technological advances in genomics research are enabling fundamental studies on these plants. The use of laser capture microdissection followed by transcriptomic analysis is a powerful tool for unravelling the molecular and functional organization of conifer tissues and specialized cells...
June 21, 2017: Plant Journal: for Cell and Molecular Biology
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