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Database SoyDB: a knowledge database of soybean transcription factors Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry T Nguyen, Dong Xu, Gary Stacey, and Jianlin Cheng PMCID: PMC2826334 Research articles Identification of genes differentially expressed during interaction of resistant and susceptible apple cultivars (Malus × domestica) with Erwinia amylovora Angela Baldo, Jay L Norelli, Robert E Farrell, Jr, Carole L Bassett, Herb S Aldwinckle, and Mickael Malnoy PMCID: PMC2827420 QTLs and candidate genes for desiccation and abscisic acid content in maize kernels Valérie Capelle, Carine Remoué, Laurence Moreau, Agnès Reyss, Aline Mahé, Agnès Massonneau, Matthieu Falque, Alain Charcosset, Claudine Thévenot, Peter Rogowsky, Sylvie Coursol, and Jean-Louis Prioul PMCID: PMC2826337 Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.) Chuan-Zhi Zhao, Han Xia, Taylor Price Frazier, Ying-Yin Yao, Yu-Ping Bi, Ai-Qin Li, Meng-Jun Li, Chang-Sheng Li, Bao-Hong Zhang, and Xing-Jun Wang PMCID: PMC2826338 Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida Izaskun Mallona, Sandra Lischewski, Julia Weiss, Bettina Hause, and Marcos Egea-Cortines PMCID: PMC2827423 DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits Grit Haseneyer, Silke Stracke, Hans-Peter Piepho, Sascha Sauer, Hartwig H Geiger, and Andreas Graner PMCID: PMC2822787 Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa × O. glaberrima introgression lines Andrés Gonzalo Gutiérrez, Silvio James Carabalí, Olga Ximena Giraldo, César Pompilio Martínez, Fernando Correa, Gustavo Prado, Joe Tohme, and Mathias Lorieux PMCID: PMC2824796 Analysis of expressed sequence tags from a single wheat cultivar facilitates interpretation of tandem mass spectrometry data and discrimination of gamma gliadin proteins that may play different functional roles in flour Susan B Altenbach, William H Vensel, and Frances M DuPont PMCID: PMC2827424 Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris Falk Zakrzewski, Torsten Wenke, Daniela Holtgräwe, Bernd Weisshaar, and Thomas Schmidt PMCID: PMC2820488 Differential gene expression in incompatible interaction between wheat and stripe rust fungus revealed by cDNA-AFLP and comparison to compatible interaction Xiaojie Wang, Wei Liu, Xianming Chen, Chunlei Tang, Yanling Dong, Jinbiao Ma, Xueling Huang, Guorong Wei, Qingmei Han, Lili Huang, and Zhensheng Kang PMCID: PMC2817678 Transcription profiles of mitochondrial genes correlate with mitochondrial DNA haplotypes in a natural population of Silene vulgaris Hosam O Elansary, Karel Müller, Matthew S Olson, and Helena Štorchová PMCID: PMC2820487 Polymorphisms in monolignol biosynthetic genes are associated with biomass yield and agronomic traits in European maize (Zea mays L.) Yongsheng Chen, Imad Zein, Everton Alen Brenner, Jeppe Reitan Andersen, Mathias Landbeck, Milena Ouzunova, and Thomas Lübberstedt PMCID: PMC2827421 Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis) Jeffrey T Foster, Gerard J Allan, Agnes P Chan, Pablo D Rabinowicz, Jacques Ravel, Paul J Jackson, and Paul Keim PMCID: PMC2832895 Genetic relationships among seven sections of genus Arachis studied by using SSR markers Ravi Koppolu, Hari D Upadhyaya, Sangam L Dwivedi, David A Hoisington, and Rajeev K Varshney PMCID: PMC2826335 Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress Kil-Young Yun, Myoung Ryoul Park, Bijayalaxmi Mohanty, Venura Herath, Fuyu Xu, Ramil Mauleon, Edward Wijaya, Vladimir B Bajic, Richard Bruskiewich, and Benildo G de los Reyes PMCID: PMC2826336 A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome Yanbin Hong, Xiaoping Chen, Xuanqiang Liang, Haiyan Liu, Guiyuan Zhou, Shaoxiong Li, Shijie Wen, C Corley Holbrook, and Baozhu Guo PMCID: PMC2835713 Identification and functional characterisation of the promoter of the calcium sensor gene CBL1 from the xerophyte Ammopiptanthus mongolicus Lili Guo, Yanhua Yu, Xinli Xia, and Weilun Yin PMCID: PMC2844064 Factors influencing the production of stilbenes by the knotweed, Reynoutria × bohemica Marcela Kovářová, Kristýna Bartůňková, Tomáš Frantík, Helena Koblihová, Kateřina Prchalová, and Miroslav Vosátka PMCID: PMC2834697 The Arabidopsis pop2-1 mutant reveals the involvement of GABA transaminase in salt stress tolerance Hugues Renault, Valérie Roussel, Abdelhak El Amrani, Matthieu Arzel, David Renault, Alain Bouchereau, and Carole Deleu PMCID: PMC2825238 Identification and characterisation of CYP75A31, a new flavonoid 3'5'-hydroxylase, isolated from Solanum lycopersicum Kristine M Olsen, Alain Hehn, Hélène Jugdé, Rune Slimestad, Romain Larbat, Frédéric Bourgaud, and Cathrine Lillo PMCID: PMC2825239 The origin of populations of Arabidopsis thaliana in China, based on the chloroplast DNA sequences Ping Yin, Juqing Kang, Fei He, Li-Jia Qu, and Hongya Gu PMCID: PMC2827422 Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance Deepti Jain and Debasis Chattopadhyay PMCID: PMC2831037 Identification of genes associated with growth cessation and bud dormancy entrance using a dormancy-incapable tree mutant Sergio Jiménez, Zhigang Li, Gregory L Reighard, and Douglas G Bielenberg PMCID: PMC2829590 Iron and ferritin accumulate in separate cellular locations in Phaseolus seeds Cristina Cvitanich, Wojciech J Przybyłowicz, Dorian F Urbanski, Anna M Jurkiewicz, Jolanta Mesjasz-Przybyłowicz, Matthew W Blair, Carolina Astudillo, Erik Ø Jensen, and Jens Stougaard PMCID: PMC2831038 Polymorphisms in O-methyltransferase genes are associated with stover cell wall digestibility in European maize (Zea mays L.) Everton A Brenner, Imad Zein, Yongsheng Chen, Jeppe R Andersen, Gerhard Wenzel, Milena Ouzunova, Joachim Eder, Birte Darnhofer, Uschi Frei, Yves Barrière, and Thomas Lübberstedt PMCID: PMC2829591 Traditional agroecosystems as conservatories and incubators of cultivated plant varietal diversity: the case of fig (Ficus carica L.) in Morocco Hafid Achtak, Mohammed Ater, Ahmed Oukabli, Sylvain Santoni, Finn Kjellberg, and Bouchaib Khadari PMCID: PMC2844065 Exposure of beta-tubulin regions defined by antibodies on an Arabidopsis thaliana microtubule protofilament model and in the cells Yaroslav Blume, Alla Yemets, Yarina Sheremet, Alexey Nyporko, Vadym Sulimenko, Tetyana Sulimenko, and Pavel Dráber PMCID: PMC2844066 Functional characterization of Arabidopsis thaliana transthyretin-like protein João Pessoa, Zsuzsa Sárkány, Frederico Ferreira-da-Silva, Sónia Martins, Maria R Almeida, Jianming Li, and Ana M Damas PMCID: PMC2834698 Novel induced mlo mutant alleles in combination with site-directed mutagenesis reveal functionally important domains in the heptahelical barley Mlo protein Anja Reinstädler, Judith Müller, Jerzy H Czembor, Pietro Piffanelli, and Ralph Panstruga PMCID: PMC2844067 Mechanistic insights from a quantitative analysis of pollen tube guidance Shannon F Stewman, Matthew Jones-Rhoades, Prabhakar Bhimalapuram, Martin Tchernookov, Daphne Preuss, and Aaron R Dinner PMCID: PMC2844068 STIL, a peculiar molecule from styles, specifically dephosphorylates the pollen receptor kinase LePRK2 and stimulates pollen tube growth in vitro Diego L Wengier, María A Mazzella, Tamara M Salem, Sheila McCormick, and Jorge P Muschietti PMCID: PMC2844069 Salicylic acid alleviates decreases in photosynthesis under heat stress and accelerates recovery in grapevine leaves Li-Jun Wang, Ling Fan, Wayne Loescher, Wei Duan, Guo-Jie Liu, Jian-Shan Cheng, Hai-Bo Luo, and Shao-Hua Li PMCID: PMC2848757 Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo) José R Hernandez Mora, Eric Rivals, Hakim Mireau, and Françoise Budar PMCID: PMC2848758 Cellular localization of ROS and NO in olive reproductive tissues during flower development Adoración Zafra, María Isabel Rodríguez-García, and Juan de Dios Alché PMCID: PMC2838403 Potential chromosomal introgression barriers revealed by linkage analysis in a hybrid of Pinus massoniana and P. hwangshanensis Shuxian Li, Ying Chen, Handong Gao, and Tongming Yin PMCID: PMC2844070 The Botrytis cinerea xylanase Xyn11A contributes to virulence with its necrotizing activity, not with its catalytic activity Judith Noda, Nélida Brito, and Celedonio González PMCID: PMC2844071 An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of Oryza sativa L. subsp. indica Srirupa Das, Supriya Sen, Anirban Chakraborty, Papia Chakraborti, Mrinal K Maiti, Asitava Basu, Debabrata Basu, and Soumitra K Sen PMCID: PMC2848759 Pb-induced cellular defense system in the root meristematic cells of Allium sativum L Wusheng Jiang and Donghua Liu PMCID: PMC2848760 Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean Yung-Tsi Bolon, Bindu Joseph, Steven B Cannon, Michelle A Graham, Brian W Diers, Andrew D Farmer, Gregory D May, Gary J Muehlbauer, James E Specht, Zheng Jin Tu, Nathan Weeks, Wayne W Xu, Randy C Shoemaker, and Carroll P Vance PMCID: PMC2848761 Effects of manganese-excess on CO2 assimilation, ribulose-1,5-bisphosphate carboxylase/oxygenase, carbohydrates and photosynthetic electron transport of leaves, and antioxidant systems of leaves and roots in Citrus grandis seedlings Qing Li, Li-Song Chen, Huan-Xin Jiang, Ning Tang, Lin-Tong Yang, Zheng-He Lin, Yan Li, and Gang-Hua Yang PMCID: PMC2848762 Small chloroplast-targeted DnaJ proteins are involved in optimization of photosynthetic reactions in Arabidopsis thaliana Kun-Ming Chen, Maija Holmström, Wuttinun Raksajit, Marjaana Suorsa, Mirva Piippo, and Eva-Mari Aro PMCID: PMC2844072 The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization Patrick PC Tam, Isabelle H Barrette-Ng, Dawn M Simon, Michael WC Tam, Amanda L Ang, and Douglas G Muench PMCID: PMC2848763 The Arabidopsis EAR-motif-containing protein RAP2.1 functions as an active transcriptional repressor to keep stress responses under tight control Chun-Juan Dong and Jin-Yuan Liu PMCID: PMC2848764 A mutation in the cytosolic O-acetylserine (thiol) lyase induces a genome-dependent early leaf death phenotype in Arabidopsis Reza Shirzadian-Khorramabad, Hai-Chun Jing, Gerja E Everts, Jos HM Schippers, Jacques Hille, and Paul P Dijkwel PMCID: PMC2890954 An examination of targeted gene neighborhoods in strawberry Thomas M Davis, Melanie E Shields, Qian Zhang, Denise Tombolato-Terzić, Jeffrey L Bennetzen, Ana C Pontaroli, Hao Wang, Qin Yao, Phillip SanMiguel, and Kevin M Folta PMCID: PMC2890015 Uncovering the evolutionary origin of plant molecular processes: comparison of Coleochaete (Coleochaetales) and Spirogyra (Zygnematales) transcriptomes Ruth E Timme and Charles F Delwiche PMCID: PMC2890016 Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain James Breen, Dora Li, David S Dunn, Ferenc Békés, Xiuying Kong, Juncheng Zhang, Jizeng Jia, Thomas Wicker, Rohit Mago, Wujun Ma, Matthew Bellgard, and Rudi Appels PMCID: PMC2887456 Phylogeny and expression profiling of CAD and CAD-like genes in hybrid Populus (P. deltoides × P. nigra): evidence from herbivore damage for subfunctionalization and functional divergence Abdelali Barakat, Agnieszka Bagniewska-Zadworna, Christopher J Frost, and John E Carlson PMCID: PMC2887455 Research Articles Dynamics of DNA methylation and Histone H4 acetylation during floral bud differentiation in azalea Mónica Meijón, Isabel Feito, Luis Valledor, Roberto Rodríguez, and María Jesús Cañal PMCID: PMC2923518 Can differences in phosphorus uptake kinetics explain the distribution of cattail and sawgrass in the Florida Everglades? Hans Brix, Bent Lorenzen, Irving A Mendelssohn, Karen L McKee, and ShiLi Miao PMCID: PMC2923519 The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.) Nikku L Raju, Belaghihalli N Gnanesh, Pazhamala Lekha, Balaji Jayashree, Suresh Pande, Pavana J Hiremath, Munishamappa Byregowda, Nagendra K Singh, and Rajeev K Varshney PMCID: PMC2923520 Functional analysis of B and C class floral organ genes in spinach demonstrates their role in sexual dimorphism D Noah Sather, Maja Jovanovic, and Edward M Golenberg PMCID: PMC2923521 Transmission ratio distortion results in asymmetric introgression in Louisiana Iris Shunxue Tang, Rebecca A Okashah, Steven J Knapp, Michael L Arnold, and Noland H Martin PMCID: PMC2923522 Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data Sinara Artico, Sarah M Nardeli, Osmundo Brilhante, Maria Fátima Grossi-de-Sa, and Marcio Alves-Ferreira PMCID: PMC2923523 An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae Kui Lin-Wang, Karen Bolitho, Karryn Grafton, Anne Kortstee, Sakuntala Karunairetnam, Tony K McGhie, Richard V Espley, Roger P Hellens, and Andrew C Allan PMCID: PMC2923524 A plant natriuretic peptide-like molecule of the pathogen Xanthomonas axonopodis pv. citri causes rapid changes in the proteome of its citrus host Betiana S Garavaglia, Ludivine Thomas, Tamara Zimaro, Natalia Gottig, Lucas D Daurelio, Bongani Ndimba, Elena G Orellano, Jorgelina Ottado, and Chris Gehring PMCID: PMC2923525 Accumulation of phenanthrene by roots of intact wheat (Triticum acstivnm L.) seedlings: passive or active uptake? Xin-Hua Zhan, Heng-Liang Ma, Li-Xiang Zhou, Jian-Ru Liang, Ting-Hui Jiang, and Guo-Hua Xu PMCID: PMC2923526 Disruption of actin filaments induces mitochondrial Ca2+ release to the cytoplasm and [Ca2+]c changes in Arabidopsis root hairs Yuqing Wang, Yingfang Zhu, Yu Ling, Haiyan Zhang, Peng Liu, František Baluška, Jozef Šamaj, Jinxing Lin, and Qinli Wang PMCID: PMC2923527 Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers Charlotte J Allender and Graham J King PMCID: PMC2923528 A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica Satoko Yoshida, Juliane K Ishida, Nasrein M Kamal, Abdelbagi M Ali, Shigetou Namba, and Ken Shirasu PMCID: PMC2923529 The YlmG protein has a conserved function related to the distribution of nucleoids in chloroplasts and cyanobacteria Yukihiro Kabeya, Hiromitsu Nakanishi, Kenji Suzuki, Takanari Ichikawa, Youichi Kondou, Minami Matsui, and Shin-ya Miyagishima PMCID: PMC2923531 Salt tolerance in Solanum pennellii: antioxidant response and related QTL Anne Frary, Deniz Göl, Davut Keleş, Bilal Ökmen, Hasan Pınar, Hasan Ö Şığva, Ahmet Yemenicioğlu, and Sami Doğanlar PMCID: PMC2923532 Transcriptional responses to polycyclic aromatic hydrocarbon-induced stress in Arabidopsis thaliana reveal the involvement of hormone and defense signaling pathways David Weisman, Merianne Alkio, and Adán Colón-Carmona PMCID: PMC2923533 Genetic and transformation studies reveal negative regulation of ERS1 ethylene receptor signaling in Arabidopsis Qian Liu, Chan Xu, and Chi-Kuang Wen PMCID: PMC2923534 Isolation and functional characterization of Lycopene β-cyclase (CYC-B) promoter from Solanum habrochaites Monika Dalal, Viswanathan Chinnusamy, and Kailash C Bansal PMCID: PMC2923535 Dissecting grain yield pathways and their interactions with grain dry matter content by a two-step correlation approach with maize seedling transcriptome Junjie Fu, Alexander Thiemann, Tobias A Schrag, Albrecht E Melchinger, Stefan Scholten, and Matthias Frisch PMCID: PMC2923537 Phloem small RNAs, nutrient stress responses, and systemic mobility Anja Buhtz, Janin Pieritz, Franziska Springer, and Julia Kehr PMCID: PMC2923538 A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas Isabelle Hippolyte, Frederic Bakry, Marc Seguin, Laetitia Gardes, Ronan Rivallan, Ange-Marie Risterucci, Christophe Jenny, Xavier Perrier, Françoise Carreel, Xavier Argout, Pietro Piffanelli, Imtiaz A Khan, Robert NG Miller, Georgios J Pappas, Didier Mbéguié-A-Mbéguié, Takashi Matsumoto, Veronique De Bernardinis, Eric Huttner, Andrzej Kilian, Franc-Christophe Baurens, Angélique D'Hont, François Cote, Brigitte Courtois, and Jean-Christophe Glaszmann PMCID: PMC2923539 Methodology Articles Defining reference genes in Oryza sativa using organ, development, biotic and abiotic transcriptome datasets Reena Narsai, Aneta Ivanova, Sophia Ng, and James Whelan PMCID: PMC2923530 A rich TILLING resource for studying gene function in Brassica rapa Pauline Stephenson, David Baker, Thomas Girin, Amandine Perez, Stephen Amoah, Graham J King, and Lars Østergaard PMCID: PMC2923536 Other Issues: Journal List
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