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    B-BOX genes: genome-wide identification, evolution and their contribution to pollen growth in pear (Pyrus bretschneideri Rehd.).
    BMC Plant Biol 2017 Sep 19;17(1):156. Epub 2017 Sep 19.
    School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
    Background: The B-BOX (BBX) proteins have important functions in regulating plant growth and development. In plants, the BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, there still lack a genome-wide survey of BBX genes in pear. Read More

    Transcriptome analysis of Pseudostellaria heterophylla in response to the infection of pathogenic Fusarium oxysporum.
    BMC Plant Biol 2017 Sep 18;17(1):155. Epub 2017 Sep 18.
    Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
    Background: Pseudostellaria heterophylla (P. heterophylla), a herbaceous perennial, belongs to Caryophyllaceae family and is one of the Chinese herbal medicine with high pharmacodynamic value. It can be used to treat the spleen deficiency, anorexia, weakness after illness and spontaneous perspiration symptoms. Read More

    Seed maturation associated transcriptional programs and regulatory networks underlying genotypic difference in seed dormancy and size/weight in wheat (Triticum aestivum L.).
    BMC Plant Biol 2017 Sep 16;17(1):154. Epub 2017 Sep 16.
    Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada.
    Background: Maturation forms one of the critical seed developmental phases and it is characterized mainly by programmed cell death, dormancy and desiccation, however, the transcriptional programs and regulatory networks underlying acquisition of dormancy and deposition of storage reserves during the maturation phase of seed development are poorly understood in wheat. The present study performed comparative spatiotemporal transcriptomic analysis of seed maturation in two wheat genotypes with contrasting seed weight/size and dormancy phenotype.

    Results: The embryo and endosperm tissues of maturing seeds appeared to exhibit genotype-specific temporal shifts in gene expression profile that might contribute to the seed phenotypic variations. Read More

    Visualization of chromosome condensation in plants with large chromosomes.
    BMC Plant Biol 2017 Sep 12;17(1):153. Epub 2017 Sep 12.
    Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia.
    Background: Most data concerning chromosome organization have been acquired from studies of a small number of model organisms, the majority of which are mammals. In plants with large genomes, the chromosomes are significantly larger than the animal chromosomes that have been studied to date, and it is possible that chromosome condensation in such plants was modified during evolution. Here, we analyzed chromosome condensation and decondensation processes in order to find structural mechanisms that allowed for an increase in chromosome size. Read More

    Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses.
    BMC Plant Biol 2017 Sep 11;17(1):152. Epub 2017 Sep 11.
    Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China.
    Background: Sesame (Sesamum indicum L.) is one of the world's most important oil crops. However, it is susceptible to abiotic stresses in general, and to waterlogging and drought stresses in particular. Read More

    Differentially expressed genes during the imbibition of dormant and after-ripened seeds - a reverse genetics approach.
    BMC Plant Biol 2017 Sep 11;17(1):151. Epub 2017 Sep 11.
    Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands.
    Background: Seed dormancy, defined as the incapability of a viable seed to germinate under favourable conditions, is an important trait in nature and agriculture. Despite extensive research on dormancy and germination, many questions about the molecular mechanisms controlling these traits remain unanswered, likely due to its genetic complexity and the large environmental effects which are characteristic of these quantitative traits. To boost research towards revealing mechanisms in the control of seed dormancy and germination we depend on the identification of genes controlling those traits. Read More

    microRNAs participate in gene expression regulation and phytohormone cross-talk in barley embryo during seed development and germination.
    BMC Plant Biol 2017 Sep 6;17(1):150. Epub 2017 Sep 6.
    Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China.
    Background: Small RNA and degradome sequencing have identified a large number of miRNA-target pairs in plant seeds. However, detailed spatial and temporal studies of miRNA-mediated regulation, which can reflect links between seed development and germination are still lacking.

    Results: In this study, we extended our investigation on miRNAs-involved gene regulation by a combined analysis of seed maturation and germination in barley. Read More

    Characterization of the role of sodium nitroprusside (SNP) involved in long vase life of different carnation cultivars.
    BMC Plant Biol 2017 Sep 6;17(1):149. Epub 2017 Sep 6.
    Department of Horticultural Science, Kyungpook National University, Daegu, 4165122, South Korea.
    Background: Sodium nitroprusside (SNP) has been previously shown to extend the vase life of various cut flowers; however, its positive effect on extending vase life of carnations has not been well documented. Moreover, the role of SNP in the mechanisms underlying determination of vase life of cut carnations has also not been well addressed.

    Results: SNP increased vase life of Tico Viola carnations along with their relative fresh weight (RFW). Read More

    The lysin motif-containing proteins, Lyp1, Lyk7 and LysMe3, play important roles in chitin perception and defense against Verticillium dahliae in cotton.
    BMC Plant Biol 2017 Sep 4;17(1):148. Epub 2017 Sep 4.
    State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China.
    Background: Lysin motif (LysM)-containing proteins are important pattern recognition receptors (PRRs) in plants, which function in the perception of microbe-associated molecular patterns (MAMPs) and in the defense against pathogenic attack. To date, the LysM genes have not been systematically analyzed in cotton or effectively utilized for disease resistance.

    Results: Here, we identified 29, 30, 60, and 56 LysM genes in the four sequenced cotton species, diploid Gossypium raimondii, diploid G. Read More

    Identification of a methyltransferase catalyzing the final step of methyl anthranilate synthesis in cultivated strawberry.
    BMC Plant Biol 2017 Aug 31;17(1):147. Epub 2017 Aug 31.
    Horticultural Sciences Department, University of Florida, 1251 Fifield Hall, Gainesville, FL, 32611, USA.
    Background: Methyl anthranilate (MA) contributes an attractive fruity note to the complex flavor and aroma of strawberry (Fragaria spp.), yet it is rare in modern cultivars. The genetic basis for its biosynthesis has not been elucidated. Read More

    Expression patterns of flowering genes in leaves of 'Pineapple' sweet orange [Citrus sinensis (L.) Osbeck] and pummelo (Citrus grandis Osbeck).
    BMC Plant Biol 2017 Aug 30;17(1):146. Epub 2017 Aug 30.
    Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, 2550 Hull Road, Gainesville, FL, 32611, USA.
    Background: In citrus the transition from juvenility to mature phase is marked by the capability of a tree to flower and fruit consistently. The long period of juvenility in citrus severely impedes the use of genetic based strategies to improve fruit quality, disease resistance, and responses to abiotic environmental factors. One of the genes whose expression signals flower development in many plant species is FLOWERING LOCUS T (FT). Read More

    The core regulatory network of the abscisic acid pathway in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress.
    BMC Plant Biol 2017 Aug 29;17(1):145. Epub 2017 Aug 29.
    Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
    Background: Abscisic acid (ABA) signaling plays a crucial role in developmental and environmental adaptation processes of plants. However, the PYL-PP2C-SnRK2 families that function as the core components of ABA signaling are not well understood in banana.

    Results: In the present study, 24 PYL, 87 PP2C, and 11 SnRK2 genes were identified from banana, which was further supported by evolutionary relationships, conserved motif and gene structure analyses. Read More

    Specificity versus redundancy in the RAP2.4 transcription factor family of Arabidopsis thaliana: transcriptional regulation of genes for chloroplast peroxidases.
    BMC Plant Biol 2017 Aug 23;17(1):144. Epub 2017 Aug 23.
    Dahlem Center of Plant Sciences, Plant Physiology, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195, Berlin, Germany.
    Background: The Arabidopsis ERFIb / RAP2.4 transcription factor family consists of eight members with highly conserved DNA binding domains. Selected members have been characterized individually, but a systematic comparison is pending. Read More

    GaMYB85, an R2R3 MYB gene, in transgenic Arabidopsis plays an important role in drought tolerance.
    BMC Plant Biol 2017 Aug 22;17(1):142. Epub 2017 Aug 22.
    State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, 455000, China.
    Background: MYB transcription factors (TFs) are one of the largest families of TFs in higher plants and are involved in diverse biological, functional, and structural processes. Previously, very few functional validation studies on R2R3 MYB have been conducted in cotton in response to abiotic stresses. In the current study, GaMYB85, a cotton R2R3 MYB TF, was ectopically expressed in Arabidopsis thaliana (Col-0) and was functionally characterized by overexpression in transgenic plants. Read More

    Comparative transcriptome analysis reveals differentially expressed genes associated with sex expression in garden asparagus (Asparagus officinalis).
    BMC Plant Biol 2017 Aug 22;17(1):143. Epub 2017 Aug 22.
    College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
    Background: Garden asparagus (Asparagus officinalis) is a highly valuable vegetable crop of commercial and nutritional interest. It is also commonly used to investigate the mechanisms of sex determination and differentiation in plants. However, the sex expression mechanisms in asparagus remain poorly understood. Read More

    Comparative studies on tolerance of rice genotypes differing in their tolerance to moderate salt stress.
    BMC Plant Biol 2017 Aug 17;17(1):141. Epub 2017 Aug 17.
    State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
    Background: Moderate salt stress, which often occurs in most saline agriculture land, suppresses crop growth and reduces crop yield. Rice, as an important food crop, is sensitive to salt stress and rice genotypes differ in their tolerance to salt stress. Despite extensive studies on salt tolerance of rice, a few studies have specifically investigated the mechanism by which rice plants respond and tolerate to moderate salt stress. Read More

    Overexpression of Arabidopsis P3B increases heat and low temperature stress tolerance in transgenic sweetpotato.
    BMC Plant Biol 2017 Aug 14;17(1):139. Epub 2017 Aug 14.
    Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, South Korea.
    Background: Sweetpotato (Ipomoea batatas [L.] Lam) is suitable for growth on marginal lands due to its abiotic stress tolerance. However, severe environmental conditions including low temperature pose a serious threat to the productivity and expanded cultivation of this crop. Read More

    Mapping of a major QTL for salt tolerance of mature field-grown maize plants based on SNP markers.
    BMC Plant Biol 2017 Aug 15;17(1):140. Epub 2017 Aug 15.
    Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China.
    Background: Salt stress significantly restricts plant growth and production. Maize is an important food and economic crop but is also a salt sensitive crop. Identification of the genetic architecture controlling salt tolerance facilitates breeders to select salt tolerant lines. Read More

    Genome-wide transcriptome profiling provides overwintering mechanism of Agropyron mongolicum.
    BMC Plant Biol 2017 Aug 10;17(1):138. Epub 2017 Aug 10.
    Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China.
    Background: The mechanism of winter survival for perennials involves multiple levels of gene regulation, especially cold resistance. Agropyron mongolicum is one important perennial grass species, but there is little information regarding its overwintering mechanism. We performed a comprehensive transcriptomics study to evaluate global gene expression profiles regarding the winter survival of Agropyron mongolicum. Read More

    Genetic architecture and temporal patterns of biomass accumulation in spring barley revealed by image analysis.
    BMC Plant Biol 2017 Aug 10;17(1):137. Epub 2017 Aug 10.
    Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Germany.
    Background: Genetic mapping of phenotypic traits generally focuses on a single time point, but biomass accumulates continuously during plant development. Resolution of the temporal dynamics that affect biomass recently became feasible using non-destructive imaging.

    Results: With the aim to identify key genetic factors for vegetative biomass formation from the seedling stage to flowering, we explored growth over time in a diverse collection of two-rowed spring barley accessions. Read More

    Erratum to: transcriptional responses and flavor volatiles biosynthesis in methyl jasmonate-treated tea leaves.
    BMC Plant Biol 2017 Aug 9;17(1):136. Epub 2017 Aug 9.
    Key Laboratory of Tea Biology and Resource Utilization of Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, 9th South Meiling Road, Hangzhou, Zhejiang, 310008, People's Republic of China.

    Catalytic and functional aspects of different isozymes of glycolate oxidase in rice.
    BMC Plant Biol 2017 Aug 8;17(1):135. Epub 2017 Aug 8.
    State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
    Background: Glycolate oxidase (GLO) is a key enzyme for photorespiration in plants. There are four GLO genes encoding and forming different isozymes in rice, but their functional differences are not well understood. In this study, enzymatic and physiological characteristics of the GLO isozymes were comparatively analyzed. Read More

    Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions.
    BMC Plant Biol 2017 Aug 4;17(1):134. Epub 2017 Aug 4.
    Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
    Background: The narrow genetic basis of resistance in modern wheat cultivars and the strong selection response of pathogen populations have been responsible for periodic and devastating epidemics of the wheat rust diseases. Characterizing new sources of resistance and incorporating multiple genes into elite cultivars is the most widely accepted current mechanism to achieve durable varietal performance against changes in pathogen virulence. Here, we report a high-density molecular characterization and genome-wide association study (GWAS) of stripe rust and stem rust resistance in 190 Ethiopian bread wheat lines based on phenotypic data from multi-environment field trials and seedling resistance screening experiments. Read More

    Effect of volatile compounds produced by Ralstonia solanacearum on plant growth promoting and systemic resistance inducing potential of Bacillus volatiles.
    BMC Plant Biol 2017 Aug 2;17(1):133. Epub 2017 Aug 2.
    Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Weigang No.1, Nanjing, 210095, People's Republic of China.
    Background: Microbial volatiles play an expedient role in the agricultural ecological system by enhancing plant growth and inducing systemic resistance against plant pathogens, without causing hazardous effects on the environment. To explore the effects of VOCs of Ralstonia solanacearum TBBS1 (Rs) on tobacco plant growth and on plant growth promoting efficiency of VOCs produced by Bacillus subtilis SYST2, experiments were conducted both in vitro and in planta.

    Results: The VOCs produced by SYST2 significantly enhanced the plant growth and induced the systemic resistance (ISR) against wilt pathogen Rs in all experiments. Read More

    Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response.
    BMC Plant Biol 2017 Aug 1;17(1):131. Epub 2017 Aug 1.
    State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, China.
    Background: The advent of big data in biology offers opportunities while poses challenges to derive biological insights. For maize, a large amount of publicly available transcriptome datasets have been generated but a comprehensive analysis is lacking.

    Results: We constructed a maize gene co-expression network based on the graphical Gaussian model, using massive RNA-seq data. Read More

    Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes.
    BMC Plant Biol 2017 Aug 1;17(1):132. Epub 2017 Aug 1.
    The New Zealand Institute for Plant & Food Research Limited, PO Box 4704, Christchurch, New Zealand.
    Background: Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea. Read More

    New insights into the roles of cucumber TIR1 homologs and miR393 in regulating fruit/seed set development and leaf morphogenesis.
    BMC Plant Biol 2017 Jul 26;17(1):130. Epub 2017 Jul 26.
    State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
    Background: TIR1-like proteins act as auxin receptors and play essential roles in auxin-mediated plant development processes. The number of auxin receptor family members varies among species. While the functions of auxin receptor genes have been widely studied in Arabidopsis, the distinct functions of cucumber (Cucumis sativus L. Read More

    Comparative RNA-seq based transcriptome profiling of waterlogging response in cucumber hypocotyls reveals novel insights into the de novo adventitious root primordia initiation.
    BMC Plant Biol 2017 Jul 26;17(1):129. Epub 2017 Jul 26.
    Department of horticulture, School of Horticulture and Plant Protection, Yangzhou University, 48 wenhui eastroad, Yangzhou, Jiangsu, 225009, China.
    Background: Waterlogging is a serious abiotic stress to plant growth because it results in the decline in the supplement of oxygen to submerged tissues. Although cucumber (Cucumis sativus L.) is sensitive to waterlogging, its ability to generate adventitious roots (ARs) facilitates gas diffusion and increases plant survival when the oxygen concentration is decreased. Read More

    Identification and characterization of suppressor mutants of stop1.
    BMC Plant Biol 2017 Jul 24;17(1):128. Epub 2017 Jul 24.
    Robert W. Holley Center, US Department of Agriculture-Agricultural Research Service, Ithaca, NY, 14853, USA.
    Background: Proton stress and aluminum (Al) toxicity are major constraints limiting crop growth and yields on acid soils (pH < 5). In Arabidopsis, STOP1 is a master transcription factor that controls the expression of a set of well-characterized Al tolerance genes and unknown processes involved in low pH resistance. As a result, loss-of-function stop1 mutants are extremely sensitive to low pH and Al stresses. Read More

    Characterization of four rice UEV1 genes required for Lys63-linked polyubiquitination and distinct functions.
    BMC Plant Biol 2017 Jul 17;17(1):126. Epub 2017 Jul 17.
    College of Life Sciences, Capital Normal University, Beijing, 100048, China.
    Background: The error-free branch of the DNA-damage tolerance (DDT) pathway is orchestrated by Lys63-linked polyubiquitination of proliferating cell nuclear antigen (PCNA), and this polyubiquitination is mediated by a Ubc13-Uev complex in yeast. We have previously cloned OsUBC13 from rice, whose product functions as an E2 to promote Lys63-linked ubiquitin chain assembly in the presence of yeast or human Uev.

    Results: Here we identify four highly conserved UEV1 genes in rice whose products are able to form stable heterodimers with OsUbc13 and mediate Lys63-linked ubiquitin chain assembly. Read More

    Suppression of the phytoene synthase gene (EgcrtB) alters carotenoid content and intracellular structure of Euglena gracilis.
    BMC Plant Biol 2017 Jul 17;17(1):125. Epub 2017 Jul 17.
    Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi, 320-8551, Japan.
    Background: Photosynthetic organisms utilize carotenoids for photoprotection as well as light harvesting. Our previous study revealed that high-intensity light increases the expression of the gene for phytoene synthase (EgcrtB) in Euglena gracilis (a unicellular phytoflagellate), the encoded enzyme catalyzes the first committed step of the carotenoid biosynthesis pathway. To examine carotenoid synthesis of E. Read More

    Combined biotic stresses trigger similar transcriptomic responses but contrasting resistance against a chewing herbivore in Brassica nigra.
    BMC Plant Biol 2017 Jul 17;17(1):127. Epub 2017 Jul 17.
    Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.
    Background: In nature, plants are frequently exposed to simultaneous biotic stresses that activate distinct and often antagonistic defense signaling pathways. How plants integrate this information and whether they prioritize one stress over the other is not well understood.

    Results: We investigated the transcriptome signature of the wild annual crucifer, Brassica nigra, in response to eggs and caterpillars of Pieris brassicae butterflies, Brevicoryne brassicae aphids and the bacterial phytopathogen Xanthomonas campestris pv. Read More

    Spatial regulation of monolignol biosynthesis and laccase genes control developmental and stress-related lignin in flax.
    BMC Plant Biol 2017 Jul 14;17(1):124. Epub 2017 Jul 14.
    University of Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France.
    Background: Bast fibres are characterized by very thick secondary cell walls containing high amounts of cellulose and low lignin contents in contrast to the heavily lignified cell walls typically found in the xylem tissues. To improve the quality of the fiber-based products in the future, a thorough understanding of the main cell wall polymer biosynthetic pathways is required. In this study we have carried out a characterization of the genes involved in lignin biosynthesis in flax along with some of their regulation mechanisms. Read More

    Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum.
    BMC Plant Biol 2017 Jul 11;17(1):123. Epub 2017 Jul 11.
    Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
    Background: Quantitative trait loci (QTLs) detected in one mapping population may not be detected in other mapping populations at all the time. Therefore, before being used for marker assisted breeding, QTLs need to be validated in different environments and/or genetic backgrounds to rule out statistical anomalies. In this regard, we mapped the QTLs controlling various agronomic traits in a recombinant inbred line (RIL) population in response to Nitrogen (N) stress and validated these with the reported QTLs in our earlier study to find the stable and consistent QTLs across populations. Read More

    Identification of QTLs controlling grain protein concentration using a high-density SNP and SSR linkage map in barley (Hordeum vulgare L.).
    BMC Plant Biol 2017 Jul 11;17(1):122. Epub 2017 Jul 11.
    State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
    Background: Grain protein concentration (GPC) is a major determinant of quality in barley (Hordeum vulgare L.). Breeding barley cultivars with high GPC has practical value for feed and food properties. Read More

    Three members of Medicago truncatula ST family are ubiquitous during development and modulated by nutritional status (MtST1) and dehydration (MtST2 and MtST3).
    BMC Plant Biol 2017 Jul 10;17(1):117. Epub 2017 Jul 10.
    Departamento de Botánica y Fisiología Vegetal. Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca. C/ Licenciado Méndez Nieto s/n, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
    Background: ShooT specific/Specific Tissue (ST) belong to a protein family of unknown function characterized by the DUF2775 domain and produced in specific taxonomic plant families, mainly Fabaceae and Asteraceae, with the Medicago truncatula ST family being the largest. The putative roles proposed for this family are cell elongation, biotic interactions, abiotic stress and N reserve. The aim of this work was to go deeper into the role of three M. Read More

    Evolution, gene expression profiling and 3D modeling of CSLD proteins in cotton.
    BMC Plant Biol 2017 Jul 10;17(1):119. Epub 2017 Jul 10.
    Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002, China.
    Background: Among CESA-like gene superfamily, the cellulose synthase-like D (CSLD) genes are most similar to cellulose synthase genes and have been reported to be involved in tip-growing cell and stem development. However, there has been no genome-wide characterization of this gene subfamily in cotton. We thus sought to analyze the evolution and functional characterization of CSLD proteins in cotton based on fully sequenced cotton genomes. Read More

    Indole-3-butyric acid promotes adventitious rooting in Arabidopsis thaliana thin cell layers by conversion into indole-3-acetic acid and stimulation of anthranilate synthase activity.
    BMC Plant Biol 2017 Jul 11;17(1):121. Epub 2017 Jul 11.
    Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Roma, Italy.
    Background: Indole-3-acetic acid (IAA), and its precursor indole-3-butyric acid (IBA), control adventitious root (AR) formation in planta. Adventitious roots are also crucial for propagation via cuttings. However, IBA role(s) is/are still far to be elucidated. Read More

    Relationships between drought, heat and air humidity responses revealed by transcriptome-metabolome co-analysis.
    BMC Plant Biol 2017 Jul 10;17(1):120. Epub 2017 Jul 10.
    Helmholtz Zentrum München, Department of Environmental Sciences, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
    Background: Elevated temperature and reduced water availability are frequently linked abiotic stresses that may provoke distinct as well as interacting molecular responses. Based on non-targeted metabolomic and transcriptomic measurements from Arabidopsis rosettes, this study aims at a systematic elucidation of relevant components in different drought and heat scenarios as well as relationships between molecular players of stress response.

    Results: In combined drought-heat stress, the majority of single stress responses are maintained. Read More

    Differential proteomic analysis of replanted Rehmannia glutinosa roots by iTRAQ reveals molecular mechanisms for formation of replant disease.
    BMC Plant Biol 2017 Jul 10;17(1):116. Epub 2017 Jul 10.
    College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
    Background: The normal growth of Rehmannia glutinosa, a widely used medicinal plant in China, is severely disturbed by replant disease. The formation of replant disease commonly involves interactions among plants, allelochemicals and microbes; however, these relationships remain largely unclear. As a result, no effective measures are currently available to treat replant disease. Read More

    Jasmonate-mediated defence responses, unlike salicylate-mediated responses, are involved in the recovery of grapevine from bois noir disease.
    BMC Plant Biol 2017 Jul 10;17(1):118. Epub 2017 Jul 10.
    Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c, I-01100, Viterbo, Italy.
    Background: Bois noir is an important disease of grapevine (Vitis vinifera L.), caused by phytoplasmas. An interesting, yet elusive aspect of the bois noir disease is "recovery", i. Read More

    Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses.
    BMC Plant Biol 2017 Jul 6;17(1):113. Epub 2017 Jul 6.
    Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052, China.
    Background: WUSCHEL-related homeobox (WOX) family members play significant roles in plant growth and development, such as in embryo patterning, stem-cell maintenance, and lateral organ formation. The recently published cotton genome sequences allow us to perform comprehensive genome-wide analysis and characterization of WOX genes in cotton.

    Results: In this study, we identified 21, 20, and 38 WOX genes in Gossypium arboreum (2n = 26, A2), G. Read More

    Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana.
    BMC Plant Biol 2017 Jul 6;17(1):114. Epub 2017 Jul 6.
    Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120, Halle (Saale), Germany.
    Background: Global increase in ambient temperatures constitute a significant challenge to wild and cultivated plant species. Forward genetic analyses of individual temperature-responsive traits have resulted in the identification of several signaling and response components. However, a comprehensive knowledge about temperature sensitivity of different developmental stages and the contribution of natural variation is still scarce and fragmented at best. Read More

    Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions.
    BMC Plant Biol 2017 Jul 6;17(1):115. Epub 2017 Jul 6.
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
    Background: Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. Read More

    Genetic diversity, population structure and marker-trait associations for agronomic and grain traits in wild diploid wheat Triticum urartu.
    BMC Plant Biol 2017 Jul 1;17(1):112. Epub 2017 Jul 1.
    State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
    Background: Wild diploid wheat, Triticum urartu (T. urartu) is the progenitor of bread wheat, and understanding its genetic diversity and genome function will provide considerable reference for dissecting genomic information of common wheat.

    Results: In this study, we investigated the morphological and genetic diversity and population structure of 238 T. Read More

    Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.).
    BMC Plant Biol 2017 Jun 30;17(1):111. Epub 2017 Jun 30.
    Area de Genética, Departamento de Biología Molecular, Universidad de León, 24071, León, Spain.
    Background: Frost is one of the main abiotic stresses limiting plant distribution and crop production. To cope with the stress, plants evolved adaptations known as cold acclimation or chilling tolerance to maximize frost tolerance. Cold acclimation is a progressive acquisition of freezing tolerance by plants subjected to low non-freezing temperatures which subsequently allows them to survive exposure to frost. Read More

    Evaluating the accuracy of genomic prediction of growth and wood traits in two Eucalyptus species and their F1 hybrids.
    BMC Plant Biol 2017 Jun 29;17(1):110. Epub 2017 Jun 29.
    Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Umeå, SE-90187, Sweden.
    Background: Genomic prediction is a genomics assisted breeding methodology that can increase genetic gains by accelerating the breeding cycle and potentially improving the accuracy of breeding values. In this study, we use 41,304 informative SNPs genotyped in a Eucalyptus breeding population involving 90 E.grandis and 78 E. Read More

    Molecular cloning, structure, phylogeny and expression analysis of the invertase gene family in sugarcane.
    BMC Plant Biol 2017 Jun 23;17(1):109. Epub 2017 Jun 23.
    Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
    Background: Invertases (INVs) are key enzymes regulating sucrose metabolism and are here revealed to be involved in responses to environmental stress in plants. To date, individual members of the invertase gene family and their expression patterns are unknown in sugarcane due to its complex genome despite their significance in sucrose metabolism.

    Results: In this study, based on comparative genomics, eleven cDNA and twelve DNA sequences belonging to 14 non-redundant members of the invertase gene family were successfully cloned from sugarcane. Read More

    Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.).
    BMC Plant Biol 2017 Jun 20;17(1):108. Epub 2017 Jun 20.
    Department of Agricultural, Food and Nutritional Science, University of Alberta, 410 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
    Background: The resistance to leaf rust (Lr) caused by Puccinia triticina in wheat (Triticum aestivum L.) has been well studied over the past decades with over 70 Lr genes being mapped on different chromosomes and numerous QTLs (quantitative trait loci) being detected or mapped using DNA markers. Such resistance is often divided into race-specific and race-nonspecific resistance. Read More

    Residual transpiration as a component of salinity stress tolerance mechanism: a case study for barley.
    BMC Plant Biol 2017 Jun 19;17(1):107. Epub 2017 Jun 19.
    School of Land and Food, University of Tasmania, Private Bag 54, Hobart, Tas, 7001, Australia.
    Background: While most water loss from leaf surfaces occurs via stomata, part of this loss also occurs through the leaf cuticle, even when the stomata are fully closed. This component, termed residual transpiration, dominates during the night and also becomes critical under stress conditions such as drought or salinity. Reducing residual transpiration might therefore be a potentially useful mechanism for improving plant performance when water availability is reduced (e. Read More

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