Correction: Dissecting the plant genome: through new generation molecular markers

Genetic Resources and Crop Evolution -     

Identification of new stock [Matthiola incana (L.) R. Br] cultivars with high fertility through morphological and molecular markers

Genetic Resources and Crop Evolution - Garden stock [Matthiola incana (L.) R. Br.] is a commercially important horticultural crop owing to its ornamental effect. There are different stock cultivars...     

Toward fish and seafood traceability: anchovy species determination in fish products by molecular markers and support through a public domain database

Traceability in the fish food sector plays an increasingly important role for consumer protection and confidence building. This is reflected by the introduction of legislation and rules covering traceability on national and international levels. Although traceability through labeling is well established and supported by respective regulations, monitoring and enforcement of these rules are still hampered by the lack of efficient diagnostic tools. We describe protocols using a direct sequencing method based on 212-274-bp diagnostic sequences derived from species-specific mitochondria DNA cytochrome b, 16S rRNA, and cytochrome oxidase subunit I sequences which can efficiently be applied to unambiguously determine even closely related fish species in processed food products labeled "anchovy". Traceability of anchovy-labeled products is supported by the public online database AnchovyID ( http://anchovyid.jrc.ec.europa.eu), which provided data obtained during our study and tools for analytical purposes.     

植物离子组学: 植物营养研究的新方向

离子组是指有机体内所有离子的总和,包括所有的金属、类金属和非金属。现代高通量的元素分析手段(如ICP-MS/OES)的出现,使得同时定量分析多个元素的含量成为可能。植物离子组学正是利用这一高通量的分析手段,在全基因组的规模上对植物体内的离子组进行分析和对比研究,从而系统地研究揭示植物体内控制离子平衡的遗传网络与分子机制。近年来,该研究领域发展迅速,并广泛地应用于植物功能基因组研究等方面,成为植物营养研究发展的一个热点领域。本文从离子组及离子组学的概念、 离子组学的技术平台、 离子组学研究的技术路线、信息管理及其应用等方面进行综述,并对这一新兴研究领域进行了展望。     

Articulating beneficial rhizobacteria-mediated plant defenses through induced systemic resistance: A review

Induced systemic resistance (ISR) is a mechanism by which certain plant beneficial rhizobacteria and fungi produce immunity, which can stimulate crop growth and resilience against various phytopathogens, insects, and parasites. These beneficial rhizobacteria and fungi improve plant performance by regulating hormone signaling, including salicylic acid (SA), jasmonic acid (JA), prosystemin, pathogenesis-related gene 1, and ethylene (ET) pathways,which activate the gene expression of ISR, the synth...     

Tracing the origin of Spanish common bean cultivars using biochemical and molecular markers

Fifty-four accessions of Phaseolus vulgaris cultivated in Spain and representing a broad variability for this country, were studied together with 30 samples of wild forms of American origin. Two reference cultivars (from the Andes and Mesoamerica) plus two outgroups (P. coccineus and Vigna unguiculata) were also included. RAPD analysis of DNA leaf extracts were carried out with four selected primers. We also studied morphological characters of the seeds and the phaseolin electrophoretic patterns. Multivariate analysis with the UPGMA method using RAPD data clustered the samples in four groups and, comparing with morphological data and phaseolin types, showed that the Spanish cultivars were mainly of Andean origin. Nevertheless, occurrence of introgression in Spain and the consideration of the country as a second center of variability for beans can also explain the obtained results.     

cis-Configuration: a new tactic/rationale for neonicotinoid molecular design

Resistance development and limited lepidopteran activities call for the discovery of "super-neonicotinoids" solving these problems. Compounds with the cis-configuration offer an opportunity for further optimization. Fixing the nitro group in the cis-configuration provided a new approach for neonicotinoid molecular design. Introductions of the heterocycle or a bulky group are two synthesis concepts to fix the cis-configuration of the nitro group. The design, synthesis, bioactivity, and preliminary modes of action of five types of cis-neonicotinoids are reviewed. cis- and trans-neonicotinoids have some differences in bioactivities and modes of action. This study focused, especially, on the reaction diversities of nitromethylene analogues of imidacloprid with various aldehydes.     

The role of creatine in the generation of N-methylacrylamide: a new toxicant in cooked meat

Investigations of different sources of acrylamide formation in model systems consisting of amino acids and sugars have indicated the presence of two pathways of acrylamide generation; the main pathway specifically involves asparagine to directly produce acrylamide after a sugar-assisted decarboxylation step, and the second, nonspecific pathway involves the initial formation of acrylic acid from different sources and its subsequent interaction with ammonia and/or amines to produce acrylamide or its N-alkylated derivatives. Aspartic acid, beta-alanine, and carnosine were found to follow the acrylic acid pathway. Labeling studies using [(13)C-4]aspartic acid have confirmed the occurrence in this amino acid of a previously proposed sugar-assisted decarboxylation mechanism identified in the asparagine/glucose model system. In addition, creatine was found to be a good source of methylamine in model systems and was responsible for the formation of N-methylacrylamide through the acrylic acid pathway. Labeling studies using creatine (methyl-d(3)) and (15)NH(4)Cl have indicated that both the nitrogen and the methyl groups of methylamine had originated from creatine. Furthermore, analysis of cooked meat samples has also confirmed the formation of N-methylacrylamide during cooking.     

Development of a new high-performance liquid chromatography-electrospray ionization time-of-flight mass spectrometry method for the determination of low molecular mass organic acids in plant tissue extracts

A liquid chromatography-electrospray ionization time-of-flight mass spectrometry method has been developed for the direct and simultaneous determination of 10 low molecular mass organic acids in different plant tissue extracts. The method does not include a derivatization step. Quantification was accomplished using (13)C-labeled malic and succinic acids as internal standards. Good limits of detection (0.05-1.27 pmol) were obtained for malic, 2-oxoglutaric, succinic, quinic, shikimic, cis-aconitic, and citric acids, whereas for oxalic, ascorbic, and fumaric acids limits of detection were 255, 25, and 11 pmol, respectively. Repeatability values for the retention time and peak area were <5%, with the exception of ascorbic acid. Analyte recovery was between 92% and 110% in most cases, with the exception of oxalic (39-108%), 2-oxoglutaric (44-69%), and ascorbic (22-86%) acids, which may require specific extraction procedures and use of the corresponding (13)C-labeled organic acid as internal standards to improve accuracy. The method was applied to three types of plant materials: sugar beet leaf extracts, tomato xylem sap, and commercial orange juice.     

Effects of plant growth-promoting rhizobacteria on the molecular responses of maize under drought and heat stresses: A review

Drought and heat are major environmental stresses that continually influence plant growth and development. Under field conditions, these stresses occur more frequently in combination than alone, which magnifies corresponding detrimental effects on the growth and productivity of agriculturally important crops. Plant responses to such abiotic stresses are quite complex and manifested in a range of developmental, molecular, and physiological modifications that lead either to stress sensitivity or tolerance/resistance. Maize (Zea mays L.) is known for its sensitivity to abiotic stresses, which often results in substantial loss in crop productivity. Bioaugmentation with plant growth-promoting rhizobacteria (PGPR) has the potential to mitigate the adverse effects of drought and heat stresses on plants. Hence, this is considered a promising and eco-friendly strategy to ensure sustainable and long-term maize production under adverse climatic conditions. These microorganisms possess various plant growth-promoting (PGP) characteristics that can induce drought and heat tolerance in maize plants by directly or indirectly influencing molecular, metabolic, and physiological stress responses of plants. This review aims to assess the current knowledge regarding the ability of PGPR to induce drought and heat stress tolerance in maize plants. Furthermore, the drought and heat stress-induced expression of drought and heat stress response genes for this crop is discussed with the mechanisms through which PGPR alter maize stress response gene expression.     

Identification of artichoke SSR markers: molecular variation and patterns of diversity in genetically cohesive taxa and wild allies

A set of 24 microsatellite markers was identified in the artichoke genome, using various approaches. A genomic library allowed the development of 14 SSR markers, whereas the other 10 were obtained from gene intron/UTR regions or from other species. Allelic variation was scored in C. cardunculus (artichoke, cultivated cardoon, and wild cardoon) samples, and in other wild Cynara allies. For the 23 polymorphic loci, a total of 165 alleles were scored, 135 of which in the artichoke primary genepool, and the remaining ones in the other Cynara species. Some allele combinations were able to identify artichoke varietal types, and some alleles were unique to specific groups. This makes these markers potentially useful in product traceability and in contributing to the saturation of genetic maps. The percentage of shared alleles between C. cardunculus taxonomic groups, and Nei’s genetic distances indicated that wild cardoons from the Eastern Mediterranean were more closely related to artichoke and less to cultivated cardoon in comparison to wild cardoons from the Western Mediterranean, and the genetic distance between the two wild cardoon genepools was rather high. The UPGMA dendrogram based on Nei’s genetic distances revealed that artichokes formed a fairly defined cluster, whereas Eastern wild cardoons occupied another branch, and Western wild cardoons were clustered together with cultivated cardoons. The transferability of microsatellite markers to other Cynara wild species was quite good. Sequencing alleles at three loci showed that, apart from microsatellite length variation, point mutations and insertion/deletions were quite abundant especially when comparing C. cardunculus to the other Cynara species. In the sequenced regions, some SNPs were identified which distinguished artichoke on one side, and cultivated and wild cardoon on the other, while other SNPs were apportioned according to the geographic distribution of Cynara wild species.     

Iron transport in plants: Future research in view of a plant nutritionist and a molecular biologist

Iron is attractive to plant physiologists since J. Sachs has proven in 1868 the essentiality and the possible leaf uptake of Fe. It lasted about 100 years before the principal processes for Fe mobilization in the rhizosphere were discovered and classified as two distinct strategies for Fe acquisition. During the 80's and 90's of the last century the uptake of Fe²⁺ and Fe^III-phytosiderophores by specific transporters in strategy I- and strategy II-plants, respectively, were postulated without any application of the new approaching molecular techniques. In the following decade, the various transporters for Fe uptake by roots, such as AtIRT1 in Arabidopsis or ZmYS1 in maize and their possible regulation were characterized. In the following years with fast developing molecular approaches further Fe trans ortsrs were genetically described with often only vague physiological functions. In view of a plant nutritionist, besides uptake processes by roots, the following transport processes within the respective target tissue have to be considered by molecular biologists in more detail: 1) radial transfer of Fe from the root cortex through the endodermis, 2) xylem loading in roots, 3) transfer of Fe from xylem to phloem via transfer cells, 4) phloem loading with Fe in source leaves and retranslocation to sink organs, and 5) remobilization and retranslocation via the phloem during senescence of perennial plants. The importance of these various specific transport processes for a well-regulated Fe homeostasis in plants and new strategies to identify and characterize proteins involved in Fe transport and homeostasis will be discussed.     

Improvement of mining soil properties through the use of a new bio-conditioner prototype: a greenhouse trial

Journal of Soils and Sediments - The effect of a prototype of humic bio-conditioner (H-BC) was assessed on the development of edaphic properties and the growth of maize plants in an edaphic...     

Canopy herbivory can mediate the influence of plant genotype on soil processes through frass deposition

The ecosystem consequences of intraspecific genetic variation is an emerging field of research that strengthens the link between population and ecosystem ecology. Despite recent advances, it remains unclear under what conditions (abiotic and biotic) plant genetic variation will be important to belowground processes. Forest canopy herbivores can have large influences on soil processes by altering the timing, quantity, and quality of forest floor inputs. We demonstrate that the frass inputs from canopy folivores (forest tent caterpillars and gypsy moths) reflect the intraspecific variation in green leaf chemistry (C:N, condensed tannins) of the aspen clones on which they fed. We then varied the genotype and nutrient availability of aspen and monitored the decomposition of both gypsy moth frass and senesced leaf litter in laboratory microcosms for 63 days. Aspen genotype influenced the short-term, frass-induced soil respiration as well as the longer-term, litter-induced respiration. In addition, aspen genotype interacted with nutrient availability to influence the activity of extracellular enzymes measured at the end of the experiment. These results suggest that in aspen forests, canopy herbivores can mediate the influence of intraspecific variation on ecosystem processes through frass deposition. Intraspecific variation is likely more important to ecosystem functioning than previously thought when trophic interactions are also taken into account. The potential for genetic variation within a single plant species to influence the ecosystem effects of herbivores highlights the importance of understanding how and when genetic variation matters to ecosystem processes.     

Fitting plants to soil through mycorrhizal fungi: Mycorrhiza effects on plant growth and soil organic matter

Summary Vesicular-arbuscular mycorrhizal (VAM) fungi affect diverse aspects of plant form and function. Since mycorrhiza-mediated changes in host-plant responses to root colonization by different VAM fungi vary widely, it is important to assess each endophyte for each specific effect it can elicit from its host as part of the screening process for effectiveness. Three species of VAM fungi and a mixture of species were compared with non-VAM controls for their effects on soil organic matter contents and on nutrition and morphology in two varieties (native and hybrid) of corn (Zea mays L.) and one of sunflower (Helianthus annuus L.) in P-sufficient and N-deficient soil in pot cultures. Differences in soil organic matter due to the fungal applications were highly significant with all host plants. Native corn responded more to VAM colonization than the hybrid did; differences in treatments were significant in leaf area, plant biomass, and root: shoot ratio in the former, but not in the latter. Responses in the sunflower were similar to those in the native corn. Significant VAM treatment-related differences in shoot N and P contents were not reflected in shoot biomass, which was invariant. Correlations between plant or soil parameters and the intensity of VAM colonization were found only in soil organic matter with the native corn, in specific leaf area in the hybrid corn, and in plant biomass in the sunflower. The presence of the different endophytes and not the intensity of colonization apparently elicited different host responses.     

Silicon-mediated genotoxic alterations in Brassica juncea under arsenic stress: A comparative study of biochemical and molecular markers

Arsenic (As), one of the most harmful toxicant at the global level, severely affects plant metabolism when taken up. Interestingly, the presence of silicon (Si) as a fertilizer in As-contaminated soil is an effective strategy to decrease As accumulation in plants. Brassica juncea (var. Varuna) were grown hydroponically to investigate the role of Si at biochemical and molecular levels under arsenite (As³⁺) stress. Seedlings of B. juncea were exposed to As³⁺, Si, and a combination of both elements. Our data demonstrated that seedlings exposed to As³⁺ showed an inhibition in shoot length, chlorophyll, carotenoid, and protein, while co-application of Si improved these growth parameters. Silicon supplementation reduced As accumulation in shoot. Increase/decrease was observed in stress-related parameters (cysteine and proline), antioxidant enzymes (superoxide dismutase, ascorbate peroxidase, and catalase), and oxidative stress markers (malondialdehyde and H₂O₂), which were improved upon co-application of Si as compared to As³⁺ alone treatment. Random amplified polymorphic DNA (RAPD) is a suitable biomarker assay for plants for assessing the genotoxicity. Seven RAPD primers produced a total of 39 and 48 bands in the leaves of the untreated and treated seedlings, respectively. The RAPD band-profiles and genomic template stability were consistent with other growth and physiological parameters. In conclusion, the genotoxic alterations along with the biochemical parameters indicate that the exposure to Si mitigates As³⁺-induced oxidative stress by improving the stress-related parameters and antioxidant system in B. juncea.     

植物低温胁迫响应的生化与分子生物学机制研究进展

综述了植物对低温胁迫响应的生化与分子生物学机制 ,即低温信号激活某些抗冻基因的表达 ,产生特异蛋白和渗透调节物质 ,使植物抗氧化胁迫能力和渗透调节能力提高 ,保护了植物细胞。而植物抗寒性的提高决定于抗冻基因的表达 ,如何通过分子生物学手段提高植物抗冻基因表达的效应是培育植物抗寒品系的关键。并展望了该领域今后研究的方向。     

Fitting plants to soil through mycorrhizal fungi: plant nutrition in host-endophyte combinations evaluated by the diagnosis and recommendation integrated system

Summary Vesicular-arbuscular mycorrhizal (VAM) fungi improve plant growth in marginal soils. This study was conducted to determine the effects of three species of VAM fungi on plant nutrition in two cultivars of corn (Zea mays L.) and one of sunflower (Helianthus annus L.). Plants were grown in pot cultures under controlled (greenhouse) conditions in a soil high in K, Mg, and P, and low in Ca and N, and were supplied with amounts of VAM-fungal inocula in which equal numbers of infective propagules had previously been determined. Analysis of variance showed highly significant main effects and interactions due to both factors (plant and fungus) for N, P, Ca, and Mg. For K, only plant effects were significant (P<0.043). The uptake of nutrients was selectively enhanced or inhibited by one or the other VAM fungus relative to non-VAM control plants. In sunflower, N concentration was markedly enhanced (73%) by the mixed inoculum of the three fungi, even though individual effects were not significant. Evaluation of leaf nutrient analyses by the Diagnosis and Recommendation Integrated System (DRIS) revealed the utility of this system to rank nutritional effects by VAM fungi in an order of relative nutrient deficiency. The DRIS therefore is seen as a useful tool in evaluating and selecting VAM fungi for the alleviation of specific nutrient disorders.Work was funded by the Program in Science and Technology Cooperation, Office of the Science Advisor, Agency for International Development, as Project No. 8.055, and was conducted in collaboration at the Colegio de Postgraduados and the Western Regional Research Center