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Agency: Cordis | Branch: FP7 | Program: CP-TP | Phase: KBBE.2013.3.1-01 | Award Amount: 9.55M | Year: 2013

Plants synthesize a staggering variety of secondary metabolites, and this chemodiversity is a poorly used pool of natural molecules with bioactive properties of importance for applications in the pharma and food industries. BacHBerry focusses on phenolic compounds, a large and diverse class of plant metabolites, which are currently in the spotlight due to their claimed beneficial effects in prevention and treatment of chronic diseases, but that also have applications as cosmetics, flavours and food colorants etc. Berries are soft and colourful fruits, with great diversity, high content and unique profiles in phenolic compounds, making them a major source of these high-value metabolites. The BacHBerry project aims to develop a portfolio of sustainable methodologies to mine the potential of the untapped biodiversity of the bioactive phenolic compounds in an extensive collection of berry species. Full exploitation of this unrivalled natural resource requires an integrated and comprehensive effort from bioprospecting in berries using SMART high-throughput screens for the valorisation of phenolic bioactivities aligned with their identification using cutting edge analytics and subsequent elucidation of their biosynthetic pathways. This knowledge will facilitate metabolic engineering of suitable bacterial hosts for high-value phenolics production in scalable fermentation bioprocesses, ultimately serving as commercial production platforms. The consortium comprises a full chain of research and innovation, with 12 research groups, 5 SMEs and a large enterprise, representing 10 countries including partners from ICPC countries Russia, Chile and China, with the capacity to exploit novel bioactivities from berry fruits diversity. BacHBerry develops a pipeline of sustainable and cost-effective processes to facilitate production of added-value berry phenolics with immediate potential for commercialization and consequent socio-economic benefits for the European community and beyond.

At present, plant molecular systematics and DNA barcoding techniques rely heavily on the use of chloroplast gene sequences. Because of the relatively low evolutionary rates of chloroplast genes, there are very few choices suitable for molecular studies on angiosperms at low taxonomic levels, and for DNA barcoding of species. We scanned the entire chloroplast genomes of 12 genera to search for highly variable regions. The sequence data of 9 genera were from GenBank and 3 genera were of our own. We identified nearly 5% of the most variable loci from all variable loci in the chloroplast genomes of each genus, and then selected 23 loci that were present in at least three genera. The 23 loci included 4 coding regions, 2 introns, and 17 intergenic spacers. Of the 23 loci, the most variable (in order from highest variability to lowest) were intergenic regions ycf1-a, trnK, rpl32-trnL, and trnH-psbA, followed by trnS(UGA)-trnG(UCC), petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnS(UGA)-trnG(UCC), trnT-psbD, and trnW-psaJ, showed very high nucleotide diversity per site (π values) across three genera. Other loci may have strong potential for resolving phylogenetic and species identification problems at the species level. The loci accD-psaI, rbcL-accD, rpl32-trnL, rps16-trnQ, and ycf1 are absent from some genera. To amplify and sequence the highly variable loci identified in this study, we designed primers from their conserved flanking regions. We tested the applicability of the primers to amplify target sequences in eight species representing basal angiosperms, monocots, eudicots, rosids, and asterids, and confirmed that the primers amplified the desired sequences of these species. Chloroplast genome sequences contain regions that are highly variable. Such regions are the first consideration when screening the suitable loci to resolve closely related species or genera in phylogenetic analyses, and for DNA barcoding.

Yang X.,CAS Institute of Botany
PloS one | Year: 2012

The success of seedling establishment of desert plants is determined by seedling emergence response to an unpredictable precipitation regime. Sand burial is a crucial and frequent environmental stress that impacts seedling establishment on sand dunes. However, little is known about the ecological role of seed mucilage in seedling emergence in arid sandy environments. We hypothesized that seed mucilage enhances seedling emergence in a low precipitation regime and under conditions of sand burial. In a greenhouse experiment, two types of Artemisia sphaerocephala achenes (intact and demucilaged) were exposed to different combinations of burial depth (0, 5, 10, 20, 40 and 60 mm) and irrigation regimes (low, medium and high, which simulated the precipitation amount and frequency in May, June and July in the natural habitat, respectively). Seedling emergence increased with increasing irrigation. It was highest at 5 mm sand burial depth and ceased at burial depths greater than 20 mm in all irrigation regimes. Mucilage significantly enhanced seedling emergence at 0, 5 and 10 mm burial depths in low irrigation, at 0 and 5 mm burial depths in medium irrigation and at 0 and 10 mm burial depths in high irrigation. Seed mucilage also reduced seedling mortality at the shallow sand burial depths. Moreover, mucilage significantly affected seedling emergence time and quiescence and dormancy percentages. Our findings suggest that seed mucilage plays an ecologically important role in successful seedling establishment of A. sphaerocephala by improving seedling emergence and reducing seedling mortality in stressful habitats of the sandy desert environment.

Bennetzen J.L.,CAS Institute of Botany | Wang H.,CAS Institute of Botany
Annual Review of Plant Biology | Year: 2014

Transposable elements (TEs) are the key players in generating genomic novelty by a combination of the chromosome rearrangements they cause and the genes that come under their regulatory sway. Genome size, gene content, gene order, centromere function, and numerous other aspects of nuclear biology are driven by TE activity. Although the origins and attitudes of TEs have the hallmarks of selfish DNA, there are numerous cases where TE components have been co-opted by the host to create new genes or modify gene regulation. In particular, epigenetic regulation has been transformed from a process to silence invading TEs and viruses into a key strategy for regulating plant genes. Most, perhaps all, of this epigenetic regulation is derived from TE insertions near genes or TE-encoded factors that act in trans. Enormous pools of genome data and new technologies for reverse genetics will lead to a powerful new era of TE analysis in plants. Copyright © 2014 by Annual Reviews.

Chi W.,CAS Institute of Botany | Sun X.,CAS Institute of Botany | Zhang L.,CAS Institute of Botany
Annual Review of Plant Biology | Year: 2013

Intracellular signaling from plastids to the nucleus, called retrograde signaling, coordinates the expression of nuclear and plastid genes and is essential for plastid biogenesis and for maintaining plastid function at optimal levels. Recent identification of several components involved in plastid retrograde generation, transmission, and control of nuclear gene expression has provided significant insight into the regulatory network of plastid retrograde signaling. Here, we review the current knowledge of multiple plastid retrograde signaling pathways, which are derived from distinct sources, and of possible plastid signaling molecules. We describe the retrograde signaling-dependent regulation of nuclear gene expression, which involves multilayered transcriptional control, as well as the transcription factors involved. We also summarize recent advances in the identification of key components mediating signal transduction from plastids to the nucleus. © Copyright ©2013 by Annual Reviews. All rights reserved.

Ma Q.-H.,CAS Institute of Botany
Journal of Experimental Botany | Year: 2010

Cinnamyl alcohol dehydrogenase (CAD) catalyses the final step in the biosynthesis of monolignols. In the present study, a cDNA encoding a CAD was isolated from wheat, designated as TaCAD1. A genome-wide data mining in the wheat EST database revealed another 10 CAD-like homologues, namely TaCAD2 to TaCAD11. A phylogenetic analysis showed that TaCAD1 belonged to the bona fide CAD group involved in lignin synthesis. Two other putative CADs from the wheat genome (TaCAD2 and TaCAD4) also belonged to this group and were very close to TaCAD1, but lacked C-terminal domain, suggesting that they are pseudogenes. DNA gel blot analysis for the wheat genome showed two to three copies of CAD related to TaCAD1, but RNA gel blot analysis revealed only single band for TaCAD1, which was highly expressed in stem, with quite low expression in leaf and undetectable expression in root. The predicted three-dimension structure of TaCAD1 resembled that of AtCAD5, but two amino acid substitutions were identified in the substrate binding region. Recombinant TaCAD1 protein used coniferyl aldehyde as the most favoured substrate, also showed high efficiencies toward sinapyl and p-coumaryl aldehydes. TaCAD1 was an enzyme being pH-dependent and temperature-sensitive, and showing a typical random catalysing mechanism. At the milky stage of wheat, TaCAD1 mRNA abundance, protein level and enzyme activity in stem tissues were higher in a lodging-resistant cultivar (H4546) than in lodging-sensitive cultivar (C6001). These properties were correlated to the lignin contents and lodging indices of the two cultivars. These data suggest that TaCAD1 is the predominant CAD in wheat stem for lignin biosynthesis and is critical for lodging resistance. © 2010 The Author(s).

Warming, watering and elevated atmospheric CO2-concentration effects have been extensively studied separately; however, their combined impact on plants is not well understood. In the current research, we examined plant growth and physiological responses of three dominant species from the Eurasian Steppe with different functional traits to a combination of elevated CO2, high temperature, and four simulated precipitation patterns. Elevated CO2 stimulated plant growth by 10.8-41.7 % for a C3 leguminous shrub, Caragana microphylla, and by 33.2-52.3 % for a C3 grass, Stipa grandis, across all temperature and watering treatments. Elevated CO2, however, did not affect plant biomass of a C4 grass, Cleistogenes squarrosa, under normal or increased precipitation, whereas a 20.0-69.7 % stimulation of growth occurred with elevated CO2 under drought conditions. Plant growth was enhanced in the C3 shrub and the C4 grass by warming under normal precipitation, but declined drastically with severe drought. The effects of elevated CO2 on leaf traits, biomass allocation and photosynthetic potential were remarkably species-dependent. Suppression of photosynthetic activity, and enhancement of cell peroxidation by a combination of warming and severe drought, were partly alleviated by elevated CO2. The relationships between plant functional traits and physiological activities and their responses to climate change were discussed. The present results suggested that the response to CO2 enrichment may strongly depend on the response of specific species under varying patterns of precipitation, with or without warming, highlighting that individual species and multifactor dependencies must be considered in a projection of terrestrial ecosystem response to climatic change.

Liu S.,CAS Institute of Botany
Nature Genetics | Year: 2016

Maize production is threatened by drought stress worldwide. Identification of the genetic components underlying drought tolerance in maize is of great importance. Here we report a genome-wide association study (GWAS) of maize drought tolerance at the seedling stage that identified 83 genetic variants, which were resolved to 42 candidate genes. The peak GWAS signal showed that the natural variation in ZmVPP1, encoding a vacuolar-type H+ pyrophosphatase, contributes most significantly to the trait. Further analysis showed that a 366-bp insertion in the promoter, containing three MYB cis elements, confers drought-inducible expression of ZmVPP1 in drought-tolerant genotypes. Transgenic maize with enhanced ZmVPP1 expression exhibits improved drought tolerance that is most likely due to enhanced photosynthetic efficiency and root development. Taken together, this information provides important genetic insights into the natural variation of maize drought tolerance. The identified loci or genes can serve as direct targets for both genetic engineering and selection for maize trait improvement. © 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

CAS Institute of Botany | Date: 2014-07-18

The present invention provides a method of producing transgenic plants which are drought resistant, plants obtainable by the method and uses thereof.

CAS Institute of Botany | Date: 2014-10-15

The present invention relates to a method for preparing fertility-lowered plant. The present invention provides an RNA interference vector and a method for obtaining a transgenic plant by introducing said RNA interference vector into a target plant; said transgenic plant is the following 1) or 2): 1) Sterile transgenic plant or 2) The fertility of said transgenic plant is lower than said target plant; the present invention also provides a method for cultivating a target plant to a sterile mutant or fertility-lowered mutant by sodium azide mutagenesis. The experiments of the present invention proved that the present invention provides various methods for preparing sterile lines or fertility-lowered lines; including RNA interference or TILLING (Targeting Induced Local Lesions IN Genomes) technology selection; sterile lines prepared by the methods of the present invention establish the basis of rice heterosis and crossbreeding.

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