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Integration of promoters, inverted repeat sequences and proteomic data into a model for high silencing efficiency of coeliac disease related gliadins in bread wheat

Background: Wheat gluten has unique nutritional and technological characteristics, but is also a major trigger of allergies and intolerances. One of the most severe diseases caused by gluten is coeliac disease. The peptides produced in the digestive tract by the incomplete digestion of gluten proteins trigger the disease. The majority of the epitopes responsible reside in the gliadin fraction of gluten. The location of the multiple gliadin genes in blocks has to date complicated their elimination by classical breeding techniques or by the use of biotechnological tools.As an approach to silence multiple gliadin genes we have produced 38 transgenic lines of bread wheat containing combinations of two endosperm-specific promoters and three different inverted repeat sequences to silence three fractions of gliadins by RNA interference. Results: The effects of the RNA interference constructs on the content of the gluten proteins, total protein and starch, thousand seed weights and SDSS quality tests of flour were analyzed in these transgenic lines in two consecutive years. The characteristics of the inverted repeat sequences were the main factor that determined the efficiency of silencing. The promoter used had less influence on silencing, although a synergy in silencing efficiency was observed when the two promoters were used simultaneously. Genotype and the environment also influenced silencing efficiency. Conclusions: We conclude that to obtain wheat lines with an optimum reduction of toxic gluten epitopes one needs to take into account the factors of inverted repeat sequences design, promoter choice and also the wheat background used.

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Vernalization requirement duration in winter wheat is controlled by TaVRN-A1 at the protein level

Vernalization requirement duration in winter wheat is controlled by TaVRN-A1 at the protein level | Plant Breeding and Genomics News | Scoop.it

Winter wheat requires a period of low temperatures to accelerate flowering (vernalization). This requirement could make winter wheat more vulnerable to elevated global temperature via insufficient vernalization. All known vernalization genes are cloned according to qualitative variation in vernalization requirement between spring and winter wheat, but genes controlling quantitative variation for more or less vernalization requirement among winter wheat cultivars remain unknown. We report here that the gene for the vernalization requirement duration in winter wheat was cloned using a BC1F2:3 population that was segregated in a 3:1 ratio of the early flowered plants and the late flowered plants after vernalized for 3 weeks. The positional cloning of the gene for vernalization requirement duration demonstrated that this trait is controlled by TaVRN-A1 at the protein level. The Ala180 in vrn-A1a encoded by the dominant allele for 3-week vernalization was mutated to Val180 in vrn-A1b encoded by the recessive allele for 6-week vernalization. Further studies indicated that the mutated Val180 in vrn-A1b protein decreased ability to bind with TaHOX1 (the first homeobox protein in T. aestivum) by in vitro protein pulldown assays and immunoprecipitation analyses. The direct binding of TaVRN-A1 and TaHOX1 proteins was confirmed in the nucleus of living plant cells by bimolecular fluorescence complementation (BiFC) analyses. The TaHOX1 gene was found to be up-regulated by low temperature and have significant genetic effect on heading date, suggesting that TaHOX1 functions in the flowering pathway in winter wheat.

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Integrating place-specific livelihood and equity outcomes into global assessments of bioenergy deployment

http://bcove.me/u16ma8o3 video

 

Integrated assessment models suggest that the large-scale deployment of bioenergy could contribute to ambitious climate change mitigation efforts. However, such a shift would intensify the global competition for land, with possible consequences for 1.5 billion smallholder livelihoods that these models do not consider. Maintaining and enhancing robust livelihoods upon bioenergy deployment is an equally important sustainability goal that warrants greater attention. The social implications of biofuel production are complex, varied and place-specific, difficult to model, operationalize and quantify. However, a rapidly developing body of social science literature is advancing the understanding of these interactions. In this letter we link human geography research on the interaction between biofuel crops and livelihoods in developing countries to integrated assessments on biofuels. We review case-study research focused on first-generation biofuel crops to demonstrate that food, income, land and other assets such as health are key livelihood dimensions that can be impacted by such crops and we highlight how place-specific and global dynamics influence both aggregate and distributional outcomes across these livelihood dimensions. We argue that place-specific production models and land tenure regimes mediate livelihood outcomes, which are also in turn affected by global and regional markets and their resulting equilibrium dynamics. The place-specific perspective suggests that distributional consequences are a crucial complement to aggregate outcomes; this has not been given enough weight in comprehensive assessments to date. By narrowing the gap between place-specific case studies and global models, our discussion offers a route towards integrating livelihood and equity considerations into scenarios of future bioenergy deployment, thus contributing to a key challenge in sustainability sciences.

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Wasted: How America Is Losing Up to 40 Percent of Its Food from Farm to Fork to Landfill

Wasted: How America Is Losing Up to 40 Percent of Its Food from Farm to Fork to Landfill | Plant Breeding and Genomics News | Scoop.it

NRCD Issue Paper

http://www.nrdc.org/food/files/wasted-food-ip.pdf

 

Getting food from the farm to our fork eats up 10 percent of the total U.S. energy budget, uses 50 percent of U.S. land, and swallows 80 percent of all freshwater consumed in the United States. Yet, 40 percent of food in the United States today goes uneaten. This not only means that Americans are throwing out the equivalent of $165 billion each year, but also that the uneaten food ends up rotting in landfills as the single largest component of U.S. municipal solid waste where it accounts for a large portion of U.S. methane emissions. Reducing food losses by just 15 percent would be enough food to feed more than 25 million Americans every year at a time when one in
six Americans lack a secure supply of food to their tables. Increasing the efficiency of our food system is a triplebottom-line solution that requires collaborative efforts by businesses, governments and consumers. The U.S.
government should conduct a comprehensive study of losses in our food system and set national goals for waste reduction; businesses should seize opportunities to streamline their own operations, reduce food losses and save
money; and consumers can waste less food by shopping wisely, knowing when food goes bad, buying produce that is perfectly edible even if it’s less cosmetically attractive, cooking only the amount of food they need, and eating
their leftovers.

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PLOS ONE: Increasing Seriousness of Plant Invasions in Croplands of Eastern China in Relation to Changing Farming Practices: A Case Study

PLOS ONE: Increasing Seriousness of Plant Invasions in Croplands of Eastern China in Relation to Changing Farming Practices: A Case Study | Plant Breeding and Genomics News | Scoop.it

Arable areas are commonly susceptible to alien plant invasion because they experience dramatic environmental influences and intense anthropogenic activity. However, the limited reports on relevant factors in plant invasion of croplands have addressed single or a few invasive species and environmental factors. To elucidate key factors affecting plant invasions in croplands, we analyzed the relationship between 11 effective factors and changes in composition of alien plants, using field surveys of crop fields in Anhui Province conducted during 1987–1990 (historical dataset) and 2005–2010 (recent dataset), when rapid urbanization was occurring in China. We found that in the past few decades, the dominance and richness of alien plant populations approximately doubled, despite differences among the 4 regions of Anhui Province. Among the 38 alien invasive plant species observed in the sites, the dominance values of 11 species increased significantly, while the dominance of 4 species decreased significantly. The quantity of chemical fertilizer and herbicide applied, population density, agricultural machinery use, traffic frequency, and annual mean temperature were significantly related to increased richness and annual dominance values of alien plant species. Our findings suggest that the increase in alien plant invasions during the past few decades is primarily a result of increased application of chemical fertilizer and herbicides.

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FAO - News Article: Bridging the information gap in agriculture

FAO - News Article: Bridging the information gap in agriculture | Plant Breeding and Genomics News | Scoop.it

Ten years after its launch in 2003, AGORA (Access to Global Online Research in Agriculture) now provides free or low-cost access to over 3 500 key journals and 3 300 books in food, nutrition, agriculture and related biological, environmental and social sciences.

 

"Lack of access to knowledge is a major bottleneck for many poor countries to develop their agricultural sector and ensure food security," said FAO Director-General José Graziano da Silva celebrating AGORA's 10th anniversary in Rome.

 

Graziano da Silva added that knowledge is only valuable to the extent that those who need it can access it.

 
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Phytochrome C Is A Key Factor Controlling Long-day Flowering in Barley (Hordeum vulgare L.)

The spring-type near isogenic line (NIL) of the winter-type barley (Hordeum vulgare ssp. vulgare L.) variety Hayakiso 2 (HK2) was developed by introducing Vrn-H1 for spring growth habit from a spring-type variety Indo Omugi. Contrary to expectations, the spring-type NIL flowered later than winter-type HK2. This phenotypic difference was controlled by a single gene which co-segregated only with phytochrome C (HvPhyC) among three candidates around the Vrn-H1 region (Vrn-H1, HvPhyC, and HvCK2alpha), indicating that HvPhyC was the most likely candidate gene. Compared to the late-flowering allele HvPhyC-l from the NIL, the early-flowering allele HvPhyC-e from HK2 had a single nucleotide polymorphism T1139C in exon 1, which caused a non-synonymous amino acid substitution Phe380Ser in the functionally essential GAF domain. Functional assay using a rice (Oryza sativa L.) phyA phyC double mutant line showed that both of the HvPhyC alleles are functional but HvPhyC-e may have a hyperfunction. Expression analysis using NILs carrying HvPhyC-e and HvPhyC-l (NIL (HvPhyC-e) and NIL (HvPhyC-l), respectively) showed that HvPhyC-e up-regulated only the flowering promoter HvFT1 by bypassing the circadian clock genes and flowering integrator HvCO1 under a long photoperiod. Consistent with the up-regulation, NIL (HvPhyC-e) flowered earlier than NIL (HvPhyC-l) under long photoperiods. These results implied that HvPhyC is a key factor to control long-day flowering directly.

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PLOS ONE: Cerebroside C Increases Tolerance to Chilling Injury and Alters Lipid Composition in Wheat Roots

PLOS ONE: Cerebroside C Increases Tolerance to Chilling Injury and Alters Lipid Composition in Wheat Roots | Plant Breeding and Genomics News | Scoop.it

Chilling tolerance was increased in seed germination and root growth of wheat seedlings grown in media containing 20 µg/mL cerebroside C (CC), isolated from the endophytic Phyllosticta sp. TG78. Seeds treated with 20 µg/mL CC at 4°C expressed the higher germination rate (77.78%), potential (23.46%), index (3.44) and the shorter germination time (6.19 d); root growth was also significantly improved by 13.76% in length, 13.44% in fresh weight and 6.88% in dry mass compared to controls. During the cultivation process at 4°C for three days and the followed 24 h at 25°C, lipid peroxidation, expressed by malondialdehyde (MDA) content and relative membrane permeability (RMP) was significantly reduced in CC-treated roots; activities of lipoxygenase (LOX), phospholipid C (PLC) and phospholipid D (PLD) were inhibited by 13.62–62.26%, 13.54–63.93% and 13.90–61.17%, respectively; unsaturation degree of fatty acids was enhanced through detecting the contents of CC-induced linoleic acid, linolenic acid, palmitic acid and stearic acid using GC-MS; capacities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) were individually increased by 7.69–46.06%, 3.37–37.96%, and −7.00–178.07%. These results suggest that increased chilling tolerance may be due, in part, to the reduction of lipid peroxidation and alternation of lipid composition of roots in the presence of CC.

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Fertilization and uniparental chromosome elimination during crosses with maize haploid inducers

Producing maternal haploids via a male inducer can greatly accelerate maize breeding process. The mechanism underlying haploid formation, though, remains unclear. In our study, we constructed two inducer lines containing cytogenetic marker B chromosome or alien CENH3-YFP vector to investigate the mechanism. The two inducer lines as the pollinators were crossed with a hybrid ZD958, respectively. B chromosomes were detected in F1 haploids at a low frequency, which was direct evidence to support the occurrence of selective chromosome elimination during haploid formation. We found that most of the inducer chromosomes were eliminated in haploid embryonic cells during the first week after pollination. The gradual elimination of chromosomes was also detected in the endosperm of defective kernels, although it occurred only in some endosperm cells as late as 15 days after pollination. We also performed a genome-wide identification of SNP markers in the inducers, non-inducer inbred lines and 42 derived haploids using a 50K SNP array. We found a ~44Mb heterozygous fragment from the male parent was detected in a single haploid, which further supported the occurrence of paternal introgression. Our results suggest that selective elimination of uniparental chromosomes leads to the formation of haploid and possible defective kernels in maize as well, which is accompanied with unusual paternal introgression in haploid cells.

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Herbivore exploits orally secreted bacteria to suppress plant defenses

Induced plant defenses in response to herbivore attack are modulated by cross-talk between jasmonic acid (JA)- and salicylic acid (SA)-signaling pathways. Oral secretions from some insect herbivores contain effectors that overcome these antiherbivore defenses. Herbivores possess diverse microbes in their digestive systems and these microbial symbionts can modify plant-insect interactions; however, the specific role of herbivore-associated microbes in manipulating plant defenses remains unclear. Here, we demonstrate that Colorado potato beetle (Leptinotarsa decemlineata) larvae exploit bacteria in their oral secretions to suppress antiherbivore defenses in tomato (Solanum lycopersicum). We found that antibiotic-untreated larvae decreased production of JA and JA-responsive antiherbivore defenses, but increased SA accumulation and SA-responsive gene expression. Beetles benefit from down-regulating plant defenses by exhibiting enhanced larval growth. In SA-deficient plants, suppression was not observed, indicating that suppression of JA-regulated defenses depends on the SA-signaling pathway. Applying bacteria isolated from larval oral secretions to wounded plants confirmed that three microbial symbionts belonging to the genera Stenotrophomonas, Pseudomonas, and Enterobacter are responsible for defense suppression. Additionally, reinoculation of these bacteria to antibiotic-treated larvae restored their ability to suppress defenses. Flagellin isolated from Pseudomonas sp. was associated with defense suppression. Our findings show that the herbivore exploits symbiotic bacteria as a decoy to deceive plants into incorrectly perceiving the threat as microbial. By interfering with the normal perception of herbivory, beetles can evade antiherbivore defenses of its host.

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Light at the End of a Tunnel: International Atomic Energy Agency Contributes to Global Fight to Stop a Wheat Killer

Light at the End of a Tunnel: International Atomic Energy Agency Contributes to Global Fight to Stop a Wheat Killer | Plant Breeding and Genomics News | Scoop.it

The IAEA in collaboration with the FAO sought to help nations produce mutant wheat varieties resistant to Ug99 through support undertaken at the FAO/IAEA laboratory in Austria. The FAO/IAEA plant breeding and genetics experts use radiation induced mutation techniques, to develop varieties that can withstand drought, saline soil conditions and diseases. Pierre Lagoda, Head of the Plant Breeding and Genetics Section, said, "The robust varieties of rice, wheat, barley, bananas, cassava, indigenous grains and other staple crops that we have developed are contributing to greater food security and agricultural sustainability."

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PLOS ONE: Randomly Detected Genetically Modified (GM) Maize (Zea mays L.) near a Transport Route Revealed a Fragile 45S rDNA Phenotype

PLOS ONE: Randomly Detected Genetically Modified (GM) Maize (Zea mays L.) near a Transport Route Revealed a Fragile 45S rDNA Phenotype | Plant Breeding and Genomics News | Scoop.it

Monitoring of genetically modified (GM) crops has been emphasized to prevent their potential effects on the environment and human health. Monitoring of the inadvertent dispersal of transgenic maize in several fields and transport routes in Korea was carried out by qualitative multiplex PCR, and molecular analyses were conducted to identify the events of the collected GM maize. Cytogenetic investigations through fluorescence in situhybridization (FISH) of the GM maize were performed to check for possible changes in the 45S rDNA cluster because this cluster was reported to be sensitive to replication and transcription stress. Three GM maize kernels were collected from a transport route near Incheon port, Korea, and each was found to contain NK603, stacked MON863 x NK603, and stacked NK603 x MON810 inserts, respectively. Cytogenetic analysis of the GM maize containing the stacked NK603 x MON810 insert revealed two normal compact 5S rDNA signals, but the 45S rDNA showed a fragile phenotype, demonstrating a “beads-on-a-string” fragmentation pattern, which seems to be a consequence of genetic modification. Implications of the 45S rDNA cluster fragility in GM maize are also discussed.

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PLOS ONE: A Test for Pre-Adapted Phenotypic Plasticity in the Invasive Tree Acer negundo L.

PLOS ONE: A Test for Pre-Adapted Phenotypic Plasticity in the Invasive Tree Acer negundo L. | Plant Breeding and Genomics News | Scoop.it

Phenotypic plasticity is a key mechanism associated with the spread of exotic plants and previous studies have found that invasive species are generally more plastic than co-occurring species. Comparatively, the evolution of phenotypic plasticity in plant invasion has received less attention, and in particular, the genetic basis of plasticity is largely unexamined. Native from North America, Acer negundo L. is aggressively impacting the riparian forests of southern and eastern Europe thanks to higher plasticity relative to co-occurring native species. We therefore tested here whether invasive populations have evolved increased plasticity since introduction. The performance of 1152 seedlings from 8 native and 8 invasive populations was compared in response to nutrient availability. Irrespective of nutrients, invasive populations had higher growth and greater allocation to above-ground biomass relative to their native conspecifics. More importantly, invasive genotypes did not show increased plasticity in any of the 20 traits examined. This result suggests that the high magnitude of plasticity to nutrient variation of invasive seedlings might be pre-adapted in the native range. Invasiveness of A. negundo could be explained by higher mean values of traits due to genetic differentiation rather than by evolution of increased plasticity.

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BMC Genomics | Abstract | Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress

Background: Drought tolerance is an attribute maintained in plants by cross-talk between multiple and cascading metabolic pathways. Without a sequenced genome available for horse gram, it is difficult to comprehend such complex networks and intercalated genes associated with drought tolerance of horse gram (Macrotyloma uniflorum). Therefore, de novo transcriptome discovery and associated analyses was done for this highly drought tolerant yet under exploited legume to decipher its genetic makeup. Results: Eight samples comprising of shoot and root tissues of two horse gram genotypes (drought-sensitive; M-191 and drought-tolerant; M-249) were used for comparison under control and polyethylene glycol-induced drought stress conditions. Using Illumina sequencing technology, a total of 229,297,896 paired end read pairs were generated and utilized for de novo assembly of horse gram. Significant BLAST hits were obtained for 26,045 transcripts while, 3,558 transcripts had no hits but contained important conserved domains. A total of 21,887 unigenes were identified. SSRs containing sequences covered 16.25% of the transcriptome with predominant tri- and mono-nucleotides (43%). The total GC content of the transcriptome was found to be 43.44%. Under Gene Ontology response to stimulus, DNA binding and catalytic activity was highly expressed during drought stress conditions. Serine/threonine protein kinase was found to dominate in Enzyme Classification while pathways belonging to ribosome metabolism followed by plant pathogen interaction and plant hormone signal transduction were predominant in Kyoto Encyclopedia of Genes and Genomes analysis. Independent search on plant metabolic network pathways suggested valine degradation, gluconeogenesis and purine nucleotide degradation to be highly influenced under drought stress in horse gram. Transcription factors belonging to NAC, MYB-related, and WRKY families were found highly represented under drought stress. qRT-PCR validated the expression profile for 9 out of 10 genes analyzed in response to drought stress. Conclusions: De novo transcriptome discovery and analysis has generated enormous information over horse gram genomics. The genes and pathways identified suggest efficient regulation leading to active adaptation as a basal defense response against drought stress by horse gram. The knowledge generated can be further utilized for exploring other underexploited plants for stress responsive genes and improving plant tolerance.

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Genetic dissection of a TIR-NB-LRR locus from the wild North American grapevine species Muscadinia rotundifolia identifies paralogous genes conferring resistance to major fungal and oomycete pathog...

Genetic dissection of a TIR-NB-LRR locus from the wild North American grapevine species Muscadinia rotundifolia identifies paralogous genes conferring resistance to major fungal and oomycete pathog... | Plant Breeding and Genomics News | Scoop.it

The most economically important diseases of grapevine cultivation worldwide are caused by the fungal pathogen powdery mildew (Erysiphe necator syn. Uncinula necator) and the oomycete pathogen downy mildew (Plasmopara viticola). Currently, grapegrowers rely heavily on the use of agrochemicals to minimise the potentially devastating impact of these pathogens on grape yield and quality. The wild North American grapevine species Muscadinia rotundifolia was recognised as early as 1889 to be resistant to both powdery and downy mildew. We have now mapped resistance to these two mildew pathogens in M. rotundifolia to a single locus on chromosome 12 that contains a family of seven TIR-NB-LRR genes. We further demonstrate that two highly homologous (86% amino acid identity) members of this gene family confer strong resistance to these unrelated pathogens following genetic transformation into susceptible V. vinifera winegrape cultivars. These two genes designated Resistance to Uncinula necator (MrRUN1) and Resistance to Plasmopara viticola (MrRPV1) are the first resistance genes to be cloned from a grapevine species. Both MrRUN1 and MrRPV1 were found to confer resistance to multiple powdery and downy mildew isolates from France, North America and Australia. However, a single powdery mildery isolate collected from the south-eastern region of North America, to which M rotundifolia is native, was capable of breaking MrRUN1-mediated resistance. Comparisons of gene organisation and coding sequences between M. rotundifolia and the cultivated grapevine V. vinifera at the MrRUN1/MrRPV1 locus revealed a high level of synteny suggesting that the TIR-NB-LRR genes at this locus share a common ancestor. This article is protected by copyright. All rights reserved.

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International Conference on Next Generation Genomic View On Plants, Animals and Microbes

International Conference on Next Generation Genomic View On Plants, Animals and Microbes | Plant Breeding and Genomics News | Scoop.it

5 - 7 March 2014 in Singapore

 

The International Conference on Next Generation Genomic View on Plants, Animals and Microbes will focus on four main areas: genomics technology, plant genomes, animal genomes and microbial genomes.

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Evaluation of five peanut (Arachis hypogaea) genotypes to identify drought responsive mechanisms utilising candidate-gene approach

Drought can significantly limit yield and quality in peanut (Arachis hypogaea L.), depending on its timing, duration and severity. The objective of this study was to identify potential molecular mechanism(s) utilising a candidate-gene approach in five peanut genotypes with contrasting drought responses. An early season drought stress treatment was applied under environmentally controlled rain-out shelters. When water was completely withheld for 3 weeks, no physical differences were observed for treated plants compared with their fully irrigated counterparts as indicated by relative water content; however, yield, grades (total sound mature kernel, TSMK), specific leaf area, and leaf dry matter content showed significant differences. Comparing expression levels of candidate genes, ‘C76–16’ exhibited significantly higher levels for CuZnSOD, NsLTP and drought protein 1 week earlier compared to the other genotypes, followed by significantly lower levels for the same genes. This suggested an early recognition of drought in C76–16 followed by an acclimation response. Cultivar ‘Georgia Green’ showed different patterns of gene-expression than C76–16. AP-3, a susceptible genotype, showed generally lower levels of gene-expression than C76–16 and Georgia Green.Myo-inositol phosphate synthase gene-expression showed high levels in irrigated treatment, ranging from 4-fold for 08T-12 to 12-fold for Georgia Green, but were significantly inhibited in drought treatment after 2 weeks of drought and after recovery.

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Economic mitigation challenges: how further delay closes the door for achieving climate targets - IOPscience

Economic mitigation challenges: how further delay closes the door for achieving climate targets - IOPscience | Plant Breeding and Genomics News | Scoop.it
While the international community aims to limit global warming to below 2 ° C to prevent dangerous climate change, little progress has been made towards a global climate agreement to implement the emissions reductions required to reach this target.
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Varietal Differences in the Flavonol Content of Mulberry (Morus spp.) Leaves and Genetic Analysis of Quercetin 3-(6-Malonylglucoside) for Component Breeding - Journal of Agricultural and Food Chemi...

Varietal Differences in the Flavonol Content of Mulberry (Morus spp.) Leaves and Genetic Analysis of Quercetin 3-(6-Malonylglucoside) for Component Breeding - Journal of Agricultural and Food Chemi... | Plant Breeding and Genomics News | Scoop.it

The varietal differences in the flavonol glycosides rutin, isoquercitrin, kaempferol 3-(6-rhamnosylglucoside), quercetin 3-(6-malonylglucoside), astragalin, quercetin 3-(6-acetylglucoside), and kaempferol 3-(6-malonylglucoside) contained in mulberry leaves were elucidated. This information was used for breeding mulberry cultivars with a high concentration of functional components. The flavonol content, composition, and proportion in leaves varied widely. ‘Kobuchizawa 1’ had the highest level of total flavonols (1819 mg/100 g of dry weight), 5 times higher than that of ‘Mikurasima 15’ (393 mg/100 g of dry weight). Quercetin 3-(6-malonylglucoside) was the most abundant flavonol, although it was not found in all cultivars. Quercetin 3-(6-acetylglucoside) was only found in ‘Keguwa’. From the quercetin 3-(6-malonylglucoside) content in crossbred offspring, malonyltransferase, an enzyme involved in quercetin 3-(6-malonylglucoside) synthesis, was acquired according to Mendelian inheritance. An offspring with a higher quercetin 3-(6-malonylglucoside) level than both parents was obtained from the crossing. This suggested that crossbreeding was effective for acquiring cultivars with a higher content of quercetin 3-(6-malonylglucoside).

 
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BMC Genomics | Abstract | Leaf cDNA-AFLP analysis of two citrus species differing in manganese tolerance in response to long-term manganese-toxicity

Background: Very little is known about manganese (Mn)-toxicity-responsive genes in citrus plants. Seedlings of 'Xuegan' (Citrus sinensis) and 'Sour pummelo' (Citrus grandis) were irrigated for 17 weeks with nutrient solution containing 2 muM (control) or 600 muM (Mn-toxicity) MnSO4. The objectives of this study were to understand the mechanisms of citrus Mn-tolerance and to identify differentially expressed genes, which might be involved in Mn-tolerance. Results: Under Mn-toxicity, the majority of Mn in seedlings was retained in the roots; C. sinensis seedlings accumulated more Mn in roots and less Mn in shoots (leaves) than C. grandis ones and Mn concentration was lower in Mn-toxicity C. sinensis leaves compared to Mn-toxicity C. grandis ones. Mn-toxicity affected C. grandis seedling growth, leaf CO2 assimilation, total soluble concentration, phosphorus (P) and magenisum (Mg) more than C. sinensis. Using cDNA-AFLP, we isolated 42 up-regulated and 80 down-regulated genes in Mn-toxicity C. grandis leaves. They were grouped into the following functional categories: biological regulation and signal transduction, carbohydrate and energy metabolism, nucleic acid metabolism, protein metabolism, lipid metabolism, cell wall metabolism, stress responses and cell transport. However, only 7 up-regulated and 8 down-regulated genes were identified in Mn-toxicity C. sinensis ones. The responses of C. grandis leaves to Mn-toxicity might include following several aspects: (1) accelerating leaf senescence; (2) activating the metabolic pathway related to ATPase synthesis and reducing power production; (3) decreasing cell transport; (4) inhibiting protein and nucleic acid metabolisms; (5) impairing the formation of cell wall; and (6) triggering multiple signal transduction pathways. We also identified many new Mn-toxicity-responsive genes involved in biological and signal transduction, carbohydrate and protein metabolisms, stress responses and cell transport. Conclusions: Our results demonstrated that C. sinensis was more tolerant to Mn-toxicity than C. grandis, and that Mn-toxicity affected gene expression far less in C. sinensis leaves. This might be associated with more Mn accumulation in roots and less Mn accumulation in leaves of Mn-toxicity C. sinensis seedlings than those of C. grandis seedlings. Our findings increase our understanding of the molecular mechanisms involved in the responses of plants to Mn-toxicity.  
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Upcoming Webinar: Use of GAPIT in Genome-Wide Association Studies - eXtension

Upcoming Webinar: Use of GAPIT in Genome-Wide Association Studies - eXtension | Plant Breeding and Genomics News | Scoop.it

Register now. Thursday, October 3, 2013 at 1:00 pm EDT

 

This webinar given by Duke Pauli will demonstrate the use of the R package, GAPIT, in a barley genome-wide association study.

 

https://www1.gotomeeting.com/register/533600505

 

 

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BMC Genetics | Abstract | Genomic prediction of trait segregation in a progeny population: a case study of Japanese pear (Pyrus pyrifolia)

Background: In cross breeding, it is important to choose a good parental combination that has high probability of generating offspring with desired characteristics. This study examines a method for predicting the segregation of target traits in a progeny population based on genome-wide markers and phenotype data of parental cultivars. Results: The proposed method combines segregation simulation and Bayesian modeling for genomic selection. Marker segregation in a progeny population was simulated based on parental genotypes. Posterior marker effects sampled via Markov Chain Monte Carlo were used to predict the segregation pattern of target traits. The posterior distribution of the proportion of progenies that fulfill selection criteria was calculated and used for determining a promising cross and the necessary size of the progeny population. We applied the proposed method to Japanese pear (Pyrus pyrifolia Nakai) data to demonstrate the method and to show how it works in the selection of a promising cross. Verification using an actual breeding population suggests that the segregation of target traits can be predicted with reasonable accuracy, especially in a highly heritable trait. The uncertainty in predictions was reflected on the posterior distribution of the proportion of progenies that fulfill selection criteria. A simulation study based on the real marker data of Japanese pear cultivars also suggests the potential of the method. Conclusions: The proposed method is useful to provide objective and quantitative criteria for choosing a parental combination and the breeding population size. 
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PLOS ONE: Transcriptome Analysis of Yellow Horn (Xanthoceras sorbifolia Bunge): A Potential Oil-Rich Seed Tree for Biodiesel in China

PLOS ONE: Transcriptome Analysis of Yellow Horn (Xanthoceras sorbifolia Bunge): A Potential Oil-Rich Seed Tree for Biodiesel in China | Plant Breeding and Genomics News | Scoop.it
Background

Yellow horn (Xanthoceras sorbifolia Bunge) is an oil-rich seed shrub that grows well in cold, barren environments and has great potential for biodiesel production in China. However, the limited genetic data means that little information about the key genes involved in oil biosynthesis is available, which limits further improvement of this species. In this study, we describe sequencing and de novo transcriptome assembly to produce the first comprehensive and integrated genomic resource for yellow horn and identify the pathways and key genes related to oil accumulation. In addition, potential molecular markers were identified and compiled.

Methodology/Principal Findings

Total RNA was isolated from 30 plants from two regions, including buds, leaves, flowers and seeds. Equal quantities of RNA from these tissues were pooled to construct a cDNA library for 454 pyrosequencing. A total of 1,147,624 high-quality reads with total and average lengths of 530.6 Mb and 462 bp, respectively, were generated. These reads were assembled into 51,867 unigenes, corresponding to a total of 36.1 Mb with a mean length, N50 and median of 696, 928 and 570 bp, respectively. Of the unigenes, 17,541 (33.82%) were unmatched in any public protein databases. We identified 281 unigenes that may be involved in de novo fatty acid (FA) and triacylglycerol (TAG) biosynthesis and metabolism. Furthermore, 6,707 SSRs, 16,925 SNPs and 6,201 InDels with high-confidence were also identified in this study.

Conclusions

This transcriptome represents a new functional genomics resource and a foundation for further studies on the metabolic engineering of yellow horn to increase oil content and modify oil composition. The potential molecular markers identified in this study provide a basis for polymorphism analysis of Xanthoceras, and even Sapindaceae; they will also accelerate the process of breeding new varieties with better agronomic characteristics.

  
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Airborne imaging could revolutionise agriculture

Airborne imaging could revolutionise agriculture | Plant Breeding and Genomics News | Scoop.it
An airborne camera capable of photographing the condition of certain crops over many acres of land could provide agriculturalists with the information they need to improve production.
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PLOS ONE: Impact of Single and Stacked Insect-Resistant Bt-Cotton on the Honey Bee and Silkworm

PLOS ONE: Impact of Single and Stacked Insect-Resistant Bt-Cotton on the Honey Bee and Silkworm | Plant Breeding and Genomics News | Scoop.it

Transgenic insect-resistant cotton (Bt cotton) has been extensively planted in China, but its effects on non-targeted insect species such as the economically important honey bee (Apis mellifera) and silkworm (Bombyx mori) currently are unknown. In this study, pollen from two Bt cotton cultivars, one expressing Cry1Ac/EPSPS and the other expressing Cry1Ac/Cry2Ab, were used to evaluate the effects of Bt cotton on adult honey bees and silkworm larvae. Laboratory feeding studies showed no adverse effects on the survival, cumulative consumption, and total hemocyte count (THC) of A. mellifera fed with Bt pollen for 7 days. No effects on the survival or development of B. mori larvae were observed either. A marginally significant difference between Cry1Ac/Cry2Ab cotton and the conventional cotton on the THC of the 3rd day of 5th B. mori instar larvae was observed only at the two highest pollen densities (approximately 900 and 8000 grains/cm2), which are much higher than the pollen deposition that occurs under normal field conditions. The results of this study show that pollen of the tested Bt cotton varieties carried no lethal or sublethal risk for A. mellifera, and the risk for B. mori was negligible.

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