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What Jeremy Grantham Gets Horribly, Horribly, Wrong About Resource Availability - Forbes

Response to recent Nature opinion peice on fertilizer resources

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GMO's Jeremy Grantham warns about impending food crisis | top1000funds.com

"Global investors should have as much as 30 per cent of their portfolios exposed to natural resources, more than double the current market average, because of a burgeoning worldwide food crisis, GMO’s Jeremy Grantham says."

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BMC Plant Biology | Abstract | 'Le Rouge et le Noir': A decline in flavone formation correlates with the rare color of black dahlia (Dahlia variabilis hort.) flowers

"An increased accumulation of anthocyanins establishes the black flowering phenotypes. In the majority of black cultivars this is due to decreased flavone accumulation and thus a lack of competition for flavanones as the common precursors of flavone formation and the anthocyanin pathway. The low FNS II activity is reflected by decreased FNS II expression."

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Trait Diversity and Potential for Selection Indices Based on Variation Among Regionally Adapted Processing Tomato Germplasm

Trait Diversity and Potential for Selection Indices Based on Variation Among Regionally Adapted Processing Tomato Germplasm | Plant Breeding and Genomics News | Scoop.it

"For many horticultural crops, selection is based on quality as well as yield. To investigate the distribution of trait variation and identify those attributes appropriate for developing selection indices, we collected and organized information related to fruit size, shape, color, soluble solids, acid, and yield traits for 143 processing tomato (Solanum lycopersicum L.) lines from North America. Evaluation of the germplasm panel was conducted in a multiyear, multilocation trial. Data were stored in a flat-file format and in a trait ontology database, providing a public archive. We estimated variance components and proportion of variance resulting from genetics for each trait. Genetic variance was low to moderate (range, 0.03–0.51) for most traits, indicating high environmental influence on trait expression and/or complex genetic architecture. Phenotypic values for each line were estimated across environments as best linear unbiased predictors (BLUPs). Principal components (PC) analysis using the trait BLUPs provided a means to assess which traits explained variation in the germplasm. The first two PCs explained 28.0% and 16.2% of the variance and were heavily weighted by measures of fruit shape and size. The third PC explained 12.9% of the phenotypic variance and was determined by fruit color and yield components. Trait BLUPs and the first three PCs were also used to explore the relationship between phenotypes and the origin of the accessions. We were able to differentiate germplasm for fruit size, fruit shape, yield, soluble solids, and color based on origin, indicating regional breeding programs provide a source of trait variation. These analyses suggest that multitrait selection indices could be established that encompass quality traits in addition to yield. However, such indices will need to balance trait correlations and be consistent with market valuation."

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International plant molecular biology: a bright future for green science

Meeting Report

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BMC Genomics | Abstract | De Novo characterization of the banana root transcriptome and analysis of gene expression under Fusarium oxysporum f. sp. Cubense tropical race 4 infection

"The combination of RNA-Seq and DGE analysis provides a powerful method for analyzing the banana root transcriptome and investigating the transcriptional changes during the response of banana genes to Foc TR4 infection. The assembled banana transcriptome provides an important resource for future investigations about the banana crop as well as the diseases that plague this valuable staple food."

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Birch tree genome sequenced for first time

Birch tree genome sequenced for first time | Plant Breeding and Genomics News | Scoop.it
Scientists have sequenced the genetic code of a birch tree for the first time, which could help protect birch populations.
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Call for Manuscripts: Sustainability | Special Issue: Underutilized Plant Species: Leveraging Food and Nutritional Security, and Income Generation

"The world is precariously dependent on a limited number of food crop species despite its wealth of traditional, locally-adapted underutilized species. In many cases, the underutilised species have a much higher nutrient content than globally known species or varieties, even though they may not be fully suited to conventional production systems. With climate uncertainty, there is an urgent need to diversify our food base to a wider range of food crop species for greater system resilience. Promoting the use of underutilized species (vegetables, fruit, starchy crops and condiments) needs to be achieved by highlighting their importance in their current production areas as well as exploiting further opportunities to extend their production and consumption. Promotion of these species, and the development of their value chains, must be based on rigorous scientific methods which will enable us to remove the stigma of ‘food for the poor’ which often hinders their popularization and new demand creation. More research for development including conservation, selection, breeding, production, nutrition studies, postharvest value-addition and advocating consumption as part of a balanced diet will facilitate some of these underutilized species transitioning into crops that can better support development and the quality of life."

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Herbivores can select for mixed defensive strategies in plants - Carmona - 2012 - New Phytologist - Wiley Online Library

Herbivores can select for mixed defensive strategies in plants - Carmona - 2012 - New Phytologist - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

"In our experimental population, natural selection imposed by herbivores can favor the evolution of mixed defense strategies in plants, accounting for the presence of intermediate levels of tolerance and resistance."

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PLOS ONE: Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis

PLOS ONE: Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis | Plant Breeding and Genomics News | Scoop.it

"The rice leaf folder (RLF), Cnaphalocrocis medinalis (Guenee) (Lepidoptera: Pyralidae), is one of the most destructive pests affecting rice in Asia. Although several studies have been performed on the ecological and physiological aspects of this species, the molecular mechanisms underlying its developmental regulation, behavior, and insecticide resistance remain largely unknown. Presently, there is a lack of genomic information for RLF; therefore, studies aimed at profiling the RLF transcriptome expression would provide a better understanding of its biological function at the molecular level."

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Why size really matters when sequencing plant genomes

Why size really matters when sequencing plant genomes | Plant Breeding and Genomics News | Scoop.it

"Genome sequencing has been restricted to species with a small genome size. With the advent of second- and third-generation sequencing technologies, the potential to sequence genomes of all sizes is becoming a reality. As the field of whole genome sequencing has developed, there has been a growing appreciation of the need to better represent the major lineages of the plant tree of life, rather than just those that contain economically important taxa. We argue that as well as accounting for phylogenetic diversity when selecting species to analyse, in order to gain a comprehensive understanding of genome evolution, large-scale sequencing projects also need to reflect the diversity of genome sizes in plants. In this art"icle we briefly outline evidence from the literature to support this view.

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Variation in carbon availability, defense chemistry and susceptibility to fungal invasion along the stems of mature trees - Goodsman - 2012 - New Phytologist - Wiley Online Library

Variation in carbon availability, defense chemistry and susceptibility to fungal invasion along the stems of mature trees - Goodsman - 2012 - New Phytologist - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

"If carbon (C) sinks withdraw carbohydrates as they are transported along tree stems, carbohydrate availability may depend on local sink strength and distance from sources. Defenses, including monoterpenes – a major component of resin – limit the invasibility of pines. Since carbohydrate reserves fund monoterpene synthesis, we hypothesized that monoterpene concentrations in pine stems would decrease from the crown to the lower stem, and susceptibility to fungal infection would increase.

Here, we measured carbohydrate and monoterpene concentrations along the stems of lodgepole pine trees (Pinus contorta var. latifolia) before inoculating with a blue-stain fungus at different heights. After 6 wk, we assessed tree responses to fungal infection based on lesion length and carbohydrate mobilization.

Concentrations of carbohydrates and monoterpenes in the phloem before inoculation decreased with distance from the crown, whereas lesion lengths after inoculation increased. However, trees mobilized sugars in response to fungal infection such that carbohydrate reserves near lesions were similar at all heights.

 

Despite C mobilization, the lower stem was more vulnerable than the upper stem. Consistent with predictions based on sink–source relationships, vulnerability occurred where carbohydrates were less available, and likely resulted from C withdrawal by sinks higher in the supply chain."

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Emerging role for RNA-based regulation in plant immunity - Staiger - 2012 - New Phytologist - Wiley Online Library

Emerging role for RNA-based regulation in plant immunity - Staiger - 2012 - New Phytologist - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

"Infection by phytopathogenic bacteria triggers massive changes in plant gene expression, which are thought to be mostly a result of transcriptional reprogramming. However, evidence is accumulating that plants additionally use post-transcriptional regulation of immune-responsive mRNAs as a strategic weapon to shape the defense-related transcriptome. Cellular RNA-binding proteins regulate RNA stability, splicing or mRNA export of immune-response transcripts. In particular, mutants defective in alternative splicing of resistance genes exhibit compromised disease resistance. Furthermore, detection of bacterial pathogens induces the differential expression of small non-coding RNAs including microRNAs that impact the host defense transcriptome. Phytopathogenic bacteria in turn have evolved effector proteins to inhibit biogenesis and/or activity of cellular microRNAs. Whereas RNA silencing has long been known as an antiviral defense response, recent findings also reveal a major role of this process in antibacterial defense. Here we review the function of RNA-binding proteins and small RNA-directed post-transcriptional regulation in antibacterial defense. We mainly focus on studies that used the model system Arabidopsis thaliana and also discuss selected examples from other plants."

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Effects of Homoeologous Wheat Starch Synthase IIa Genes on Starch Properties - Journal of Agricultural and Food Chemistry (ACS Publications)

"Near-isogenic lines (NILs) of the eight haplotypes of starch synthase IIa (SSIIa) were used to analyze the effects of SSIIa gene dosage on branch chain length, gelatinization, pasting, retrogradation, and enzymatic hydrolysis of starches. Compared to wild-type, the amylopectin of lines missing one or more active SSIIa enzymes had increases in the proportion of short branch chains (DP6–10) and decreases in midlength chains (DP11–24), and the size of these differences depended on the dosage of active SSIIa enzymes. Of the three loci, SSIIa-A1 had the smallest contribution to amylopectin structure and SSIIa-B1 the largest. The different effects of the three SSIIa enzymes on starch properties were also seen in gelatinization, retrogradation, pasting, and enzymatic hydrolysis properties. Such differences in starch properties might be useful in influencing the texture and shelf life of food products."

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Metabolic engineering of tomato fruit organic ... [Plant Physiol. 2012] - PubMed - NCBI

"Organic acid content is regarded as one of the most important quality traits of fresh tomatoes. However, the complexity of carboxylic acid metabolism and storage means that it is difficult to predict the best way to engineer altered carboxylic acid levels. Here we have used a biochemical analysis of a tomato introgression line with increased levels of fruit citrate and malate at breaker stage to identify a metabolic engineering target that was subsequently tested in transgenic plants. Increased carboxylic acid levels in introgression line 2-5 were not accompanied by changes in the pattern of carbohydrate oxidation by pericarp discs or the catalytic capacity of TCA cycle enzymes measured in isolated mitochondria. However, there was a significant decrease in the maximum catalytic activity of aconitase in total tissue extracts suggesting that a cytosolic isoform of aconitase was affected. To test the role of cytosolic aconitase in controlling fruit citrate levels, we analysed fruit of transgenic lines expressing an antisense construct against SlAco3b, one of the two tomato genes encoding aconitase. A GFP-fusion of SlAco3b was dual targeted to cytosol and mitochondria, while the other aconitase, SlAco3a was exclusively mitochondrial when transiently expressed in tobacco leaves. Both aconitase transcripts were decreased in fruit from transgenic lines and aconitase activity was reduced by about 30% in the transgenic lines. Other measured enzymes of carboxylic acid metabolism were not significantly altered. Both citrate and malate levels were increased in ripe fruit of the transgenic plants and, as a consequence, total carboxylic acid content was increased by 50% at maturity."

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Experimental support of the stress-gradient hypothesis in herbivore–herbivore interactions - Dangles - 2012 - New Phytologist - Wiley Online Library

Experimental support of the stress-gradient hypothesis in herbivore–herbivore interactions - Dangles - 2012 - New Phytologist - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

"The stress-gradient hypothesis (SGH) postulates an increase in the frequency of positive species interactions at increasing amounts of stress. While the SGH has been extensively tested in plant–plant interactions along abiotic stresses, it remains unclear whether this hypothesis could apply to higher trophic levels, such as herbivores, along biotic stress gradients.


To address this issue, we investigated how the interaction between two potato herbivores may change along a stress gradient created by an assortment of potato varieties with different tuber palatability. We used a tuber resistance trait as a measure for biotic stress and one herbivore as the facilitator to gain access to the tuber of the other herbivore.


Our experiment revealed a switch from neutral to positive interactions with increasing stress, confirming for the first time the predictions of the SGH for herbivores. Moreover, the intensity of facilitation decreased at high stress levels, suggesting that benefits by the facilitating species were dampened in the most stressful environment.


In view of the ubiquitous role played by positive interactions among herbivores, broadening our search image for facilitative effects among other plant enemies will allow a better awareness of the importance of the SGH in structuring plant communities."

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Strategies towards sequencing complex crop genomes

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BMC Genomics | Abstract | Transcriptome database resource and gene expression atlas for the rose

"Here, we used a combination of Illumina and 454 sequencing technologies to generate information on Rosa sp. transcripts using RNA from various tissues and in response to biotic and abiotic stresses. A total of 80714 transcript clusters were identified and 76611 peptides have been predicted among which 20997 have been clustered into 13900 protein families. BLASTp hits in closely related Rosaceae species revealed that about half of the predicted peptides in the strawberry and peach genomes have orthologs in Rosa dataset. Digital expression was obtained using RNA samples from organs at different development stages and under different stress conditions. qPCR validated the digital expression data for a selection of 23 genes with high or low expression levels. Comparative gene expression analyses between the different tissues and organs allowed the identification of clusters that are highly enriched in given tissues or under particular conditions, demonstrating the usefulness of the digital gene expression analysis. A web interface ROSAseq was created that allows data interrogation by BLAST, subsequent analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis. The rose peptides dataset was used to create the ROSAcyc resource pathway database that allows access to the putative genes and enzymatic pathways."

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PLOS ONE: Reference-Free Comparative Genomics of 174 Chloroplasts

PLOS ONE: Reference-Free Comparative Genomics of 174 Chloroplasts | Plant Breeding and Genomics News | Scoop.it

"Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across genomes [1]. We then assemble de novo contigs centered on informative variation. The localized de novo contigs can be separated into two major classes: tip = unique to a single genome and group = shared by a subset of genomes. Prior to assembly, we found that ~18% of the chloroplast was duplicated in the inverted repeat (IR) region across a four-fold difference in genome sizes, from a highly reduced parasitic orchid [2] to a massive algal chloroplast [3], including gnetophytes [4] and cycads [5]. The conservation of this ratio between single copy and duplicated sequence was basal among green plants, independent of photosynthesis and mechanism of genome size change, and different in gymnosperms and lower plants. Major lineages in the angiosperm clade differed in the pattern of shared kmers and de novo contigs. For example, parasitic plants demonstrated an expected accelerated overall rate of evolution, while the hemi-parasitic genomes contained a great deal more novel sequence than holo-parasitic plants, suggesting different mechanisms at different stages of genomic contraction. Additionally, the legumes are diverging more quickly and in different ways than other major families. Small duplicated fragments of the rrn23 genes were deeply conserved among seed plants, including among several species without the IR regions, indicating a crucial functional role of this duplication. Localized de novo assembly of informative kmers greatly reduces the complexity of large comparative analyses by confining the analysis to a small partition of data and genomes relevant to the specific question, allowing direct analysis of next-gen sequence data from previously unstudied genomes and rapid discovery of informative candidate regions."

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Source population characteristics affect heterosis following genetic rescue of fragmented plant populations

"Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations."

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BMC Plant Biology | Abstract | The Plant Short-Chain Dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns

"Wide-scale analyses were performed on ten plant genomes. The combination of hidden Markov model (HMM) based analyses and similarity searches led to the construction of an exhaustive inventory of plant SDR. With 68 to 315 members found in each analysed genome, the inventory confirmed the over-representation of SDRs in plants compared to animals, fungi and prokaryotes. The plant SDRs were first classified into three major types --- 'classical', 'extended' and 'divergent' --- but a minority (10 % of the predicted SDRs) could not be classified into these general types ('unknown' or 'atypical' types). In a second step, we could categorize the vast majority of land plant SDRs into a set of 49 families. Out of these 49 families, 35 appeared early during evolution since they are commonly found through all the Green Lineage. Yet, some SDR families --- tropinone reductase-like proteins (SDR65C), 'ABA2-like'-NAD dehydrogenase (SDR110C), 'salutaridine/menthone-reductase-like' proteins (SDR114C), 'dihydroflavonol 4-reductase'-like proteins (SDR108E) and 'isoflavone-reductase-like' (SDR460A) proteins --- have undergone significant functional diversification within vascular plants since they diverged from Bryophytes. Interestingly, these diversified families are either involved in the secondary metabolism routes (terpenoids, alkaloids, phenolics) or participate in developmental processes (hormone biosynthesis or catabolism, flower development), in opposition to SDR families involved in primary metabolism which are poorly diversified."

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PLOS ONE: Differential Gene Expression in Soybean Leaf Tissues at Late Developmental Stages under Drought Stress Revealed by Genome-Wide Transcriptome Analysis

PLOS ONE: Differential Gene Expression in Soybean Leaf Tissues at Late Developmental Stages under Drought Stress Revealed by Genome-Wide Transcriptome Analysis | Plant Breeding and Genomics News | Scoop.it

"The availability of complete genome sequence of soybean has allowed research community to design the 66 K Affymetrix Soybean Array GeneChip for genome-wide expression profiling of soybean. In this study, we carried out microarray analysis of leaf tissues of soybean plants, which were subjected to drought stress from late vegetative V6 and from full bloom reproductive R2 stages. Our data analyses showed that out of 46093 soybean genes, which were predicted with high confidence among approximately 66000 putative genes, 41059 genes could be assigned with a known function. Using the criteria of a ratio change > = 2 and a q-value<0.05, we identified 1458 and 1818 upregulated and 1582 and 1688 downregulated genes in drought-stressed V6 and R2 leaves, respectively. These datasets were classified into 19 most abundant biological categories with similar proportions. There were only 612 and 463 genes that were overlapped among the upregulated and downregulated genes, respectively, in both stages, suggesting that both conserved and unconserved pathways might be involved in regulation of drought response in different stages of plant development. A comparative expression analysis using our datasets and that of drought stressed Arabidopsis leaves revealed the existence of both conserved and species-specific mechanisms that regulate drought responses. Many upregulated genes encode either regulatory proteins, such as transcription factors, including those with high homology to Arabidopsis DREB, NAC, AREB and ZAT/STZ transcription factors, kinases and two-component system members, or functional proteins, e.g. late embryogenesis-abundant proteins, glycosyltransferases, glycoside hydrolases, defensins and glyoxalase I family proteins. A detailed analysis of the GmNAC family and the hormone-related gene category showed that expression of many GmNAC and hormone-related genes was altered by drought in V6 and/or R2 leaves. Additionally, the downregulation of many photosynthesis-related genes, which contribute to growth retardation under drought stress, may serve as an adaptive mechanism for plant survival. This study has identified excellent drought-responsive candidate genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans."

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Crop Scientists Warn of Need for Climate Change Action: Scientific American

Crop Scientists Warn of Need for Climate Change Action: Scientific American | Plant Breeding and Genomics News | Scoop.it

"A group of scientists in the top U.S. grain-growing state of Iowa said on Monday that this year's harsh drought was a sign of things to come and should spur more action to prepare for the challenges of a warming climate."

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BMC Plant Biology | Abstract | Stress inducible proteinase inhibitor diversity in Capsicum annuum

"Wound-inducible Pin-II Proteinase inhibitors (PIs) are one of the important plant serine PIs which have been studied extensively for their structural and functional diversity and relevance in plant defense against insect pests."

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Chemical and Bioactive Quality Traits During Fruit Ripening in Eggplant (S. melongena L.) and Allied Species - Journal of Agricultural and Food Chemistry (ACS Publications)

"A chemical and bioactive quality evaluation of phytochemicals content of 10 eggplant lines and three allied species (S. sodomaeum, S. aethiopicum and S. integrifolium) was performed. The eggplant lines were divided into the two subgroups of delphinidin-3-rutinoside (D3R) and nasunin (NAS) typologies, on the basis of the anthocyanin detected in their fruit skin. The allied species had higher glycoalkaloids content, lower soluble solids and PPO activity and absence of anthocyanins compared to the eggplant lines; S. sodomaeum stood out for high phenols content. Orthogonal contrast revealed a higher sugar content and low PPO activity in NAS- compared to D3R-typologies, whereas higher chlorogenic acid and anthocyanin contents were present in D3R-typologies. The main effect of the ripening was a decrease in phenols and in the PPO activity, not evidenced in S. sodomaeum, and an increase of glycoalkaloids in overripe fruits."

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