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Clonal differences in susceptibility to the dieback of Fraxinus excelsior in southern Sweden

Clonal differences in susceptibility to the dieback of Fraxinus excelsior in southern Sweden | Plant Breeding and Genomics News | Scoop.it

"Ash dieback damage was assessed and analysed on 16–22 year-old grafts in two ash seed orchards (Fraxinus excelsior L.). The grafts originated from 106 plus-tree clones selected from 27 stands in southern Sweden based on their phenotypes. The results obtained indicate that ash dieback disease is strongly genotypically controlled. There was considerable genotypic variation among individuals. None of the clones seemed to be totally resistant, but some exhibited reduced susceptibility and retained this resistance after 6 years under heavy infection pressure."

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Rosette Tracker: An Open Source Image Analysis Tool for Automatic Quantification of Genotype Effects

"..Rosette Tracker allows us to simultaneously quantify plant growth, photosynthesis, and leaf temperature-related parameters through the analysis of visual, chlorophyll fluorescence, and/or thermal infrared time-lapse sequences. Freely available, Rosette Tracker facilitates the rapid understanding of Arabidopsis genotype effects. "

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Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China - Sun - 2012 - New Phytologist - Wiley Online Library

Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China - Sun - 2012 - New Phytologist - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

"Weedy rice is a unique system with which to investigate how weedy plants adapt to an agricultural environment. Our finding that extensive introgression from local cultivars, combined with the continuing ability to maintain weedy genes, is characteristic of weedy rice in northern China provides a clue for the field control of weedy rice."

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Genome-wide analysis of Stowaway-like MITEs in... [Plant Physiol. 2012] - PubMed - NCBI

Genome-wide analysis of Stowaway-like MITEs in... [Plant Physiol. 2012] - PubMed - NCBI | Plant Breeding and Genomics News | Scoop.it

"The diversity and evolution of wheat genomes is determined, in part, by the activity of transposable elements (TEs) that constitute a large fraction of the genome (up to 90%). In this study, we retrieved sequences from publicly available wheat databases, including a 454-pyrosequencing database, and analyzed 18,217 insertions of 18 Stowaway-like MITE families previously characterized in wheat and which together account for ~1.3 Mb of sequence. All 18 families showed high conservation in length, sequence and target site preference. Furthermore, ~55% of the elements were inserted in transcribed regions, into or near known wheat genes. Notably, we observed significant correlation between the mean length of the MITEs and their copy number. In addition, the genomic composition of nine MITE families was studied by real-time quantitative PCR (qPCR) analysis in 40 accessions of Triticum and Aegilops species, including diploids, tetraploids and hexaploids. The qPCR data showed massive and significant intra- and interspecific variation, as well as genome-specific proliferation and non-additive quantities in the polyploids. We also observed significant differences in the methylation status of the insertion sites among MITE families. Our data thus suggest a possible role for MITEs in generating genome diversification and in the establishment of nascent polyploid species in wheat."

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BMC Genomics | Abstract | De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes

"Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm."

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Phenotypic plasticity of plant response to herbivore eggs: effects on resistance to caterpillars and plant development

Phenotypic plasticity of plant response to herbivore eggs: effects on resistance to caterpillars and plant development | Plant Breeding and Genomics News | Scoop.it

"Herbivory induces direct resistance responses in plants that negatively affect subsequently colonizing herbivores. Moreover, eggs of herbivorous insects can also activate plant resistance, which in some cases prevents hatching larvae from feeding. Until now, plant-mediated effects of eggs on subsequent herbivory, and the specificity of such responses, have remained poorly understood. We studied the specificity and effects of plant resistance induced by herbivore egg deposition against lepidopteran larvae of species with different dietary breadths, feeding on a wild annual plant, the crucifer Brassica nigra. We examined whether this plant-mediated response affects the growth of caterpillars of a specialist (Pieris brassicae) that feeds on B. nigra leaves and flowers, and a generalist (Mamestra brassicae) that rarely attacks this wild crucifer. We measured growth rates of neonate larvae to the end of their second instar after the larvae had hatched on plants exposed to eggs vs. plants without eggs, under laboratory and semi-field conditions. Moreover, we studied the effects of egg deposition by the two herbivore species on plant height and flowering rate before and after larval hatching. Larvae of both herbivore species that developed on plants previously infested with eggs of the specialist butterfly P. brassicae gained less weight compared with larvae that developed on egg-free plants. Plants exposed to butterfly eggs showed accelerated plant growth and flowering compared to egg-free plants. Egg deposition by the generalist moth M. brassicae, in contrast, had no effect on subsequent performance by either herbivore species, or on plant development. Our results demonstrate that B. nigra plants respond differently to eggs of two herbivore species in terms of plant development and induced resistance to caterpillar attack. For this annual crucifer, the retardation of caterpillar growth in response to deposition of eggs by P. brassicae in combination with enhanced growth and flowering likely result in reproductive assurance, after being exposed to eggs from an herbivore whose larvae rapidly reduce the plant's reproductive potential through florivory

Read More: http://www.esajournals.org/doi/abs/10.1890/12-1561.1?af=R&"

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BMC Bioinformatics | Abstract | A quantitative genetic and epigenetic model of complex traits

BMC Bioinformatics | Abstract | A quantitative genetic and epigenetic model of complex traits | Plant Breeding and Genomics News | Scoop.it

"Despite our increasing recognition of the mechanisms that specify and propagate epigenetic states of gene expression, the pattern of how epigenetic modifications contribute to the overall genetic variation of a phenotypic trait remains largely elusive."

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Waterproofing crops: Effective flooding surviv... [Plant Physiol. 2012] - PubMed - NCBI

Waterproofing crops: Effective flooding surviv... [Plant Physiol. 2012] - PubMed - NCBI | Plant Breeding and Genomics News | Scoop.it

Update on the research around crop flood survival.

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Plant Cell Teaching Tool: A really useful pathogen, Agrobacterium tumefaciens (2012)

Plant Cell Teaching Tool: A really useful pathogen, Agrobacterium tumefaciens (2012) | Plant Breeding and Genomics News | Scoop.it

The soil bacterium Agrobacterium tumefaciens has a special place in plant biology. Through a rare inter-kingdom DNA transfer, the bacteria move some of their genes into their host's genome, thereby inducing the host cells to proliferate and produce opines, which are nutrients sources for the pathogen. Agrobacterium's ability to transfer DNA makes can be adapted to introduce other genes, such as those encoding useful traits, into plant genomes. The development of Agrobacterium as a tool to transform plants is a landmark event in modern plant biology. This new "Teaching Tool in Plant Biology" provides an introduction to Agrobacterium tumefaciens and related species, focusing on their modes of pathogenicity, their usefulness as tools for plant transformation, and their use as a model for the study of plant-pathogen interactions.

Find it here: http://www.plantcell.org/site/teachingtools/TTPB23.xhtml (subscription to Plant Cell or ASPB membership required).


Via Mary Williams, Kamoun Lab @ TSL
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Lidia Pérez de Obanos's curator insight, November 27, 2013 6:15 AM

Agrobacterium tumefaciens es un vector muy útil para muchos tipos de genes que se quieren introducir en distintas plantas. Gracias a ella hemos podido realizar múltiples experimentos y es muy fácil de realizar.

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Why Wiry? Tomato Mutants Reveal Connections among Small RNAs, Auxin Response Factors, Virus Infection, and Leaf Morphology

"Tomato (Solanum lycopersicum) wiry mutants posed a mystery because their phenotype, wiry or shoestring leaves that lack leaf blade expansion, resembles virus-infected tomato plants (see figure). However, the wiry mutant phenotype is not transmissible from plant to plant, as an infection would be, but is caused by mutation (Lesley and Lesley, 1928). To examine this mystery, Yifhar et al. (pages 3575–3589) characterized a set of classical and newly isolated wiry mutants and found that they correspond to four complementation groups, with multiple alleles producing a broad phenotypic series. Identification of the responsible loci showed that all four WIRY loci, tomato orthologs of RNA Dependent RNA Polymerase6, ARGONAUTE7, DICER-LIKE4, and SUPPRESSOR of GENE SILENCING3, act in biogenesis of trans-acting short interfering RNAs (ta-siRNAs). ta-siRNAs are a class of small interfering RNAs that are transcribed from TAS loci and are processed into small RNAs that regulate multiple processes, including development and stress responses (reviewed in Rubio-Somoza et al., 2009)."

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Natural variation for seed longevity and seed ... [Plant Physiol. 2012] - PubMed - NCBI

"Dormancy is a state of metabolic arrest that facilitates survival of organisms during environmental conditions incompatible with their regular course of life. Many organisms have deep dormant stages to promote an extended life span (increased longevity). In contrast, plants have seed dormancy and seed longevity described as two traits. Seed dormancy is defined as a temporary failure of a viable seed to germinate in conditions that favor germination, whereas seed longevity is defined as seed viability after dry storage (storability). In plants, the association of seed longevity with seed dormancy has not been studied in detail. This is surprising given the ecological, agronomical and economic importance of seed longevity. We studied seed longevity to reveal its genetic regulators and its association with seed dormancy in Arabidopsis. Integrated quantitative trait locus (QTL) analyses for seed longevity, in six recombinant inbred line (RIL) populations, revealed five loci: Germination ability after storage (GAAS) 1 to 5. GAAS loci co-located with seed dormancy loci, Delay of germination (DOG), earlier identified in the same six RIL populations. Both GAAS loci and their colocation with DOG loci were validated by near isogenic lines. A negative correlation was observed, deep seed dormancy correlating with low seed longevity and vice versa. Detailed analysis on the collocating GAAS5 and DOG1 QTL revealed that the DOG1-Cvi allele both reduces seed longevity and increases seed dormancy. To our knowledge, this study is the first to report a negative correlation between seed longevity and seed dormancy."

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Upcoming Webinar: Introduction to the rrBLUP Package in R for Genomewide Selection Webinar | PBGworks

Upcoming Webinar: Introduction to the rrBLUP Package in R for Genomewide Selection Webinar | PBGworks | Plant Breeding and Genomics News | Scoop.it

Plant Breeding and Genomics is pleased to announce an upcoming webinar presented by Amy Jacobson at the University of Minnesota.  October 31, 2012 at 1:00 Eastern Time.  Please register to attend.

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Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

"Consistent with the dominance model (i.e., complementation) for heterosis, 865 genes that were expressed in the hybrids were expressed in only one of the two parents. For 50 genes, it could be shown that this was a consequence of complementation of genomic presence/absence variation. For dozens of other genes, alleles from the inactive inbred were activated in the hybrid, presumably via interactions with regulatory factors from the active inbred. As a consequence of these types of complementation, both hybrids expressed more genes than did either parental inbred. Finally, in hybrids, ∼14% of expressed genes exhibited allele-specific expression (ASE) levels that differed significantly from the parental-inbred expression ratios, providing further evidence for interactions of regulatory factors from one parental genome with target genes from the other parental genome."

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Diverse Roles of Strigolactone Signaling in Maize Architecture and the Uncoupling of a Branching-Specific Subnetwork

"Analysis of the tb1 zmccd8 double mutant revealed that Tb1 functions in an SL-independent subnetwork that is not required for the other diverse roles of SL in development. Our findings indicate that in maize, uncoupling of the Tb1 subnetwork from SL signaling has profoundly altered the balance between conserved roles of SLs in branching and diverse aspects of plant architecture."

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BMC Plant Biology | Abstract | Beneficial 'unintended effects' of a cereal cystatin in transgenic lines of potato, Solanum tuberosum

"Studies reported unintended pleiotropic effects for a number of pesticidal proteins ectopically expressed in transgenic crops, but the nature and significance of such effects in planta remain poorly understood.Here we assessed the effects of corn cystatin II (CCII), a potent inhibitor of C1A cysteine (Cys) proteases considered for insect and pathogen control, on the leaf proteome and pathogen resistance status of potato lines constitutively expressing this protein"

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Adapting Agricultural Extension to Peacebuilding: Report of a Workshop by the National Academy of Engineering and the United States Institute of Peace: Roundtable on Technology, Science, and Peaceb...

Adapting Agricultural Extension to Peacebuilding: Report of a Workshop by the National Academy of Engineering and the United States Institute of Peace: Roundtable on Technology, Science, and Peaceb... | Plant Breeding and Genomics News | Scoop.it

National Academy of Engineering and United States Institute of Peace are offering the PDF version of their book for free.

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BMC Genomics | Abstract | QTL mapping of the production of wine aroma compounds by yeast

Wine aroma results from the combination of numerous volatile compounds, some produced by yeast and others produced in the grapes and further metabolized by yeast.
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BMC Genomics | Abstract | Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing

"We used transcriptome sequencing to discover large numbers of SNPs segregating in elite breeding populations of alfalfa. Little loss of SNP diversity was evident between unimproved and elite alfalfa germplasm. The EST and SNP markers generated from this study are publicly available at the Legume Information System (http://medsa.comparative-legumes.org/) and can contribute to future alfalfa research and breeding applications."

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Differing Positions on Genetic Enginnering and California’s Proposition 37 | PBGworks

Differing Positions on Genetic Enginnering and California’s Proposition 37 | PBGworks | Plant Breeding and Genomics News | Scoop.it

Genetically engineered (GE) crops have been much debated in the popular press recently due to the upcoming November 6th vote on California’s Proposition 37, which proposes mandatory labeling of GE foods. The academic community is also conflicted, and for this reason we are highlighting the evidence underlying different scientific and economic arguments on these topics, as well as differences in personal philosophy that shape GE crop policy recommendations.

 

We have invited two agricultural experts with differing positions on GE crops and Proposition 37 to outline and fully reference their positions. The differing positions of Dr. David Zilberman and Dr. Belinda Martineau underscore how evidence-interpretation and personal philosophy shape policy recommendations. Their invited submissions are presented in the order they were received.

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Quantifying introgression risk with realistic population genetics

"Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified crop regulation. Most theoretical introgression studies aimed at such quantification disregard one or more of the most important factors concerning introgression: realistic genetical mechanisms, repeated invasions and stochasticity. In addition, the use of linkage as a risk mitigation strategy has not been studied properly yet with genetic introgression models. Current genetic introgression studies fail to take repeated invasions and demographic stochasticity into account properly, and use incorrect measures of introgression risk that can be manipulated by arbitrary choices. In this study, we present proper methods for risk quantification that overcome these difficulties. We generalize a probabilistic risk measure, the so-called hazard rate of introgression, for application to introgression models with complex genetics and small natural population sizes. We illustrate the method by studying the effects of linkage and recombination on transgene introgression risk at different population sizes."

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A multivariate analysis of variation in genome size and endoreduplication in angiosperms reveals strong phylogenetic signal and association with phenotypic traits - Bainard - 2012 - New Phytologist...

A multivariate analysis of variation in genome size and endoreduplication in angiosperms reveals strong phylogenetic signal and association with phenotypic traits - Bainard - 2012 - New Phytologist... | Plant Breeding and Genomics News | Scoop.it

"Genome size (C-value) and endopolyploidy (endoreduplication index, EI) are known to correlate with various morphological and ecological traits, in addition to phylogenetic placement. A phylogenetically controlled multivariate analysis was used to explore the relationships between DNA content and phenotype in angiosperms.
Seeds from 41 angiosperm species (17 families) were grown in a common glasshouse experiment. Genome size (2C-value and 1Cx-value) and EI (in four tissues: leaf, stem, root, petal) were determined using flow cytometry. The phylogenetic signal was calculated for each measure of DNA content, and phylogenetic canonical correlation analysis (PCCA) explored how the variation in genome size and EI was correlated with 18 morphological and ecological traits.
Phylogenetic signal (λ) was strongest for EI in all tissues, and λ was stronger for the 2C-value than the 1Cx-value. PCCA revealed that EI was correlated with pollen length, stem height, seed mass, dispersal mechanism, arbuscular mycorrhizal association, life history and flowering time, and EI and genome size were both correlated with stem height and life history.
PCCA provided an effective way to explore multiple factors of DNA content variation and phenotypic traits in a phylogenetic context. Traits that were correlated significantly with DNA content were linked to plant competitive ability."

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Hybrid rye performance under natural drought stress in Europe

"Several rye growing regions of Central Europe suffered from severe drought stress in the last decade. Rye is typically grown on sandy soils with low water-holding capacity in areas with low rainfall, thus drought-tolerant varieties are urgently needed. The main objective of our study was to evaluate the drought stress tolerance of rye hybrids using large-scaled field experiments. Two biparental populations (Pop-A, Pop-B) each consisting of 220 F2:4 lines from the Petkus gene pool and their parents were evaluated for grain yield testcross performance under irrigated (I) and rainfed (R) regime in six environments. We observed for most environments severe drought stress leading to an average grain yield reduction of 23.8 % for rainfed compared to irrigated regime in drought stress environments. A decomposition of the variance revealed significant (P < 0.01) genotypic and genotype × environment interaction variances but only a minor effect of drought stress on the ranking of the genotypes with regard to grain yield. In conclusion, separate breeding programs for drought-tolerant genotypes are not superior to the currently practiced selection under rainfed conditions without irrigation in hybrid rye breeding in Central Europe."

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IFPRI invites comments on draft strategy | International Food Policy Research Institute (IFPRI)

IFPRI invites comments on draft strategy | International Food Policy Research Institute (IFPRI) | Plant Breeding and Genomics News | Scoop.it

The International Food Policy and Research Institute invites comments on their draft of strategies to address the food policy issues in developing countries.

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Open Access Week

Open Access Week | Plant Breeding and Genomics News | Scoop.it

"A global event, now in its 6th year, promoting Open Access as a new norm in scholarship and research."

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Increased greenhouse-gas intensity of rice production under future atmospheric conditions : Nature Climate Change : Nature Publishing Group

Increased greenhouse-gas intensity of rice production under future atmospheric conditions : Nature Climate Change : Nature Publishing Group | Plant Breeding and Genomics News | Scoop.it

"Increased atmospheric CO2 and rising temperatures are expected to affect rice yields and greenhouse-gas (GHG) emissions from rice paddies1, 2, 3, 4. This is important, because rice cultivation is one of the largest human-induced sources of the potent GHG methane5 (CH4) and rice is the world’s second-most produced staple crop6. The need for meeting a growing global food demand7 argues for assessing GHG emissions from croplands on the basis of yield rather than land area8, 9, 10, such that efforts to reduce GHG emissions take into consideration the consequences for food production. However, it is unclear whether or how the GHG intensity (that is, yield-scaled GHG emissions) of cropping systems will be affected by future atmospheric conditions. Here we show, using meta-analysis, that increased atmospheric CO2 (ranging from 550 to 743 ppmV) and warming (ranging from +0.8 °C to +6 °C) both increase the GHG intensity of rice cultivation. Increased atmospheric CO2 increased GHG intensity by 31.4%, because CH4 emissions are stimulated more than rice yields. Warming increased GHG intensity by 11.8% per 1 °C, largely owing to a decrease in yield. This analysis suggests that rising CO2 and warming will approximately double the GHG intensity of rice production by the end of the twenty-first century, stressing the need for management practices that optimize rice production while reducing its GHG intensity as the climate continues to change."

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