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New allelic variants found in key rice salt-tolerance genes: an association study - Negrão - 2012 - Plant Biotechnology Journal - Wiley Online Library

New allelic variants found in key rice salt-tolerance genes: an association study - Negrão - 2012 - Plant Biotechnology Journal - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

"Salt stress is a complex physiological trait affecting plants by limiting growth and productivity. Rice, one of the most important food crops, is rated as salt-sensitive. High-throughput screening methods are required to exploit novel sources of genetic variation in rice and further improve salinity tolerance in breeding programmes. To search for genotypic differences related to salt stress, we genotyped 392 rice accessions by EcoTILLING. We targeted five key salt-related genes involved in mechanisms such as Na+/K+ ratio equilibrium, signalling cascade and stress protection, and we found 40 new allelic variants in coding sequences. By performing association analyses using both general and mixed linear models, we identified 11 significant SNPs related to salinity. We further evaluated the putative consequences of these SNPs at the protein level using bioinformatic tools. Amongst the five nonsynonymous SNPs significantly associated with salt-stress traits, we found a T67K mutation that may cause the destabilization of one transmembrane domain in OsHKT1;5, and a P140A alteration that significantly increases the probability of OsHKT1;5 phosphorylation. The K24E mutation can putatively affect SalT interaction with other proteins thus impacting its function. Our results have uncovered allelic variants affecting salinity tolerance that may be important in breeding."

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Creating patches of native flowers facilitates crop pollination in large agricultural fields: mango as a case study - Carvalheiro - 2012 - Journal of Applied Ecology - Wiley Online Library

Creating patches of native flowers facilitates crop pollination in large agricultural fields: mango as a case study - Carvalheiro - 2012 - Journal of Applied Ecology - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

"Our results show that the presence of small patches of native flowers within large farms can increase pollinator-dependent crop production if combined with preservation of remaining fragments of natural habitat and judicious use of pesticides. Native flower compensation areas represent a profitable management measure for farmers, increasing cost-effectiveness of cropland while indirectly contributing to preservation of natural habitat."

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PLOS ONE: Integration of a Systems Biological Network Analysis and QTL Results for Biomass Heterosis in Arabidopsis thaliana

PLOS ONE: Integration of a Systems Biological Network Analysis and QTL Results for Biomass Heterosis in Arabidopsis thaliana | Plant Breeding and Genomics News | Scoop.it

"A chromosome-wise over-representation analysis gave rise to the hypothesis that chromosomes number 2 and 4 probably carry a majority of the genes involved in biomass heterosis in the early development of Arabidopsis thaliana."

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GmDREB2A;2, a Canonical DREB2-type Transcripti... [Plant Physiol. 2012] - PubMed - NCBI

"The heterologous expression of GmDREB2A;2 in Arabidopsis induced DRE-regulated stress-inducible genes and improved stress tolerance. However, there were variations in the growth phenotypes of the transgenic Arabidopsis, the induced genes and their induction ratios between GmDREB2A;2 and DREB2A. Therefore, the basic function and regulatory machinery of DREB2 have been maintained between Arabidopsis and soybean, although differentiation has also occurred."

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Biophysical characteristics of the stem and petiole surface of six hemlock (Tsuga) species and a hybrid: implications for resistance to Adelges tsugae - Botany

"We addressed the potential role of plant surface morphology in the adelgid–hemlock interaction by comparing four adelgid-resistant hemlock species and a hybrid with the two adelgid-susceptible hemlock species. We found that trichomes are likely not involved in conferring resistance to A. tsugae. Cuticle thickness may be involved in insertion site selection by A. tsugae and may therefore have implications for resistance. The cuticle is thinnest at the point of A. tsugae stylet insertion and thus may affect A. tsugae feeding."

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Evolutionary analyses of non-family genes in plants. [Plant J. 2012] - PubMed - NCBI

"We performed comparative studies on NF genes in 14 plant species. Based on the clustering of protein sequences, we identified ~94,000 NF genes across these species that were divided into five evolutionary groups: Viridiplantae-wide, angiosperm-specific, monocot-specific, dicot-specific, and those that were species-specific."

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IJMS | Free Full-Text | The Characterization of SaPIN2b, a Plant Trichome-Localized Proteinase Inhibitor from Solanum americanum

"Taken together, our results demonstrated that SaPIN2b is a potent serine proteinase inhibitor that may act as a protective protein in plant defense against insect attacks."

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Xylella fastidiosa Virtual Issue

Free access to key papers on the bacterial pathogen, Xylella fastidiosa, published in Phytopathology, Plant Disease, and Molecular Plant-Microbe Interactions for a limited time.

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Disease threatens Pacific coconut gene bank | Pacific Beat | ABC Radio Australia

"The international collection of the South Pacific's coconut palms is under threat from a disease outbreak close to the gene bank in Papua New Guinea."

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BMC Plant Biology | Abstract | PMRD: a curated database for genes and mutants involved in plant male reproduction

"Plant Male Reproduction Database (PMRD) is a comprehensive resource for browsing and retrieving knowledge on genes and mutants related to plant male reproduction. It is based upon literature and biological databases and includes 506 male sterile genes and 484 mutants with defects of male reproduction from a variety of plant species. Based on Gene Ontology (GO) annotations and literature, information relating to a further 3697 male reproduction related genes were systematically collected and included, and using in text curation, gene expression and phenotypic information were captured from the literature."

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New Book: Phytoplasma

New Book: Phytoplasma | Plant Breeding and Genomics News | Scoop.it

"Phytoplasmas are a group of bacteria that are capable of multiplying and causing severe diseases in a wide range of plant species and are transported between plants by insect vectors in which the bacteria can also multiply."

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BMC Bioinformatics | Abstract | Clustering of time-course gene expression profiles using normal mixture models with autoregressive random effects

"Our new model under our extension of the EMMIX-WIRE procedure is more reliable and robust for clustering time-course data because it adopts a random effects model that allows for the correlation among observations at different time points. It postulates gene-specific random effects with an auto-correlation variance structure that models coregulation within the clusters The developed R package is flexible in its specification of the randomeffects through user-input parameters that enables improved modelling and consequent clustering of time-course data."

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Rhizobial and Mycorrhizal Symbioses in Lotus j... [Plant Physiol. 2012] - PubMed - NCBI

"We propose that LNP functions at the earliest stage of the common nodulation and mycorrhization symbiosis signaling pathway downstream of the Nod-factor receptors; it may either act either by influencing signaling via changes in external nucleotides or may act in conjunction with the LysM receptor-like kinases for recognition of Nod factor."

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Diversity in global maize germplasm: Characterizati... [J Biosci. 2012] - PubMed - NCBI

"Multi-institutional efforts are required at the global level to systematically explore the maize germplasm to diversify the genetic base of elite breeding materials, create novel varieties and counter the effects of global climate changes."

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BMC Genomics | Abstract | A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)

Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools.
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Clocks are ticking and climate is changing: Increasing plant productivity in a changing climate

Scientists are looking to cellular biological clocks as a target for genetic modification for increasing plant productivity.
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Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics - Andolfo - 2012 - New Phytologist - Wiley Online Library

Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics - Andolfo - 2012 - New Phytologist - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

"Taken together, these findings have implications for improved understanding of the mechanisms of molecular adaptive selection at Solanum R loci."

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PLOS ONE: Genome-Wide Survey and Expression Analysis of Amino Acid Transporter Gene Family in Rice (Oryza sativa L.)

PLOS ONE: Genome-Wide Survey and Expression Analysis of Amino Acid Transporter Gene Family in Rice (Oryza sativa L.) | Plant Breeding and Genomics News | Scoop.it

"Comprehensive analyses were performed to investigate the expression profiles of OsAAT genes in various stages of vegetative and reproductive development by using data from EST, Microarrays, MPSS and Real-time PCR. Many OsAAT genes exhibited abundant and tissue-specific expression patterns. Moreover, 21 OsAAT genes were found to be differentially expressed under the treatments of abiotic stresses. Comparative analysis indicates that 26 AAT genes with close evolutionary relationships between rice and Arabidopsis exhibited similar expression patterns."

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RuBisCO small subunit is involved in Tobamovir... [Plant Physiol. 2012] - PubMed - NCBI

"ToMV was able to establish efficient local infection but was not able to move systemically. These findings suggest that NbRbCS plays a vital role in Tobamovirus movement and plant antiviral defenses."

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Association genetics of chemical wood properties in black poplar (Populus nigra) - Guerra - 2012 - New Phytologist - Wiley Online Library

Association genetics of chemical wood properties in black poplar (Populus nigra) - Guerra - 2012 - New Phytologist - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

"The rapid decay of LD within candidate genes in this population and the genetic associations identified suggest a close relationship between the associated SNPs and the causative polymorphisms underlying the genetic variation of lignocellulosic traits in black poplar."

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Live Chat: The Genes We Eat - ScienceNOW

AAAS is sponsoring a discussion about genetically modified foods Thursday, November 15th, 3 pm EST.

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PLOS ONE: Inferences from the Historical Distribution of Wild and Domesticated Maize Provide Ecological and Evolutionary Insight

PLOS ONE: Inferences from the Historical Distribution of Wild and Domesticated Maize Provide Ecological and Evolutionary Insight | Plant Breeding and Genomics News | Scoop.it

"The restricted and highly contrasting ecological niches of the wild teosintes differ substantially from domesticated maize. Variables determining the distributions of these taxa can inform future considerations of local adaptation and the impacts of climate change. Our assessment of the changing distributions of Zea mays taxa over time offers a unique glimpse into the history of maize, highlighting a strategy for the study of domestication that may prove useful for other species."

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The Life Cycle of Wheat Stem Rust

The Borlaug Global Rust Initiative Presents: The Life Cycle of Wheat Stem Rust.

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PLOS ONE: Abscisic Acid Refines the Synthesis of Chloroplast Proteins in Maize (Zea mays) in Response to Drought and Light

PLOS ONE: Abscisic Acid Refines the Synthesis of Chloroplast Proteins in Maize (Zea mays) in Response to Drought and Light | Plant Breeding and Genomics News | Scoop.it

"Thus, the results in the present study supported the vital role of ABA in regulating the synthesis of drought- and/or light-induced proteins in maize chloroplasts and would facilitate the functional characterization of ABA-induced chloroplast proteins in C4 plants."

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Arabidopsis ribosomal proteins cont... [Proc Natl Acad Sci U S A. 2012] - PubMed - NCBI

"Upstream ORFs are elements found in the 5'-leader sequences of specific mRNAs that modulate the translation of downstream ORFs encoding major gene products. In Arabidopsis, the translational control of auxin response factors (ARFs) by upstream ORFs has been proposed as a regulatory mechanism required to respond properly to complex auxin-signaling inputs. In this study, we identify and characterize the aberrant auxin responses in specific ribosomal protein mutants in which multiple ARF transcription factors are simultaneously repressed at the translational level. This characteristic lends itself to the use of these mutants as genetic tools to bypass the genetic redundancy among members of the ARF family in Arabidopsis. Using this approach, we were able to assign unique functions for ARF2, ARF3, and ARF6 in plant development."

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