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De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome

Andres Zurita's insight:

Olive breeding programmes are focused on selecting for traits as short juvenile period, plant architecture suited for mechanical harvest, or oil characteristics, including fatty acid composition, phenolic, and volatile compounds to suit new markets. Understanding the molecular basis of these characteristics and improving the efficiency of such breeding programmes require the development of genomic information and tools. However, despite its economic relevance, genomic information on olive or closely related species is still scarce. We have applied Sanger and 454 pyrosequencing technologies to generate close to 2 million reads from 12 cDNA libraries obtained from the Picual, Arbequina, and Lechin de Sevilla cultivars and seedlings from a segregating progeny of a Picual × Arbequina cross. The libraries include fruit mesocarp and seeds at three relevant developmental stages, young stems and leaves, active juvenile and adult buds as well as dormant buds, and juvenile and adult roots. The reads were assembled by library or tissue and then assembled together into 81 020 unigenes with an average size of 496 bases. Here, we report their assembly and their functional annotation.

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Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple

Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple | Plant Gene Seeker -PGS | Scoop.it
Fruit crops: Determining dwarfism in apples
Dwarfing revolutionized apple cultivation, but its genetic basis is poorly understood. Researchers led by Toshi Foster at the New Zealand Institute for Plant and Food Research have now analysed the basis of dwarfing and discovered two interacting genetic regions account for the reduced growth produced by most ‘dwarfing’ apple rootstocks. To distinguish genetic from environmental effects, the team analysed a large, standardized population of apple trees grown on both dwarfing and more vigorous rootstocks. Their results confirmed one previously identified dwarfing gene, Dw1, and uncovered a second, Dw2. Unlike Dw1, Dw2 alone does not cause dwarfing, suggesting it may act as an enhancer of Dw1. Foster's team found markers of Dw1 and Dw2 in most modern dwarfing apple rootstocks, implying all such rootstocks derive from a single origin. The study provides crucial information for future apple rootstock breeding.
Andres Zurita's insight:

The apple dwarfing rootstock ‘Malling9’ (‘M9’) has been used worldwide both to reduce scion vigour and as a genetic source for breeding new rootstocks. Progeny of ‘M9’ segregate for rootstock-induced dwarfing of the scion, indicating that this trait is controlled by one or more genetic factors. A quantitative trait locus (QTL) analysis of a rootstock population derived from the cross between ‘M9’ × ‘Robusta5’ (non-dwarfing) and grafted with ‘Braeburn’ scions identified a major QTL (Dw1) on linkage group (LG) 5, which exhibits a significant influence on dwarfing of the scion. A smaller-effect QTL affecting dwarfing (Dw2) was identified on LG11, and four minor-effect QTLs were found on LG6, LG9, LG10 and LG12. Phenotypic analysis indicates that the combination of Dw1 and Dw2 has the strongest influence on rootstock-induced dwarfing, and that Dw1 has a stronger effect than Dw2. Genetic markers linked to Dw1 and Dw2 were screened over 41 rootstock accessions that confer a range of effects on scion growth. The majority of the dwarfing and semi-dwarfing rootstock accessions screened carried marker alleles linked to Dw1 and Dw2. This suggests that most apple dwarfing rootstocks have been derived from the same genetic source.

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Functional characterization and developmental expression profiling of gibberellin signalling components in Vitis vinifera

Functional characterization and developmental expression profiling of gibberellin signalling components in Vitis vinifera | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Gibberellins (GAs) regulate numerous developmental processes in grapevine (Vitis vinifera) such as rachis elongation, fruit set, and fruitlet abscission. The ability of GA to promote berry enlargement has led to its indispensable use in the sternospermocarpic (‘seedless’) table grape industry worldwide. However, apart from VvGAI1 (VvDELLA1), which regulates internode elongation and fruitfulness, but not berry size of seeded cultivars, little was known about GA signalling in grapevine. We have identified and characterized two additional DELLAs (VvDELLA2 and VvDELLA3), two GA receptors (VvGID1a and VvGID1b), and two GA-specific F-box proteins (VvSLY1a and VvSLY1b), in cv. Thompson seedless. With the exception of VvDELLA3-VvGID1b, all VvDELLAs interacted with the VvGID1s in a GA-dependent manner in yeast two-hybrid assays. Additionally, expression of these grape genes in corresponding Arabidopsis mutants confirmed their functions in planta. Spatiotemporal analysis of VvDELLAs showed that both VvDELLA1 and VvDELLA2 are abundant in most tissues, except in developing fruit where VvDELLA2 is uniquely expressed at high levels, suggesting a key role in fruit development. Our results further suggest that differential organ responses to exogenous GA depend on the levels of VvDELLA proteins and endogenous bioactive GAs. Understanding this interaction will allow better manipulation of GA signalling in grapevine.

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Suppression of soil nitrification by plants

Suppression of soil nitrification by plants | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:
Highlights

• Modern agricultural systems have become high-nitrifying.


• Nitrification control is critical to improve NUE in agricultural systems.

• Release of nitrification inhibitors from plant roots is termed BNI function.• BNI-enabled food and feed crops can reduce nitrification and N2O emissions.• Next-generation production systems need to be low-nitrifying and low-N2O emitting.
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Shoot and root branch growth angle control—the wonderfulness of lateralness

Shoot and root branch growth angle control—the wonderfulness of lateralness | Plant Gene Seeker -PGS | Scoop.it
The overall shape of plants, the space they occupy above and below ground, is determined principally by the number, length, and angle of their lateral branches. The function of these shoot and root branches is to hold leaves and other organs to the sun, and below ground, to provide anchorage and facilitate the uptake of water and nutrients. While in some respects lateral roots and shoots can be considered mere iterations of the primary root-shoot axis, in others there are fundamental differences in their biology, perhaps most conspicuously in the regulation their angle of growth. Here we discuss recent advances in the understanding of the control of branch growth angle, one of the most important but least understood components of the wonderful diversity of plant form observed throughout nature.
Andres Zurita's insight:
Highlights

 • Gravitropic setpoint angles are growth angles that are maintained relative to gravity.

• Non-vertical branch growth is an important adaptive trait that is poorly understood.• Auxin is central to the gravity-dependent, non-vertical growth of lateral branches.• Non-vertical GSAs arise via balancing gravitropic and antigravitropic components.
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Rescooped by Andres Zurita from Plant Biology Teaching Resources (Higher Education)
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Resources for academic writing and publishing


I led a workshop on academic writing and publishing last week, and this is a list of resources I gave to the participants. It's not an exhaustive list, so if you have any favorites let me know and I'll add them!


Links and resources


General writing resources


Strunk, W. Jr. (1999).The Elements of Style. http://www.bartleby.com/141/


 


Guidelines and lessons for good scientific writing


Cargill, M., and O’Connor, P. (2011). Writing Scientific Research Articles: Strategy and Steps. Wiley. http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1444356216.html


Doumont, J., ed. (2010). English Communication for Scientists. Cambridge, MA: NPG Education. http://www.nature.com/wls/ebooks/english-communication-for-scientists-14053993/contents (Free ebook - very useful)


Duke University Graduate School. Scientific Writing Resource.  https://cgi.duke.edu/web/sciwriting/index.php Short, online course for graduate students with examples and worksheets


Editorial (2010). Scientific writing 101. Nat Struct Mol Biol. 17: 139-139. http://www.nature.com/nsmb/journal/v17/n2/full/nsmb0210-139.html


European Association of Science Editors. EASE Toolkit for Authors. http://www.ease.org.uk/publications/ease-toolkit-authors


Nature Scitable Effective Writing. http://www.nature.com/scitable/topicpage/effective-writing-13815989


Nature Scitable Scientific Papers. http://www.nature.com/scitable/topicpage/scientific-papers-13815490


Lichtfouse, E. (2013). Scientific Writing for Impact Factor Journals. Nova Scientific Publishers, Inc. (New York).


Moreira, A., and Haahtela, T. (2011). How to write a scientific paper--and win the game scientists play! Rev. Port. Pneumol. 17:146-149. doi: 10.1016/j.rppneu.2011.03.007. http://www.elsevier.pt/en/linkresolver/320/how-to-write-scientific-paper-and-win/90020266


Plaxco, K.W. (2010). The art of writing science. Protein Science 19: 2261 – 2266. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009394/pdf/pro0019-2261.pdf


Rogers, Silvia M. (2014). Mastering Scientific and Medical Writing: A Self-Help Guide. Springer. http://www.springer.com/medicine/book/978-3-642-39445-4 https://moodle.swarthmore.edu/pluginfile.php/179173/mod_resource/content/1/Good%20versus%20poor%20scientific%20writing%20from%20Silvia%20Rogers.pdf


Writing Center University of Wisconsin. (2014) The Writers Handbook: Reverse Outlines. http://writing.wisc.edu/Handbook/ReverseOutlines.html


 


Guidance from journals


J Exp Bot: http://www.oxfordjournals.org/our_journals/exbotj/for_authors/


Nature: http://www.nature.com/authors/author_resources/how_write.html


Plant Cell: http://www.plantcell.org/site/misc/ifora.xhtml


 


Figures preparation and ethical issues


Blatt, M. and Martin, C. (2013). Manipulation and Misconduct in the Handling of Image Data. Plant Physiology. 163: 3-4. http://www.plantphysiol.org/content/163/1/3.short


Cromey, D.W. (2010). Avoiding twisted pixels: ethical guidelines for the appropriate use and manipulation of scientific digital images. Sci. Eng. Ethics 16: 639–667


Rossner, M., and Yamada, K.M. (2004). What’s in a picture? The temptation of image manipulation. J. Cell Biol 166: 11–15. http://jcb.rupress.org/content/166/1/11.short


 


Peer Review Guidelines and Policies, Post-publication peer review


Bastian, H. (2014) A Stronger Post-Publication Culture Is Needed for Better Science. PLoS Med 11(12): e1001772. doi:10.1371/journal.pmed.1001772


F1000Research: http://blog.f1000research.com/2014/07/08/what-is-post-publication-peer-review/


F1000: http://journal.frontiersin.org/Journal/10.3389/fncom.2012.00063/full


Mole. (2007). Rebuffs and rebuttals I: how rejected is rejected? J Cell Sci. 120: 1143-1144. http://hwmaint.jcs.biologists.org/cgi/reprint/120/7/1143


Nature: http://www.nature.com/authors/policies/peer_review.html


Office of Research Integrity. (US Dept of Health and Human Services) The Lab. http://ori.hhs.gov/THELAB


Office of Research Integrity. Research Clinic Case Book. http://ori.hhs.gov/rcr-casebook-stories-about-researchers-worth-discussing


Science: http://www.sciencemag.org/site/feature/contribinfo/review.xhtml


PLOS ONE: www.plosone.org/static/reviewerGuidelines


Provenzale, J.M. and Stanley, R.J. (2006). A Systematic Guide to Reviewing a Manuscript. J. Nuclear Med.Techn.. 34: 92-99. http://tech.snmjournals.org/content/34/2/92.full.pdf+html


Times Higher Education: http://www.timeshighereducation.co.uk/news/can-post-publication-peer-review-endure/2016895.article


 


Readability


RavenBlog (2010). Ultimate list of online content readability tests. http://blog.raventools.com/ultimate-list-of-online-content-readability-tests/


 


Communicating more broadly


Kuehne, L.M., et al. (2014). Practical science communication strategies for graduate students. Conservation Biology. 28: 1225–1235. .DOI: 10.1111/cobi.12305


Osterrieder, A. (2013). The value and use of social media as communication tool in the plant sciences. Plant Methods. 9: 26. http://www.plantmethods.com/content/9/1/26


 



Via Mary Williams
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Outstanding source of fine material! Thanks Mary!
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AckerbauHalle's curator insight, February 3, 10:49 AM

Großartige Literatursammlung für wissenschaftliches Schreiben. 

Bibhya Sharma's curator insight, February 3, 8:58 PM

Very helpful for teachers and researchers. 

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PRL1 modulates root stem cell niche activity and meristem size through WOX5 and PLTs in Arabidopsis

PRL1 modulates root stem cell niche activity and meristem size through WOX5 and PLTs in Arabidopsis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The stem cell niche in the root meristem maintains pluripotent stem cells to ensure a constant supply of cells for root growth. Despite extensive progress, the molecular mechanisms through which root stem cell fates and stem cell niche activity are determined remain largely unknown. In Arabidopsis thaliana, the Pleiotropic Regulatory Locus 1 (PRL1) encodes a WD40-repeat protein subunit of the spliceosome-activating Nineteen Complex (NTC) that plays a role in multiple stress, hormone and developmental signaling pathways. Here, we show that PRL1 is involved in the control of root meristem size and root stem cell niche activity. PRL1 is strongly expressed in the root meristem and its loss of function mutation results in disorganization of the quiescent center (QC), premature stem cell differentiation, aberrant cell division, and reduced root meristem size. Our genetic studies indicate that PRL1 is required for confined expression of the homeodomain transcription factor WOX5 in the QC and acts upstream of the transcription factor PLETHORA (PLT) in modulating stem cell niche activity and root meristem size. These findings define a role for PRL1 as an important determinant of PLT signaling that modulates maintenance of the stem cell niche and root meristem size.

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The Plant Cell Reviews Dynamic Aspects of Plant Hormone Signaling and Crosstalk

The Plant Cell Reviews Dynamic Aspects of Plant Hormone Signaling and Crosstalk | Plant Gene Seeker -PGS | Scoop.it

The Roles of ROS and ABA in Systemic Acquired Acclimation

Ron Mittler and Eduardo Blumwald

Plant Cell 2015 tpc.114.133090; First Published on January 20, 2015; doi:10.1105/tpc.114.133090 OPEN

http://www.plantcell.org/content/early/2015/01/20/tpc.114.133090.abstract

 

SCFTIR1/AFB-Based Auxin Perception: Mechanism and Role in Plant Growth and Development

Mohammad Salehin, Rammyani Bagchi, and Mark Estelle

Plant Cell 2015 tpc.114.133744; First Published on January 20, 2015; doi:10.1105/tpc.114.133744

http://www.plantcell.org/content/early/2015/01/20/tpc.114.133744.abstract

 

The PB1 Domain in Auxin Response Factor and Aux/IAA Proteins: A Versatile Protein Interaction Module in the Auxin Response

Tom J. Guilfoyle

Plant Cell 2015 tpc.114.132753; First Published on January 20, 2015; doi:10.1105/tpc.114.132753 OPEN

http://www.plantcell.org/content/early/2015/01/20/tpc.114.132753.abstract

 

PIN-Dependent Auxin Transport: Action, Regulation, and Evolution

Maciek Adamowski and Jiří Friml

Plant Cell 2015 tpc.114.134874; First Published on January 20, 2015; doi:10.1105/tpc.114.134874

http://www.plantcell.org/content/early/2015/01/20/tpc.114.134874.abstract

 

The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development

G. Eric Schaller, Anthony Bishopp, and Joseph J. Kieber

Plant Cell 2015 tpc.114.133595; First Published on January 20, 2015; doi:10.1105/tpc.114.133595

http://www.plantcell.org/content/early/2015/01/20/tpc.114.133595.abstract


Via Mary Williams, Christophe Jacquet
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Spatial and temporal variation in plant hydraulic traits and their relevance for climate change impacts on vegetation

Spatial and temporal variation in plant hydraulic traits and their relevance for climate change impacts on vegetation | Plant Gene Seeker -PGS | Scoop.it

Anderegg - 2014 - New Phytologist - Wiley Online Library

Open Minireview

Andres Zurita's insight:

Plant hydraulics mediate terrestrial woody plant productivity, influencing global water, carbon, and biogeochemical cycles, as well as ecosystem vulnerability to drought and climate change. While inter-specific differences in hydraulic traits are widely documented, intra-specific hydraulic variability is less well known and is important for predicting climate change impacts. Here, I present a conceptual framework for this intra-specific hydraulic trait variability, reviewing the mechanisms that drive variability and the consequences for vegetation response to climate change. I performed a meta-analysis on published studies (n = 33) of intra-specific variation in a prominent hydraulic trait – water potential at which 50% stem conductivity is lost (P50) – and compared this variation to inter-specific variability within genera and plant functional types used by a dynamic global vegetation model. I found that intra-specific variability is of ecologically relevant magnitudes, equivalent to c. 33% of the inter-specific variability within a genus, and is larger in angiosperms than gymnosperms, although the limited number of studies highlights that more research is greatly needed. Furthermore, plant functional types were poorly situated to capture key differences in hydraulic traits across species, indicating a need to approach prediction of drought impacts from a trait-based, rather than functional type-based perspective.

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The origin and evolution of maize in the Southwestern United States

The origin and evolution of maize in the Southwestern United States | Plant Gene Seeker -PGS | Scoop.it

Nature Plants

Andres Zurita's insight:

The origin of maize (Zea maysmays) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal1,2,3,4 or highland5,6 routes of diffusion of maize into the United States. Furthermore, the genetics of adaptation to the new environmental and cultural context of the Southwest is largely uncharacterized7. To address these issues, we compared nuclear DNA from 32 archaeological maize samples spanning 6,000 years of evolution to modern landraces. We found that the initial diffusion of maize into the Southwest about 4,000 years ago is likely to have occurred along a highland route, followed by gene flow from a lowland coastal maize beginning at least 2,000 years ago. Our population genetic analysis also enabled us to differentiate selection during domestication for adaptation to the climatic and cultural environment of the Southwest, identifying adaptation loci relevant to drought tolerance and sugar content.

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Genome-wide Association Mapping Identifies a New Arsenate Reductase Enzyme Critical for Limiting Arsenic Accumulation in Plants

Genome-wide Association Mapping Identifies a New Arsenate Reductase Enzyme Critical for Limiting Arsenic Accumulation in Plants | Plant Gene Seeker -PGS | Scoop.it

PLOS Biology

Andres Zurita's insight:

Inorganic arsenic is a carcinogen, and its ingestion through foods such as rice presents a significant risk to human health. Plants chemically reduce arsenate to arsenite. Using genome-wide association (GWA) mapping of loci controlling natural variation in arsenic accumulation in Arabidopsis thaliana allowed us to identify the arsenate reductase required for this reduction, which we named High Arsenic Content 1 (HAC1). Complementation verified the identity of HAC1, and expression in Escherichia coli lacking a functional arsenate reductase confirmed the arsenate reductase activity of HAC1. The HAC1 protein accumulates in the epidermis, the outer cell layer of the root, and also in the pericycle cells surrounding the central vascular tissue. Plants lacking HAC1 lose their ability to efflux arsenite from roots, leading to both increased transport of arsenic into the central vascular tissue and on into the shoot. HAC1 therefore functions to reduce arsenate to arsenite in the outer cell layer of the root, facilitating efflux of arsenic as arsenite back into the soil to limit both its accumulation in the root and transport to the shoot. Arsenate reduction by HAC1 in the pericycle may play a role in limiting arsenic loading into the xylem. Loss of HAC1-encoded arsenic reduction leads to a significant increase in arsenic accumulation in shoots, causing an increased sensitivity to arsenate toxicity. We also confirmed the previous observation that the ACR2 arsenate reductase in A. thaliana plays no detectable role in arsenic metabolism. Furthermore, ACR2 does not interact epistatically with HAC1, since arsenic metabolism in the acr2 hac1 double mutant is disrupted in an identical manner to that described for the hac1 single mutant. Our identification of HAC1 and its associated natural variation provides an important new resource for the development of low arsenic-containing food such as rice.

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The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pathway

The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pathway | Plant Gene Seeker -PGS | Scoop.it
Alan Lloyd and colleagues identify a MYB gene in beet that acts as a key regulator of the betalain red pigmentation pathway. They further show that this gene resides at the classical Y pigmentation locus and shares homology with MYB genes that encode positive regulators of the anthocyanin pigmentation pathway in other species.
Andres Zurita's insight:

Nearly all flowering plants produce red/violet anthocyanin pigments. Caryophyllales is the only order containing families that replace anthocyanins with unrelated red and yellow betalain pigments1, 2. Close biological correlation of pigmentation patterns suggested that betalains might be regulated by a conserved anthocyanin-regulating transcription factor complex consisting of a MYB, a bHLH and a WD repeat–containing protein (the MBW complex)3. Here we show that a previously uncharacterized anthocyanin MYB-like protein, Beta vulgaris MYB1 (BvMYB1), regulates the betalain pathway in beets. Silencing BvMYB1 downregulates betalain biosynthetic genes and pigmentation, and overexpressing BvMYB1 upregulates them. However, unlike anthocyanin MYBs, BvMYB1 will not interact with bHLH members of heterologous anthocyanin MBW complexes because of identified nonconserved residues. BvMYB1 resides at the historic beet pigment-patterning locus, Y, required for red-fleshed beets4. We show that Y and y express different levels of BvMYB1 transcripts. The co-option of a transcription factor regulating anthocyanin biosynthesis would be an important evolutionary event allowing betalains to largely functionally replace anthocyanins.

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How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity

How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity | Plant Gene Seeker -PGS | Scoop.it

Tree Physiology

Andres Zurita's insight:

Tree breeding and biotechnology can enhance forest productivity and help alleviate the rising pressure on forests from climate change and human exploitation. While many physiological processes and genes are targeted in search of genetically improved tree productivity, an overarching principle to guide this search is missing. Here, we propose a method to identify the traits that can be modified to enhance productivity, based on the differences between trees shaped by natural selection and ‘improved’ trees with traits optimized for productivity. We developed a tractable model of plant growth and survival to explore such potential modifications under a range of environmental conditions, from non-water limited to severely drought-limited sites. We show how key traits are controlled by a trade-off between productivity and survival, and that productivity can be increased at the expense of long-term survival by reducing isohydric behavior (stomatal regulation of leaf water potential) and allocation to defense against pests compared with native trees. In contrast, at dry sites occupied by naturally drought-resistant trees, the model suggests a better strategy may be to select trees with slightly lower wood density than the native trees and to augment isohydric behavior and allocation to defense. Thus, which traits to modify, and in which direction, depend on the original tree species or genotype, the growth environment and wood-quality versus volume production preferences. In contrast to this need for customization of drought and pest resistances, consistent large gains in productivity for all genotypes can be obtained if root traits can be altered to reduce competition for water and nutrients. Our approach illustrates the potential of using eco-evolutionary theory and modeling to guide plant breeding and genetic technology in selecting target traits in the quest for higher forest productivity.

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How is water-use efficiency of terrestrial ecosystems distributed and changing on Earth?

How is water-use efficiency of terrestrial ecosystems distributed and changing on Earth? | Plant Gene Seeker -PGS | Scoop.it

Scientific Reports

Open Access

Andres Zurita's insight:

A better understanding of ecosystem water-use efficiency (WUE) will help us improve ecosystem management for mitigation as well as adaption to global hydrological change. Here, long-term flux tower observations of productivity and evapotranspiration allow us to detect a consistent latitudinal trend in WUE, rising from the subtropics to the northern high-latitudes. The trend peaks at approximately 51°N, and then declines toward higher latitudes. These ground-based observations are consistent with global-scale estimates of WUE. Global analysis of WUE reveals existence of strong regional variations that correspond to global climate patterns. The latitudinal trends of global WUE for Earth's major plant functional types reveal two peaks in the Northern Hemisphere not detected by ground-based measurements. One peak is located at 20° ~ 30°N and the other extends a little farther north than 51°N. Finally, long-term spatiotemporal trend analysis using satellite-based remote sensing data reveals that land-cover and land-use change in recent years has led to a decline in global WUE. Our study provides a new framework for global research on the interactions between carbon and water cycles as well as responses to natural and human impacts.

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Plant salt tolerance: adaptations in halophytes

Plant salt tolerance: adaptations in halophytes | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Background 

Most of the water on Earth is seawater, each kilogram of which contains about 35 g of salts, and yet most plants cannot grow in this solution; less than 0·2 % of species can develop and reproduce with repeated exposure to seawater. These ‘extremophiles’ are called halophytes.

Scope 

Improved knowledge of halophytes is of importance to understanding our natural world and to enable the use of some of these fascinating plants in land re-vegetation, as forages for livestock, and to develop salt-tolerant crops. In this Preface to a Special Issue on halophytes and saline adaptations, the evolution of salt tolerance in halophytes, their life-history traits and progress in understanding the molecular, biochemical and physiological mechanisms contributing to salt tolerance are summarized. In particular, cellular processes that underpin the ability of halophytes to tolerate high tissue concentrations of Na+ and Cl−, including regulation of membrane transport, their ability to synthesize compatible solutes and to deal with reactive oxygen species, are highlighted. Interacting stress factors in addition to salinity, such as heavy metals and flooding, are also topics gaining increased attention in the search to understand the biology of halophytes.

Conclusions 

Halophytes will play increasingly important roles as models for understanding plant salt tolerance, as genetic resources contributing towards the goal of improvement of salt tolerance in some crops, for re-vegetation of saline lands, and as ‘niche crops’ in their own right for landscapes with saline soils.

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Severe drought stress is affecting selected primary metabolites, polyphenols, and volatile metabolites in grapevine leaves (Vitis vinifera cv. Pinot noir)

Severe drought stress is affecting selected primary metabolites, polyphenols, and volatile metabolites in grapevine leaves (Vitis vinifera cv. Pinot noir) | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Extreme weather conditions with prolonged dry periods and high temperatures as well as heavy rain events can severely influence grapevine physiology and grape quality. The present study evaluates the effects of severe drought stress on selected primary metabolites, polyphenols and volatile metabolites in grapevine leaves. Among the 11 primary metabolites, 13 polyphenols and 95 volatiles which were analyzed, a significant discrimination between control and stressed plants of 7 primary metabolites, 11 polyphenols and 46 volatile metabolites was observed. As single parameters are usually not specific enough for the discrimination of control and stressed plants, an unsupervised (PCA) and a supervised (PLS-DA) multivariate approach were applied to combine results from different metabolic groups. In a first step a selection of five metabolites, namely citric acid, glyceric acid, ribose, phenylacetaldehyde and 2-methylbutanal were used to establish a calibration model using PLS regression to predict the leaf water potential. The model was strong enough to assign a high number of plants correctly with a correlation of 0.83. The PLS-DA provides an interesting approach to combine data sets and to provide tools for the specific evaluation of physiological plant stresses.

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Introduced and invasive cactus species: a global review

Andres Zurita's insight:

Understanding which species are introduced and become invasive, and why, are central questions in invasion science. Comparative studies on model taxa have provided important insights, but much more needs to be done to unravel the context dependencies of these findings. The cactus family (Cactaceae), one of the most popular horticultural plant groups, is an interesting case study. Hundreds of cactus species have been introduced outside their native ranges; a few of them are among the most damaging invasive plant species in the world. We reviewed the drivers of introductions and invasions in the family and seek insights that can be used to minimize future risks. We compiled a list of species in the family and determined which have been recorded as invasive. We also mapped current global distributions and modelled the potential global distributions based on distribution data of known invasive taxa. Finally, we identified whether invasiveness is phylogenetically clustered for cacti and whether particular traits are correlated with invasiveness. Only 57 of the 1922 cactus species recognized in this treatment have been recorded as invasive. There are three invasion hotspots: South Africa (35 invasive species recorded), Australia (26 species) and Spain (24 species). However, there are large areas of the world with climates suitable for cacti that are at risk of future invasion—in particular, parts of China, eastern Asia and central Africa. The invasive taxa represent an interesting subset of the total species pool. There is a significant phylogenetic signal: invasive species occur in 2 of the 3 major phylogenetic clades and in 13 of the 130 genera. This phylogenetic signal is not driven by human preference, i.e. horticultural trade, but all invasive species are from 5 of the 12 cactus growth forms. Finally, invasive species tend to have significantly larger native ranges than non-invasive species, and none of the invasive species are of conservation concern in their native range. These results suggest fairly robust correlates of invasiveness that can be used for proactive management and risk assessments.

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Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as “junk” DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up- or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress-induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive up-regulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize.

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Digging deeper: high-resolution genome-scale data yields new insights into root biology

Digging deeper: high-resolution genome-scale data yields new insights into root biology | Plant Gene Seeker -PGS | Scoop.it

Highlights•

Cell-type specific hormone signaling is important for the high-resolution salt stress response in the root.

Computational modeling of cell-type specific data illustrates the complexity of these networks.

Mutants that lack morphological phenotypes often have molecular phenotypes that are revealed with cell-type specific data.

High-resolution analysis of auxin responses identifies a bipartite auxin response along the longitudinal axis of the root.

New advances allowing simultaneous root growth and cellular imaging identify novel regulators of root growth and development.

Development in multicellular organisms is the result of designated cellular programs occurring at specific points in time and space. The root is an excellent model to address how spatio-temporal complexity impacts organ development. High-resolution ‘omic’ approaches have delineated the transcriptional, proteomic, metabolomic, and small RNA profiles of multiple cell types in the Arabidopsis root. Similar approaches have shed light on root cell-type specific transcriptional programs in rice and soybean. These data are being used to identify specific spatio-temporal mechanisms of root development, dissect regulatory networks that control cell identity, and understand hormone responses in the root. Computational modeling of these data combined with new advances in imaging technologies is generating new biological insights into root growth and development.


Via Christophe Jacquet, Fenglin Deng
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Wise words from a tree physiologist

Wise words from a tree physiologist | Plant Gene Seeker -PGS | Scoop.it

Really enjoyed reading the biographies of Dennis Hoagland and William Chander, who collaborated on studies of mineral nutrition of plants. This quote from Chandler is abridged from a speech he gave during the second world war, but it's just as appropriate now.

 

http://www.nasonline.org/publications/biographical-memoirs/memoir-pdfs/chandler-william-h.pdf

http://www.nasonline.org/publications/biographical-memoirs/memoir-pdfs/hoagland-dennis-r.pdf


Via Mary Williams
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Genomic selection in hybrid breeding

Genomic selection in hybrid breeding | Plant Gene Seeker -PGS | Scoop.it

Plant Breeding

Wiley Online Library

Open

Andres Zurita's insight:

While hybrid breeding is widely applied in outbreeding species, for many self-pollinating crop plants, it has only recently been established. This may have had its reason in the limitations of methods available for hybrid performance prediction, in particular when established heterotic pools were absent. Genomic selection has been suggested as a promising approach to resolve these limitations. In our review, we briefly introduce the principles of genomic selection as an extension of marker-assisted selection using genome-wide high-density molecular marker data and discuss the advantages and limitations of currently used algorithms. Including the outcome from a recent extended approach to hybrid wheat as a timely example, we summarize current progress in empirical studies on the application of genomic selection for prediction of hybrid performance. Here, we put emphasis on the factors affecting the accuracy of prediction, pointing in particular to the relevance of relatedness, genotype x environment interaction and experimental design. Finally, we discuss future research needs and potential applications.

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Identification of the transporter responsible for sucrose accumulation in sugar beet taproots

Identification of the transporter responsible for sucrose accumulation in sugar beet taproots | Plant Gene Seeker -PGS | Scoop.it
Nature Plants, Published online: 8 January 2015; | doi:10.1038/nplants.2014.1
Andres Zurita's insight:

Sugar beet provides around one third of the sugar consumed worldwide and serves as a significant source of bioenergy in the form of ethanol. Sucrose accounts for up to 18% of plant fresh weight in sugar beet. Most of the sucrose is concentrated in the taproot, where it accumulates in the vacuoles. Despite 30 years of intensive research, the transporter that facilitates taproot sucrose accumulation has escaped identification. Here, we combine proteomic analyses of the taproot vacuolar membrane, the tonoplast, with electrophysiological analyses to show that the transporter BvTST2.1 is responsible for vacuolar sucrose uptake in sugar beet taproots. We show that BvTST2.1 is a sucrose-specific transporter, and present evidence to suggest that it operates as a proton antiporter, coupling the import of sucrose into the vacuole to the export of protons. BvTST2.1 exhibits a high amino acid sequence similarity to members of the tonoplast monosaccharide transporter family in Arabidopsis, prompting us to rename this group of proteins ‘tonoplast sugar transporters’. The identification of BvTST2.1 could help to increase sugar yields from sugar beet and other sugar-storing plants in future breeding programs.

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Phytohormones as integrators of environmental signals in the regulation of mycorrhizal symbioses

Phytohormones as integrators of environmental signals in the regulation of mycorrhizal symbioses | Plant Gene Seeker -PGS | Scoop.it

New Phytologist

Tansley Insight

OPEN ACCESS

Andres Zurita's insight:

For survival, plants have to efficiently adjust their phenotype to environmental challenges, finely coordinating their responses to balance growth and defence. Such phenotypic plasticity can be modulated by their associated microbiota. The widespread mycorrhizal symbioses modify plant responses to external stimuli, generally improving the resilience of the symbiotic system to environmental stresses. Phytohormones, central regulators of plant development and immunity, are instrumental in orchestrating plant responses to the fluctuating environment, but also in the regulation of mycorrhizal symbioses. Exciting advances in the molecular regulation of phytohormone signalling are providing mechanistic insights into how plants coordinate their responses to environmental cues and mycorrhizal functioning. Here, we summarize how these mechanisms permit the fine-tuning of the symbiosis according to the ever-changing environment.

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An Arabidopsis gene regulatory network for secondary cell wall synthesis

An Arabidopsis gene regulatory network for secondary cell wall synthesis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein–DNA network between Arabidopsis thalianatranscription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.

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The genome sequence of the orchid Phalaenopsis equestris

The genome sequence of the orchid Phalaenopsis equestris | Plant Gene Seeker -PGS | Scoop.it

Nature Genetics

OPEN

Andres Zurita's insight:

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

 
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Salinity tolerance in soybean is modulated by natural variation in GmSALT3

Salinity tolerance in soybean is modulated by natural variation in GmSALT3 | Plant Gene Seeker -PGS | Scoop.it

The Plant Journal - Wiley Online Library

OPEN ACCESS

Andres Zurita's insight:

The identification of genes that improve the salt tolerance of crops is essential for the effective utilization of saline soils for agriculture. Here, we use fine mapping in a soybean (Glycine max (L.) Merr.) population derived from the commercial cultivars Tiefeng 8 and 85–140 to identify GmSALT3 (salt tolerance-associated gene on chromosome 3), a dominant gene associated with limiting the accumulation of sodium ions (Na+) in shoots and a substantial enhancement in salt tolerance in soybean. GmSALT3 encodes a protein from the cation/H+ exchanger family that we localized to the endoplasmic reticulum and which is preferentially expressed in the salt-tolerant parent Tiefeng 8 within root cells associated with phloem and xylem. We identified in the salt-sensitive parent, 85–140, a 3.78-kb copia retrotransposon insertion in exon 3 of Gmsalt3 that truncates the transcript. By sequencing 31 soybean landraces and 22 wild soybean (Glycine soja) a total of nine haplotypes including two salt-tolerant haplotypes and seven salt-sensitive haplotypes were identified. By analysing the distribution of haplotypes among 172 Chinese soybean landraces and 57 wild soybean we found that haplotype 1 (H1, found in Tiefeng 8) was strongly associated with salt tolerance and is likely to be the ancestral allele. Alleles H2–H6, H8 and H9, which do not confer salinity tolerance, were acquired more recently. H1, unlike other alleles, has a wide geographical range including saline areas, which indicates it is maintained when required but its potent stress tolerance can be lost during natural selection and domestication. GmSALT3 is a gene associated with salt tolerance with great potential for soybean improvement.

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