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Rescooped by Ricardo Oliva from Rice origins and cultural history
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Population structure of the primary gene pool of Oryza sativa in Thailand

Population structure of the primary gene pool of Oryza sativa in Thailand | pathogens | Scoop.it

Genetic Resources and Crop Evolution, Online First™ - SpringerLink.

The gene pool of cultivated Asian rice consists of wild rice (Oryza rufipogon Griff.), cultivated rice (O. sativa L.) and a weedy form (O. sativa f. spontanea). All three components are widespread in Thailand, frequently co-occurring within fields and providing the opportunity for gene flow and introgression. The purpose to this study is to understand the on-going evolutionary processes that affect the gene pool of rice by analysis of microsatellite variation. Results indicate that O. rufipogon, the wild ancestor of rice, has high levels of genetic variation both within and among populations. Moreover, the variation is structured predominantly by annual and perennial life history. High levels of variation are detected among cultivars indicating Thai cultivated rice has a broad genetic base with only a 20 % reduction in diversity from its wild ancestor. The weedy rice populations reveal varying levels of genetic variation, from nearly as high as wild rice to near zero. Weedy rice is genetically structured into 2 groups. Some populations of invasive weedy rice are the result of hybridization and gene flow between local wild rice and local cultivated rice in the regions of co-occurrence. Other populations of weedy rice are genetically nearly identical to the local cultivated rice. The diversity analysis indicates that the rice gene pool in Thailand is a dynamic genetic system. Gene flow is ongoing among its three main components, first between cultivated and wild rice resulting in weedy rice. Weedy rice in turn crosses with both cultivated varieties and wild rice.


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Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Rescooped by Ricardo Oliva from Rice origins and cultural history
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rice paradox: Multiple origins but single domestication in Asian rice | Molecular Biology and Evolution | Oxford Academic

rice paradox: Multiple origins but single domestication in Asian rice | Molecular Biology and Evolution | Oxford Academic | pathogens | Scoop.it
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1 – 24.1 kya, which is an order of magnitude older then the earliest archaeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 kya and archaeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice.

Via Dorian Q Fuller
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Rescooped by Ricardo Oliva from Plant Pathogens
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Papain-like cysteine proteases as hubs in plant immunity

Papain-like cysteine proteases as hubs in plant immunity | pathogens | Scoop.it
Plants deploy a sophisticated immune system to cope with different microbial pathogens and other invaders. Recent research provides an increasing body of evidence for papain-like cysteine proteases (PLCPs) being central hubs in plant immunity. PLCPs are required for full resistance of plants to various pathogens. At the same time, PLCPs are targeted by secreted pathogen effectors to suppress immune responses. Consequently, they are subject to a co-evolutionary host–pathogen arms race. When activated, PLCPs induce a broad spectrum of defense responses including plant cell death. While the important role of PLCPs in plant immunity has become more evident, it remains largely elusive how these enzymes are activated and which signaling pathways are triggered to orchestrate different downstream responses.

Via Francis Martin, Yogesh Gupta
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Rescooped by Ricardo Oliva from Rice Blast
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Current Applicable DNA Markers for Marker Assisted Breeding in Abiotic and Biotic Stress Tolerance in Rice (Oryza sativa L.)

Current Applicable DNA Markers for Marker Assisted Breeding in Abiotic and Biotic Stress Tolerance in Rice (Oryza sativa L.) | pathogens | Scoop.it
Abiotic and biotic stresses adversely affect rice (Oryza sativa L.) growth and yield. Conventional breeding is a very effective method to develop tolerant rice variety; however, it takes a decade long to establish a new rice variety. DNA-based markers have a huge potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). The large number of quantitative trait loci (QTLs) mapping studies for rice has provided an abundance of DNA marker-trait associations. The limitations of conventional breeding such as linkage drag and lengthy time consumption can be overcome by utilizing DNA markers in plant breeding. The major applications of DNA markers such as MAS, QTL mapping and gene pyramiding have been surveyed. In this review, we presented the latest markers available for some of the most important abiotic and biotic stresses in rice breeding programs. Achieving a significant impact on crop improvement by marker assisted breeding (MAB) represents the great challenge for agricultural scientists in the next few decades.

Via Elsa Ballini
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Rescooped by Ricardo Oliva from Phytophthora biology
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Genomic Analyses of Dominant U.S. Clonal Lineages of Phytophthora infestans Reveals a Shared Common Ancestry for Clonal Lineages US11 and US18 and a Lack of Recently Shared Ancestry Among All Other...

Genomic Analyses of Dominant U.S. Clonal Lineages of Phytophthora infestans Reveals a Shared Common Ancestry for Clonal Lineages US11 and US18 and a Lack of Recently Shared Ancestry Among All Other... | pathogens | Scoop.it
Populations of the potato and tomato late-blight pathogen Phytophthora infestans are well known for emerging as novel clonal lineages. These successions of dominant clones have historically been named US1 through US24, in order of appearance, since their first characterization using molecular markers. Hypothetically, these lineages can emerge through divergence from other U.S. lineages, recombination among lineages, or as novel, independent lineages originating outside the United States. We tested for the presence of phylogenetic relationships among U.S. lineages using a population of 31 whole-genome sequences, including dominant U.S. clonal lineages as well as available samples from global populations. We analyzed ancestry of the whole mitochondrial genome and samples of nuclear loci, including supercontigs 1.1 and 1.5 as well as several previously characterized coding regions. We found support for a shared ancestry among lineages US11 and US18 from the mitochondrial genome as well as from one nuclear haplotype on each supercontig analyzed. The other nuclear haplotype from each sample assorted independently, indicating an independent ancestry. We found no support for emergence of any other of the U.S. lineages from a common ancestor shared with the other U.S. lineages. Each of the U.S. clonal lineages fit a model where populations of new clonal lineages emerge via migration from a source population that is sexual in nature and potentially located in central Mexico or elsewhere. This work provides novel insights into patterns of emergence of clonal lineages in plant pathogen genomes.

Via Niklaus Grunwald
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Rescooped by Ricardo Oliva from TAL effector science
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A resistance locus in the American heirloom rice variety Carolina Gold Select is triggered by TAL
effectors with diverse predicted targets and is effective against African strains of Xanthomonas o...

A resistance locus in the American heirloom rice variety Carolina Gold Select is triggered by TAL <br/>effectors with diverse predicted targets and is effective against African strains of Xanthomonas o... | pathogens | Scoop.it

(Via T. Lahaye, thx)

Triplett et al, 2016

The rice pathogens Xanthomonas oryzae pathovar (pv.) oryzae and pv. oryzicola produce numerous transcription activator-like (TAL) effectors that increase bacterial virulence by activating expression of host susceptibility genes. Rice resistance mechanisms against TAL effectors include polymorphisms that prevent effector binding to susceptibility gene promoters, or that allow effector activation of resistance genes. This study identifies, in the heirloom variety Carolina Gold Select, a third mechanism of rice resistance involving TAL effectors. This resistance manifests through strong suppression of disease development in response to diverse TAL effectors from both X. oryzae pathovars. The resistance can be triggered by an effector with only 3.5 central repeats, is independent of the composition of the repeat variable diresidues that determine TAL effector binding specificity, and is independent of the transcriptional activation domain. We determined that the resistance is conferred by a single dominant locus, designated Xo1, that maps to a 1.09 Mbp fragment on chromosome 4. The Xo1 interval also confers complete resistance to the strains in the African clade of X. oryzae pv. oryzicola, representing the first dominant resistance locus against bacterial leaf streak in rice. The strong phenotypic similarity between the TAL effector triggered resistance conferred by Xo1 and that conferred by the tomato resistance gene Bs4 suggests that monocots and dicots share an ancient or convergently evolved mechanism to recognize analogous TAL effector epitopes.


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dromius's curator insight, May 22, 2016 9:00 AM

This is cool! Evidence for a Bs4-type recognition in rice. Bs4 is a TIR-NB-LRR, unlikely to be present in monocot rice. Mechanism behind NB-LRR recognition of diverse TALs is still not solved. Can't wait to hear what gene in the 1 Mb target interval confers this resistance.

 

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Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans

Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans | pathogens | Scoop.it
Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans Michael D. Martin*,1,2, Filipe G. Vieira1, Simon Y.W.
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Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria - Springer

Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria - Springer | pathogens | Scoop.it

Introduction Beneficial microbes in the microbiome of plant roots provide important services to the plant as they improve plant nutrition and provide protection against plant pathogens (Berendsen et al.

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Frontiers | Rice Sheath Rot: An Emerging Ubiquitous Destructive Disease Complex | Plant Biotic Interactions

Around one century ago, a rice disease characterized mainly by rotting of sheaths was reported in Taiwan. The causal agent was identified as Acrocylindrium oryzae, later known as Sarocladium oryzae. Since then it has become clear that various other organisms can cause similar disease symptoms, including Fusarium spp. and fluorescent pseudomonads. These organisms have in common that they produce a range of phytotoxins that induce necrosis in plants. The same agents also cause grain discoloration, chaffiness and sterility and are all seed-transmitted. Rice sheath rot disease symptoms are found in all rice-growing areas of the world. The disease is now getting momentum and is considered as an important emerging rice production threat. The disease can lead to variable yield losses, which can be as high as 85%. This review aims at improving our understanding of the disease etiology of rice sheath rot and mainly deals with the three most reported rice sheath rot pathogens: Sarocladium oryzae, the Fusarium fujikuroi complex and Pseudomonas fuscovaginae. Causal agents, pathogenicity determinants, interactions among the various pathogens, epidemiology, geographical distribution and control options will be discussed.
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Rice | Full text | Allele mining and enhanced genetic recombination for rice breeding

Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources.
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Acetylation of an NB-LRR Plant Immune-Effector Complex Suppresses Immunity: Cell Reports

Acetylation of an NB-LRR Plant Immune-Effector Complex Suppresses Immunity: Cell Reports | pathogens | Scoop.it
Ricardo Oliva's insight:
Highlights

 

•HopZ3 targets the RPM1 immune complex and effectors that activate this complex•HopZ3 acetylates Ser, Thr, Lys, as well as His•HopZ3 acetylates residues important for multiple facets of plant immune signaling•Bacterial effector-effector interactions are implicated in the outcome of infection

 

Summary

Modifications of plant immune complexes by secreted pathogen effectors can trigger strong immune responses mediated by the action of nucleotide binding-leucine-rich repeat immune receptors. Although some strains of the pathogen Pseudomonas syringae harbor effectors that individually can trigger immunity, the plant’s response may be suppressed by other virulence factors. This work reveals a robust strategy for immune suppression mediated by HopZ3, an effector in the YopJ family of acetyltransferases. The suppressing HopZ3 effector binds to and can acetylate multiple members of the RPM1 immune complex, as well as two P. syringaeeffectors that together activate the RPM1 complex. These acetylations modify serine, threonine, lysine, and/or histidine residues in the targets. Through HopZ3-mediated acetylation, it is possible that the whole effector-immune complex is inactivated, leading to increased growth of the pathogen.

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Single gene locus changes perturb complex microbial communities as much as apex predator loss

Nature Communications | doi:10.1038/ncomms9235
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Rescooped by Ricardo Oliva from Plants and Microbes
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Nature: Phylogenetic structure and host abundance drive disease pressure in communities (2015)

Nature: Phylogenetic structure and host abundance drive disease pressure in communities (2015) | pathogens | Scoop.it

 

Pathogens play an important part in shaping the structure and dynamics of natural communities, because species are not affected by them equally1, 2. A shared goal of ecology and epidemiology is to predict when a species is most vulnerable to disease. A leading hypothesis asserts that the impact of disease should increase with host abundance, producing a ‘rare-species advantage’3, 4, 5. However, the impact of a pathogen may be decoupled from host abundance, because most pathogens infect more than one species, leading to pathogen spillover onto closely related species6, 7. Here we show that the phylogenetic and ecological structure of the surrounding community can be important predictors of disease pressure. We found that the amount of tissue lost to disease increased with the relative abundance of a species across a grassland plant community, and that this rare-species advantage had an additional phylogenetic component: disease pressure was stronger on species with many close relatives. We used a global model of pathogen sharing as a function of relatedness between hosts, which provided a robust predictor of relative disease pressure at the local scale. In our grassland, the total amount of disease was most accurately explained not by the abundance of the focal host alone, but by the abundance of all species in the community weighted by their phylogenetic distance to the host. Furthermore, the model strongly predicted observed disease pressure for 44 novel host species we introduced experimentally to our study site, providing evidence for a mechanism to explain why phylogenetically rare species are more likely to become invasive when introduced8, 9. Our results demonstrate how the phylogenetic and ecological structure of communities can have a key role in disease dynamics, with implications for the maintenance of biodiversity, biotic resistance against introduced weeds, and the success of managed plants in agriculture and forestry.


Se also News & Views 

http://www.nature.com/nature/journal/v520/n7548/full/520446a.html


Via Kamoun Lab @ TSL
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Characterization and functional analysis of clpB gene from Acidovorax avenae subsp. avenae RS‐1

Characterization and functional analysis of clpB gene from Acidovorax avenae subsp. avenae RS‐1 | pathogens | Scoop.it
Type VI secretion system (T6SS) has been reported to be highly associated with various cellular activities in strain RS‐1 of Acidovorax avenae subsp. avenae (Aaa), the pathogen of bacterial brow
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Current Opinion in Microbiology: The cell biology of late blight disease (2016)

Current Opinion in Microbiology: The cell biology of late blight disease (2016) | pathogens | Scoop.it

• The Phytophthora haustorium is a major site of secretion during infection.

• The host endocytic cycle contributes to biogenesis of the Extra-Haustorial Membrane.
• RXLR effectors manipulate host processes at diverse subcellular locations.

• They directly manipulate the activity or location of immune proteins.

• They also promote the activity of endogenous negative regulators of immunity.

 

Late blight, caused by the oomycete Phytophthora infestans, is a major global disease of potato and tomato. Cell biology is teaching us much about the developmental stages associated with infection, especially the haustorium, which is a site of intimate interaction and molecular exchange between pathogen and host. Recent observations suggest a role for the plant endocytic cycle in specific recruitment of host proteins to the Extra-Haustorial Membrane, emphasising the unique nature of this membrane compartment. In addition, there has been a strong focus on the activities of RXLR effectors, which are delivered into plant cells to modulate and manipulate host processes. RXLR effectors interact directly with diverse plant proteins at a range of subcellular locations to promote disease.

 


Via Kamoun Lab @ TSL
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Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment

Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment | pathogens | Scoop.it
Understanding the processes that shaped contemporary pathogen populations in agricultural landscapes is quite important to define appropriate management strategies and to support crop improvement efforts.
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Frontiers | Genomics and Effectomics of the Crop Killer Xanthomonas

Frontiers | Genomics and Effectomics of the Crop Killer Xanthomonas | pathogens | Scoop.it
Phytopathogenic bacteria of the Xanthomonas genus cause severe diseases on hundreds of host plants, including economically important crops, such as bean, cabbage, cassava, citrus, hemp, pepper
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Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms

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Open access resources for genome-wide association mapping in rice : Nature Communications : Nature Publishing Group

Open access resources for genome-wide association mapping in rice : Nature Communications : Nature Publishing Group | pathogens | Scoop.it

Catch reconstructions reveal that global marine fisheries catches are higher than reported and declining Nature Communications 19 January 2016

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Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species : Nature Genetics : Nature Publishing Group

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species : Nature Genetics : Nature Publishing Group | pathogens | Scoop.it
Beat Keller, Thomas Wicker and colleagues compare the genomes of 46 isolates of powdery mildew, Blumeria graminis. They find that B. graminis f. sp. triticale, a pathogen growing on triticale (a wheat [times] rye hybrid plant), is a hybrid of B. graminis f. sp. tritici and B. graminis f. sp. secalis, which grow on wheat and rye, respectively.
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Genomic characterization of a South American Phytophthora hybrid mandates reassessment of the geographic origins of Phytophthora infestans

Genomic characterization of a South American Phytophthora hybrid mandates reassessment of the geographic origins of Phytophthora infestans | pathogens | Scoop.it
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PLOS ONE: Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot

PLOS ONE: Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot | pathogens | Scoop.it

Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

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Frontiers | Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands | Terrestrial Microbiology

Global and regional environmental changes often co-occur, creating complex gradients of disturbance on the landscape. Soil microbial communities are an important component of ecosystem response to ...
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