<i>The Plant Cell</i> Reviews Plant Immunity: Receptor-Like Kinases, ROS-RLK Crosstalk, Quantitative Resistance, and the Growth/Defense Trade-Off

Eckardt, Nancy A.

doi:10.1105/tpc.17.00289

Cited by 27 publications

(28 citation statements)

References 4 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The plant immune system machinery is complex and is composed of two tiers of extracellular and intracellular receptors (Krattinger and Keller, ,b) that efficiently detect the presence of pathogens (for review, see Greeff et al ., ; Couto and Zipfel, ; Eckardt, ). In this study, we found a significant enrichment of signals of selection at genes involved in this first level of defense in the eastern population.…”

Section: Discussionmentioning

confidence: 99%

“…More specifically, we found many of well‐characterized R‐genes, i.e. genes with NBS‐LRR domains and involved in disease resistance (Mchale et al ., ; Jacob et al ., ; Liu et al ., ; Couto and Zipfel, ; Eckardt, ; Van Ooijen et al ., ), to be under ongoing or completed positive selection in the eastern population. On the other hand, we also found additional R‐genes and genes involved in phosphorylation, a process especially important for immune signaling response in plants (for review, see Park et al ., ), to be under balancing selection.…”

Section: Discussionmentioning

confidence: 99%

“…The other type of interaction is often referred to as Red Queen dynamics or trench warfare, where alleles involved in the interaction are recycled through negative-frequency dependence and can therefore subsist for long periods of time in populations through balancing selection (Brown and Tellier, 2011). The plant immune system machinery is complex and is composed of two tiers of extracellular and intracellular receptors (Krattinger and Keller, 2016a,b) that efficiently detect the presence of pathogens (for review, see Greeff et al, 2012;Couto and Zipfel, 2016;Eckardt, 2017). In this study, we found a significant enrichment of signals of selection at genes involved in this first level of defense in the eastern population.…”

Section: Pathogens As a Potential Driving Force Of Population Evolutionmentioning

confidence: 99%

See 2 more Smart Citations

Genome‐wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

et al. 2018

View full text Add to dashboard Cite

Grasses are essential plants for ecosystem functioning. Quantifying the selective pressures that act on natural variation in grass species is therefore essential regarding biodiversity maintenance. In this study, we investigate the selection pressures that act on two distinct populations of the grass model Brachypodium distachyon without prior knowledge about the traits under selection. We took advantage of whole-genome sequencing data produced for 44 natural accessions of B. distachyon and used complementary genome-wide selection scans (GWSS) methods to detect genomic regions under balancing and positive selection. We show that selection is shaping genetic diversity at multiple temporal and spatial scales in this species, and affects different genomic regions across the two populations. Gene ontology annotation of candidate genes reveals that pathogens may constitute important factors of positive and balancing selection in B. distachyon. We eventually cross-validated our results with quantitative trait locus data available for leaf-rust resistance in this species and demonstrate that, when paired with classical trait mapping, GWSS can help pinpointing candidate genes for further molecular validation. Thanks to a near base-perfect reference genome and the large collection of freely available natural accessions collected across its natural range, B. distachyon appears as a prime system for studies in ecology, population genomics and evolutionary biology.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Pathogens As a Potential Driving Force Of Population Evolutionmentioning

confidence: 99%

See 1 more Smart Citation

Genome‐wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

et al. 2018

View full text Add to dashboard Cite

show abstract

“…The plant immune system machinery is complex and is composed of two tiers of extracellular and intracellular receptors (Krattinger and Keller 2016a; Krattinger and Keller 2016b) that efficiently detect the presence of pathogens (for review Greeff et al , 2012; Couto & Zipfel, 2016; Eckardt, 2017). In this study, we found a significant enrichment of signals of selection at genes involved in this first level of defense in the eastern population.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide scans of selection highlight the impact sof biotic and abiotic constraints in natural populations of the model grassBrachypodium distachyon

Bourgeois

Stritt

Walser

et al. 2018

Preprint

View full text Add to dashboard Cite

SummaryGrasses are essential plants for ecosystem functioning. Quantifying the selective pressures that act on natural variation in grass species is therefore essential regarding biodiversity maintenance. In this study, we investigate the selection pressures that act on two distinct populations of the grass model Brachypodium distachyon without prior knowledge about the traits under selection. We took advantage of whole-genome sequencing data produced for 44 natural accessions of B. distachyon and used complementary genome-wide scans of selection (GWSS) methods to detect genomic regions under balancing and positive selection. We show that selection is shaping genetic diversity at multiple temporal and spatial scales in this species and affects different genomic regions across the two populations. Gene Ontology annotation of candidate genes reveals that pathogens may constitute important factors of positive and balancing selection in Brachypodium distachyon. We eventually cross-validated our results with QTL data available for leaf-rust resistance in this species and demonstrate that, when paired with classical trait mapping, GWSS can help pinpointing candidate genes for further molecular validation. Thanks to a near-base perfect reference genome and the large collection of freely available natural accessions collected across its natural range, B. distachyon appears as a prime system for studies in ecology, population genomics and evolutionary biology.

show abstract

“…Opportunistic microbes can slow down growth or kill a plant, while beneficial ones can prime the plant immune system [1] , directly antagonize pathogens [2] , or indirectly inhibit pathogens by contributing to a suppressive environment [3] . Microbes may adjust plant hormone levels [4] and participate in nutrient acquisition [5,6] , among other processes [7] . Research in this area has revealed that most of the organisms present on and in healthy plant leaves are typically bacteria [8] .…”

Section: Introductionmentioning

confidence: 99%

Combining whole genome shotgun sequencing and rDNA amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves

Regalado¹,

Lundberg²,

Deusch³

et al. 2019

Preprint

View full text Add to dashboard Cite

Microorganisms from all domains of life establish associations with plants. Although some harm the plant, others antagonize pathogens or prime the plant immune system, acquire nutrients, tune plant hormone levels, or perform additional services. Most culture-independent plant microbiome research has focused on amplicon sequencing of 16S rDNA and/or the internal transcribed spacer (ITS) of rDNA loci, but the decreasing cost of high-throughput sequencing has made shotgun metagenome sequencing increasingly accessible. Here, we describe shotgun sequencing of 275 wild Arabidopsis thaliana leaf microbiomes from southwest Germany, with additional bacterial 16S rDNA and eukaryotic ITS1 amplicon data from 176 of these samples.The shotgun data were dominated by bacterial sequences, with eukaryotes contributing only a minority of reads. For shotgun and amplicon data, microbial membership showed weak associations with both site of origin and plant genotype, both of which were highly confounded in this dataset. There was large variation among microbiomes, with one extreme comprising samples of low complexity and a high load of microorganisms typical of infected plants, and the other extreme being samples of high complexity and a low microbial load. We use the 1 Regalado et al.Combining sequencing methods in plant metagenomics metagenome data, which captures the ratio of bacterial to plant DNA in leaves of wild plants, to scale the 16S rDNA amplicon data such that they reflect absolute bacterial abundance. We show that this cost-effective hybrid strategy overcomes compositionality problems in amplicon data and leads to fundamentally different conclusions about microbiome community assembly.

show abstract

The Plant Cell Reviews Plant Immunity: Receptor-Like Kinases, ROS-RLK Crosstalk, Quantitative Resistance, and the Growth/Defense Trade-Off

Cited by 27 publications

References 4 publications

Genome‐wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

Genome‐wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

Genome-wide scans of selection highlight the impact sof biotic and abiotic constraints in natural populations of the model grassBrachypodium distachyon

Combining whole genome shotgun sequencing and rDNA amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves

Contact Info

Product

Resources

About