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      Identification of a Differentially Expressed TIR-NBS-LRR Gene in a Major QTL Associated to Leaf Rust Resistance in Salix

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          Abstract

          An earlier identified major quantitative trait locus for resistance towards the willow leaf rust fungus Melampsora larici-epitea in a Salix viminalis x ( S. viminalis × S. schwerinii) population was used to identify potential resistance genes to the rust pathogen. Screening a genomic bacterial artificial chromosome library with markers from the peak position of the QTL region revealed one gene with TIR-NBS-LRR (Toll Interleukin1 Receptor-Nucleotide Binding Site-Leucine-Rich Repeat) domain structure indicative of a resistance gene. The resistance gene analog was denoted RGA1 and further analysis revealed a number of non-synonymous single nucleotide polymorphisms in the LRR domain between the resistant and susceptible Salix genotypes. Gene expression levels under controlled conditions showed a significantly lower constitutive expression of RGA1 in the susceptible genotype. In addition, the susceptible genotype showed a significantly reduced expression level of the RGA1 gene at 24 hours post inoculation with M. larici-epitea. This indicates that the pathogen may actively suppress RGA1 gene expression allowing a compatible plant-pathogen interaction and causing infection.

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          Pathogen population genetics, evolutionary potential, and durable resistance.

          We hypothesize that the evolutionary potential of a pathogen population is reflected in its population genetic structure. Pathogen populations with a high evolutionary potential are more likely to overcome genetic resistance than pathogen populations with a low evolutionary potential. We propose a flexible framework to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure. According to this framework, pathogens that pose the greatest risk of breaking down resistance genes have a mixed reproduction system, a high potential for genotype flow, large effective population sizes, and high mutation rates. The lowest risk pathogens are those with strict asexual reproduction, low potential for gene flow, small effective population sizes, and low mutation rates. We present examples of high-risk and low-risk pathogens. We propose general guidelines for a rational approach to breed durable resistance according to the evolutionary potential of the pathogen.
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            Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process.

            Classical genetic and molecular data show that genes determining disease resistance in plants are frequently clustered in the genome. Genes for resistance (R genes) to diverse pathogens cloned from several species encode proteins that have motifs in common. These motifs indicate that R genes are part of signal-transduction systems. Most of these R genes encode a leucine-rich repeat (LRR) region. Sequences encoding putative solvent-exposed residues in this region are hypervariable and have elevated ratios of nonsynonymous to synonymous substitutions; this suggests that they have evolved to detect variation in pathogen-derived ligands. Generation of new resistance specificities previously had been thought to involve frequent unequal crossing-over and gene conversions. However, comparisons between resistance haplotypes reveal that orthologs are more similar than paralogs implying a low rate of sequence homogenization from unequal crossing-over and gene conversion. We propose a new model adapted and expanded from one proposed for the evolution of vertebrate major histocompatibility complex and immunoglobulin gene families. Our model emphasizes divergent selection acting on arrays of solvent-exposed residues in the LRR resulting in evolution of individual R genes within a haplotype. Intergenic unequal crossing-over and gene conversions are important but are not the primary mechanisms generating variation.
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              Plant Nucleotide Binding Site–Leucine-Rich Repeat (NBS-LRR) Genes: Active Guardians in Host Defense Responses

              The most represented group of resistance genes are those of the nucleotide binding site–leucine-rich repeat (NBS-LRR) class. These genes are very numerous in the plant genome, and they often occur in clusters at specific loci following gene duplication and amplification events. To date, hundreds of resistance genes and relatively few quantitative trait loci for plant resistance to pathogens have been mapped in different species, with some also cloned. When these NBS-LRR genes have been physically or genetically mapped, many cases have shown co-localization between resistance loci and NBS-LRR genes. This has allowed the identification of candidate genes for resistance, and the development of molecular markers linked to R genes. This review is focused on recent genomics studies that have described the abundance, distribution and evolution of NBS-LRR genes in plant genomes. Furthermore, in terms of their expression, NBS-LRR genes are under fine regulation by cis- and trans-acting elements. Recent findings have provided insights into the roles of alternative splicing, the ubiquitin/proteasome system, and miRNAs and secondary siRNAs in the regulation of NBS-LRR gene expression at the post-transcriptional, post-translational and epigenetic levels. The possibility to use this knowledge for genetic improvement of plant resistance to pathogens is discussed.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                21 December 2016
                2016
                : 11
                : 12
                : e0168776
                Affiliations
                [1 ]Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
                [2 ]Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
                New South Wales Department of Primary Industries, AUSTRALIA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: JS BS ACRW.

                • Data curation: BS.

                • Formal analysis: BS TM.

                • Funding acquisition: JS.

                • Investigation: BS TM.

                • Methodology: BS JS TM.

                • Project administration: BS JS.

                • Resources: JS.

                • Validation: TM BS.

                • Visualization: TM BS.

                • Writing – original draft: TM BS.

                • Writing – review & editing: TM BS ACRW JS.

                Author information
                http://orcid.org/0000-0002-6456-6121
                Article
                PONE-D-16-15837
                10.1371/journal.pone.0168776
                5176316
                28002449
                30b8e6d9-eb97-4d9d-91e0-74910cafee48
                © 2016 Martin et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 19 April 2016
                : 6 December 2016
                Page count
                Figures: 6, Tables: 1, Pages: 15
                Funding
                This research was supported by the governmental Swedish Energy Agency (JS) ( http://www.energimyndigheten.se/en/) and The NLfaculty at the Swedish University of Agricultural Sciences (JS) ( http://www.slu.se/en/faculties/nj/). The two funders above had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The SNP Technology Platform, Uppsala, Sweden (JS) ( http://molmed.medsci.uu.se/SNP+SEQ+Technology+Platform/Genotyping/) performed the high-throughput sequencing.
                Categories
                Research Article
                Biology and Life Sciences
                Plant Science
                Plant Anatomy
                Leaves
                Biology and Life Sciences
                Genetics
                Gene Expression
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Library Screening
                Genomic Library Screening
                Research and Analysis Methods
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Library Screening
                Genomic Library Screening
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Library Screening
                Research and Analysis Methods
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Library Screening
                Biology and Life Sciences
                Cell Biology
                Chromosome Biology
                Chromosomes
                Chromosome Pairs
                Chromosome 17
                Biology and life sciences
                Molecular biology
                Molecular biology techniques
                Molecular biology assays and analysis techniques
                Library screening
                BAC library screening
                Research and analysis methods
                Molecular biology techniques
                Molecular biology assays and analysis techniques
                Library screening
                BAC library screening
                Biology and life sciences
                Molecular biology
                Molecular biology techniques
                Cloning
                Vector cloning
                BAC cloning
                Research and analysis methods
                Molecular biology techniques
                Cloning
                Vector cloning
                BAC cloning
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Quantitative Trait Loci
                Custom metadata
                All relevant data are within the paper and its Supporting Information files.

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