Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes

Meiotic crossover frequency varies extensively along chromosomes and is typically concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to occur at immunity genes, where variation may be beneficial. A major component of plant immunity is recognition of pathogen Avirulence (Avr) effectors by resistance (R) genes that encode NBS-LRR domain proteins. Therefore, we sought to test whether NBS-LRR genes would overlap with meiotic crossover hotspots using experimental genetics in Arabidopsis thaliana. NBS-LRR genes tend to physically cluster in plant genomes; for example, in Arabidopsis most are located in large clusters on the south arms of chromosomes 1 and 5. We experimentally mapped 1,439 crossovers within these clusters and observed NBS-LRR gene associated hotspots, which were also detected as historical hotspots via analysis of linkage disequilibrium. However, we also observed NBS-LRR gene coldspots, which in some cases correlate with structural heterozygosity. To study recombination at the fine-scale we used high-throughput sequencing to analyze ~1,000 crossovers within the RESISTANCE TO ALBUGO CANDIDA1 (RAC1) R gene hotspot. This revealed elevated intragenic crossovers, overlapping nucleosome-occupied exons that encode the TIR, NBS and LRR domains. The highest RAC1 recombination frequency was promoter-proximal and overlapped CTT-repeat DNA sequence motifs, which have previously been associated with plant crossover hotspots. Additionally, we show a significant influence of natural genetic variation on NBS-LRR cluster recombination rates, using crosses between Arabidopsis ecotypes. In conclusion, we show that a subset of NBS-LRR genes are strong hotspots, whereas others are coldspots. This reveals a complex recombination landscape in Arabidopsis NBS-LRR genes, which we propose results from varying coevolutionary pressures exerted by host-pathogen relationships, and is influenced by structural heterozygosity.

[1]  S. Raffaele,et al.  The two-speed genomes of filamentous pathogens: waltz with plants. , 2015, Current opinion in genetics & development.

[2]  Thomas J. Hardcastle,et al.  DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis , 2015, Genes & development.

[3]  N. Barkai,et al.  DNA Crossover Motifs Associated with Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis[OPEN] , 2015, Plant Cell.

[4]  I. Henderson,et al.  Meiotic recombination hotspots - a comparative view. , 2015, The Plant journal : for cell and molecular biology.

[5]  H. Yoshioka,et al.  A Receptor Pair with an Integrated Decoy Converts Pathogen Disabling of Transcription Factors to Immunity , 2015, Cell.

[6]  Jonathan D. G. Jones,et al.  A Plant Immune Receptor Detects Pathogen Effectors that Target WRKY Transcription Factors , 2015, Cell.

[7]  M. Grelon,et al.  The molecular biology of meiosis in plants. , 2015, Annual review of plant biology.

[8]  Krystyna A. Kelly,et al.  Juxtaposition of heterozygous and homozygous regions causes reciprocal crossover remodelling via interference during Arabidopsis meiosis , 2015, eLife.

[9]  Jonathan D. G. Jones,et al.  Two linked pairs of Arabidopsis TNL resistance genes independently confer recognition of bacterial effector AvrRps4 , 2015, Nature Communications.

[10]  A. Betancourt,et al.  Crossovers are associated with mutation and biased gene conversion at recombination hotspots , 2015, Proceedings of the National Academy of Sciences.

[11]  B. Staskawicz,et al.  Recognition and Activation Domains Contribute to Allele-Specific Responses of an Arabidopsis NLR Receptor to an Oomycete Effector Protein , 2015, PLoS pathogens.

[12]  D. Weigel,et al.  Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping , 2015, G3: Genes, Genomes, Genetics.

[13]  G. Rätsch,et al.  Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis , 2014, Cell.

[14]  J. Landolin,et al.  Assembling large genomes with single-molecule sequencing and locality-sensitive hashing , 2014, Nature Biotechnology.

[15]  Liping Gao,et al.  The long-term maintenance of a resistance polymorphism through diffuse interactions , 2014, Nature.

[16]  C. L. Baker,et al.  PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration , 2014, Genome research.

[17]  Jonathan D. G. Jones,et al.  Structural Basis for Assembly and Function of a Heterodimeric Plant Immune Receptor , 2014, Science.

[18]  Jonathan D. G. Jones,et al.  A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants , 2014, bioRxiv.

[19]  D. Baulcombe,et al.  Stepwise artificial evolution of a plant disease resistance gene , 2013, Proceedings of the National Academy of Sciences.

[20]  S. Wessler,et al.  Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing , 2013, Proceedings of the National Academy of Sciences.

[21]  D. Weigel,et al.  The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana , 2013, eLife.

[22]  I. Henderson,et al.  Contrasted Patterns of Crossover and Non-crossover at Arabidopsis thaliana Meiotic Recombination Hotspots , 2013, PLoS genetics.

[23]  Krystyna A. Kelly,et al.  High-throughput analysis of meiotic crossover frequency and interference via flow cytometry of fluorescent pollen in Arabidopsis thaliana , 2013, Nature Protocols.

[24]  Mark C. Field,et al.  Antigenic variation in African trypanosomes: the importance of chromosomal and nuclear context in VSG expression control , 2013, Cellular microbiology.

[25]  O. Martin,et al.  Intraspecific variation of recombination rate in maize , 2013, Genome Biology.

[26]  J. Knight,et al.  Major histocompatibility complex genomics and human disease. , 2013, Annual review of genomics and human genetics.

[27]  I. Hellmann,et al.  Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden , 2013, Nature Genetics.

[28]  B. Kobe,et al.  Intramolecular Interaction Influences Binding of the Flax L5 and L6 Resistance Proteins to their AvrL567 Ligands , 2012, PLoS pathogens.

[29]  S. Wright,et al.  Signatures of balancing selection are maintained at disease resistance loci following mating system evolution and a population bottleneck in the genus Capsella , 2012, BMC Evolutionary Biology.

[30]  Krystyna A. Kelly,et al.  Epigenetic Remodeling of Meiotic Crossover Frequency in Arabidopsis thaliana DNA Methyltransferase Mutants , 2012, PLoS genetics.

[31]  S. Raffaele,et al.  Genome evolution in filamentous plant pathogens: why bigger can be better , 2012, Nature Reviews Microbiology.

[32]  N. Young,et al.  Fine-Scale Population Recombination Rates, Hotspots, and Correlates of Recombination in the Medicago truncatula Genome , 2012, Genome biology and evolution.

[33]  Kevin Brick,et al.  Genetic recombination is directed away from functional genomic elements in mice , 2012, Nature.

[34]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[35]  A. Auton,et al.  Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel , 2011, Nature Genetics.

[36]  N. Warthmann,et al.  The recombination landscape in Arabidopsis thaliana F2 populations , 2011, Heredity.

[37]  O. Martin,et al.  Genome-Wide Crossover Distribution in Arabidopsis thaliana Meiosis Reveals Sex-Specific Patterns along Chromosomes , 2011, PLoS genetics.

[38]  Karsten M. Borgwardt,et al.  Whole-genome sequencing of multiple Arabidopsis thaliana populations , 2011, Nature Genetics.

[39]  C. Grey,et al.  Mouse PRDM9 DNA-Binding Specificity Determines Sites of Histone H3 Lysine 4 Trimethylation for Initiation of Meiotic Recombination , 2011, PLoS biology.

[40]  B. Dujon,et al.  Genome-Wide Analysis of Heteroduplex DNA in Mismatch Repair–Deficient Yeast Cells Reveals Novel Properties of Meiotic Recombination Pathways , 2011, PLoS genetics.

[41]  D. Weigel,et al.  Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes in Arabidopsis1[W][OA] , 2011, Plant Physiology.

[42]  Oscar Flores,et al.  nucleR: a package for non-parametric nucleosome positioning , 2011, Bioinform..

[43]  Richard M. Clark,et al.  The Arabidopsis lyrata genome sequence and the basis of rapid genome size change , 2011, Nature Genetics.

[44]  M. Pellegrini,et al.  Relationship between nucleosome positioning and DNA methylation , 2010, Nature.

[45]  J. Bergelson,et al.  Impact of Initial Pathogen Density on Resistance and Tolerance in a Polymorphic Disease Resistance Gene System in Arabidopsis thaliana , 2010, Genetics.

[46]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[47]  N. Warthmann,et al.  Local-Scale Patterns of Genetic Variability, Outcrossing, and Spatial Structure in Natural Stands of Arabidopsis thaliana , 2010, PLoS genetics.

[48]  K. Paigen,et al.  Prdm9 Controls Activation of Mammalian Recombination Hotspots , 2010, Science.

[49]  P. Donnelly,et al.  Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination , 2010, Science.

[50]  G. Coop,et al.  PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice , 2010, Science.

[51]  Detlef Weigel,et al.  The Scale of Population Structure in Arabidopsis thaliana , 2010, PLoS genetics.

[52]  B. Charlesworth,et al.  Elements of Evolutionary Genetics , 2010 .

[53]  Y. Narusaka,et al.  RRS1 and RPS4 provide a dual Resistance-gene system against fungal and bacterial pathogens. , 2009, The Plant journal : for cell and molecular biology.

[54]  J. Bergelson,et al.  Quantitative fitness effects of infection in a gene-for-gene system. , 2009, The New phytologist.

[55]  R. Visser,et al.  Rin4 Causes Hybrid Necrosis and Race-Specific Resistance in an Interspecific Lettuce Hybrid[W] , 2009, The Plant Cell Online.

[56]  Jonathan D. G. Jones,et al.  Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans , 2009, Nature.

[57]  C. Zipfel.  Early molecular events in PAMP-triggered immunity. , 2009, Current opinion in plant biology.

[58]  Soon Il Kwon,et al.  Resistance to the Pseudomonas syringae Effector HopA1 Is Governed by the TIR-NBS-LRR Protein RPS6 and Is Enhanced by Mutations in SRFR11[W][OA] , 2009, Plant Physiology.

[59]  S. Kamoun,et al.  From Guard to Decoy: A New Model for Perception of Plant Pathogen Effectors , 2008, The Plant Cell Online.

[60]  Jian-Min Zhou,et al.  Plant pathogenic bacterial type III effectors subdue host responses. , 2008, Current opinion in microbiology.

[61]  C. Zipfel,et al.  Plant Immunity: AvrPto Targets the Frontline , 2008, Current Biology.

[62]  R. Michelmore,et al.  Frequent sequence exchanges between homologs of RPP8 in Arabidopsis are not necessarily associated with genomic proximity. , 2008, The Plant journal : for cell and molecular biology.

[63]  D. K. Bishop,et al.  Synthesis-Dependent Strand Annealing in Meiosis , 2007, PLoS biology.

[64]  E. Buckler,et al.  Using Crossover Breakpoints in Recombinant Inbred Lines to Identify Quantitative Trait Loci Controlling the Global Recombination Frequency , 2007, Genetics.

[65]  Zhaohui S. Qin,et al.  A second generation human haplotype map of over 3.1 million SNPs , 2007, Nature.

[66]  N. Warthmann,et al.  Autoimmune Response as a Mechanism for a Dobzhansky-Muller-Type Incompatibility Syndrome in Plants , 2007, PLoS biology.

[67]  Detlef Weigel,et al.  Recombination and linkage disequilibrium in Arabidopsis thaliana , 2007, Nature Genetics.

[68]  A. Auton,et al.  Recombination rate estimation in the presence of hotspots. , 2007, Genome research.

[69]  Joseph D. Smith,et al.  Antigenic Variation in Plasmodium falciparum: Gene Organization and Regulation of the var Multigene Family , 2007, Eukaryotic Cell.

[70]  James K. M. Brown,et al.  Stability of genetic polymorphism in host–parasite interactions , 2007, Proceedings of the Royal Society B: Biological Sciences.

[71]  Luke E. Berchowitz,et al.  Pollen tetrad-based visual assay for meiotic recombination in Arabidopsis , 2007, Proceedings of the National Academy of Sciences.

[72]  Jonathan D. G. Jones,et al.  The plant immune system , 2006, Nature.

[73]  Sarah Calvo,et al.  Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis , 2006, Nature.

[74]  M. Kreitman,et al.  A Genome-Wide Survey of R Gene Polymorphisms in Arabidopsis[W] , 2006, The Plant Cell Online.

[75]  B. Kobe,et al.  Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[76]  S. Chisholm,et al.  Host-Microbe Interactions: Shaping the Evolution of the Plant Immune Response , 2022 .

[77]  Patrick S Schnable,et al.  Cis-effects on Meiotic Recombination Across Distinct a1-sh2 Intervals in a Common Zea Genetic Background Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY656756, AY656757, AY656758 and AY662984, AY662985, AY662986, AY662987. , 2005, Genetics.

[78]  M. G. Kim,et al.  Two Pseudomonas syringae Type III Effectors Inhibit RIN4-Regulated Basal Defense in Arabidopsis , 2005, Cell.

[79]  J. Beynon,et al.  Host-Parasite Coevolutionary Conflict Between Arabidopsis and Downy Mildew , 2004, Science.

[80]  Blake C Meyers,et al.  Multiple Genetic Processes Result in Heterogeneous Rates of Evolution within the Major Cluster Disease Resistance Genes in Lettucew⃞ , 2004, The Plant Cell Online.

[81]  J. Beynon,et al.  The arabidopsis TIR-NB-LRR gene RAC1 confers resistance to Albugo candida (white rust) and is dependent on EDS1 but not PAD4. , 2004, Molecular plant-microbe interactions : MPMI.

[82]  S. Keeney,et al.  Where the crossovers are: recombination distributions in mammals , 2004, Nature Reviews Genetics.

[83]  Jonathan D. G. Jones,et al.  Genetic Variation at the Tomato Cf-4/Cf-9 Locus Induced by EMS Mutagenesis and Intralocus Recombination , 2004, Genetics.

[84]  R. Michelmore,et al.  The Maintenance of Extreme Amino Acid Diversity at the Disease Resistance Gene, RPP13, in Arabidopsis thaliana , 2004, Genetics.

[85]  I. Somssich,et al.  Physical interaction between RRS1-R, a protein conferring resistance to bacterial wilt, and PopP2, a type III effector targeted to the plant nucleus , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[86]  M. Kreitman,et al.  Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana , 2003, Nature.

[87]  Blake C. Meyers,et al.  Genome-Wide Analysis of NBS-LRR–Encoding Genes in Arabidopsis Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.009308. , 2003, The Plant Cell Online.

[88]  S. Goff,et al.  A High-Throughput Arabidopsis Reverse Genetics System Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.004630. , 2002, The Plant Cell Online.

[89]  D. Baulcombe,et al.  Interaction between domains of a plant NBS–LRR protein in disease resistance‐related cell death , 2002, The EMBO journal.

[90]  Blake C Meyers,et al.  Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. , 2002, Genome research.

[91]  Eli Stahl,et al.  Signature of balancing selection in Arabidopsis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[92]  A. Melchinger,et al.  Influence of genetic background and heterozygosity on meiotic recombination in Arabidopsis thaliana. , 2001, Genome.

[93]  A. Jeffreys,et al.  Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex , 2001, Nature Genetics.

[94]  P. Dodds,et al.  Contrasting modes of evolution acting on the complex N locus for rust resistance in flax. , 2001, The Plant journal : for cell and molecular biology.

[95]  E. Stahl,et al.  Evolutionary Dynamics of Plant R-Genes , 2001, Science.

[96]  T. Pryor,et al.  Recombination between paralogues at the Rp1 rust resistance locus in maize. , 2001, Genetics.

[97]  J. Beynon,et al.  White rust (Albugo candida) resistance loci on three Arabidopsis chromosomes are closely linked to downy mildew (Peronospora parasitica) resistance loci. , 2001, Molecular plant pathology.

[98]  R. Michelmore,et al.  Recombination and spontaneous mutation at the major cluster of resistance genes in lettuce (Lactuca sativa). , 2001, Genetics.

[99]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[100]  J. Luck,et al.  Regions outside of the Leucine-Rich Repeats of Flax Rust Resistance Proteins Play a Role in Specificity Determination , 2000, Plant Cell.

[101]  M. Marra,et al.  Genetic definition and sequence analysis of Arabidopsis centromeres. , 1999, Science.

[102]  V. Sundaresan,et al.  Analysis of Flanking Sequences from Dissociation Insertion Lines: A Database for Reverse Genetics in Arabidopsis , 1999, Plant Cell.

[103]  E. A. van der Biezen,et al.  Pronounced Intraspecific Haplotype Divergence at the RPP5 Complex Disease Resistance Locus of Arabidopsis , 1999, Plant Cell.

[104]  E. Stahl,et al.  Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis , 1999, Nature.

[105]  Jonathan D. G. Jones,et al.  Recombination between diverged clusters of the tomato Cf-9 plant disease resistance gene family. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[106]  S. Goff,et al.  Intragenic Recombination and Diversifying Selection Contribute to the Evolution of Downy Mildew Resistance at the RPP8 Locus of Arabidopsis , 1998, Plant Cell.

[107]  R. Michelmore,et al.  The Major Resistance Gene Cluster in Lettuce Is Highly Duplicated and Spans Several Megabases , 1998, Plant Cell.

[108]  Jonathan D. G. Jones,et al.  Three Genes of the Arabidopsis RPP1 Complex Resistance Locus Recognize Distinct Peronospora parasitica Avirulence Determinants , 1998, Plant Cell.

[109]  B C Meyers,et al.  Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. , 1998, Genome research.

[110]  J Chory,et al.  dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. , 1998, The Plant journal : for cell and molecular biology.

[111]  D. Bouchez,et al.  Disease resistance gene homologs correlate with disease resistance loci of Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.

[112]  S. Hulbert,et al.  A novel rust resistance gene in maize showing overdominance , 1998 .

[113]  Jonathan D. G. Jones,et al.  Novel Disease Resistance Specificities Result from Sequence Exchange between Tandemly Repeated Genes at the Cf-4/9 Locus of Tomato , 1997, Cell.

[114]  G. Wang,et al.  Evolution of the rice Xa21 disease resistance gene family. , 1997, The Plant cell.

[115]  J. Messing,et al.  Region-specific cis- and trans-acting factors contribute to genetic variability in meiotic recombination in maize. , 1997, Genetics.

[116]  E. A. van der Biezen,et al.  The Arabidopsis downy mildew resistance gene RPP5 shares similarity to the toll and interleukin-1 receptors with N and L6. , 1997, The Plant cell.

[117]  E. Finnegan,et al.  Inactivation of the flax rust resistance gene M associated with loss of a repeated unit within the leucine-rich repeat coding region. , 1997, The Plant cell.

[118]  J. Bennetzen,et al.  New rust resistance specificities associated with recombination in the Rp1 complex in maize. , 1995, Genetics.

[119]  E. Finnegan,et al.  Contrasting complexity of two rust resistance loci in flax. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[120]  J. Howard.  Disease and evolution , 1991, Nature.

[121]  J. Bennetzen,et al.  Recombination at the Rp1 locus of maize , 1991, Molecular and General Genetics MGG.

[122]  J. Haber,et al.  Meiotic recombination in yeast: alteration by multiple heterozygosities. , 1987, Science.

[123]  H. Dooner,et al.  Genetic Fine Structure of the BRONZE Locus in Maize. , 1986, Genetics.

[124]  Jack W. Szostak,et al.  The double-strand-break repair model for recombination , 1983, Cell.

[125]  B. de Massy.  Initiation of meiotic recombination: how and where? Conservation and specificities among eukaryotes. , 2013, Annual review of genetics.

[126]  C. Oliver,et al.  Looking for natural variation in chiasma frequency in Arabidopsis thaliana. , 2012, Journal of experimental botany.

[127]  A. Auton,et al.  Estimating recombination rates from genetic variation in humans. , 2012, Methods in molecular biology.

[128]  J. Drouaud,et al.  Characterization of meiotic crossovers in pollen from Arabidopsis thaliana. , 2011, Methods in molecular biology.

[129]  P. Dodds,et al.  Relationships between rust resistance genes at the M locus in flax. , 2010, Molecular plant pathology.

[130]  A. Jeffreys,et al.  Analysis of meiotic recombination products from human sperm. , 2009, Methods in molecular biology.

[131]  Luke E. Berchowitz,et al.  Fluorescent Arabidopsis tetrads: a visual assay for quickly developing large crossover and crossover interference data sets , 2007, Nature Protocols.

[132]  A. Villeneuve,et al.  Whence Meiosis? , 2001, Cell.

[133]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[134]  A. Goldman,et al.  Meiotic recombination hotspots. , 1995, Annual review of genetics.

[135]  J. Bennetzen,et al.  Unequal exchange and meiotic instability of disease-resistance genes in the Rp1 region of maize. , 1993, Genetics.

[136]  Thomas J. Hardcastle,et al.  Nature Genetics Advance Online Publication Arabidopsis Meiotic Crossover Hot Spots Overlap with H2a.z Nucleosomes at Gene Promoters , 2022 .