title: Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes.
abstract: 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.
authors.affiliation: Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Kyuha
authors.initials: K
authors.lastname: Choi
authors.affiliation: Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Carsten
authors.initials: C
authors.lastname: Reinhard
authors.affiliation: Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Heïdi
authors.initials: H
authors.lastname: Serra
authors.affiliation: Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom.|Department of Biotechnology, Adam Mickiewicz University, Poznan, Poland.
authors.forename: Piotr A
authors.initials: PA
authors.lastname: Ziolkowski
authors.affiliation: Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom.|Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.
authors.forename: Charles J
authors.identifier: 0000-0001-5730-6279
authors.initials: CJ
authors.lastname: Underwood
authors.affiliation: Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Xiaohui
authors.identifier: 0000-0001-9922-2815
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Thomas J
authors.identifier: 0000-0002-9328-5011
authors.initials: TJ
authors.lastname: Hardcastle
authors.affiliation: Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Nataliya E
authors.initials: NE
authors.lastname: Yelina
authors.affiliation: Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Catherine
authors.identifier: 0000-0001-8862-1386
authors.initials: C
authors.lastname: Griffin
authors.affiliation: Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Matthew
authors.initials: M
authors.lastname: Jackson
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Mézard
authors.affiliation: The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Gil
authors.initials: G
authors.lastname: McVean
authors.affiliation: Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.|Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America.
authors.forename: Gregory P
authors.identifier: 0000-0002-7962-3862
authors.initials: GP
authors.lastname: Copenhaver
authors.affiliation: Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Ian R
authors.initials: IR
authors.lastname: Henderson
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D003433:Crosses, Genetic; D060467:Disease Resistance / Q000235:genetics*; D017343:Genes, Plant; D014644:Genetic Variation; D006579:Heterozygote; D015810:Linkage Disequilibrium; D008540:Meiosis; D005810:Multigene Family; D009693:Nucleic Acid Hybridization; D010935:Plant Diseases / Q000235:genetics; D011058:Pollen / Q000378:metabolism; D011995:Recombination, Genetic
chemical_list: D029681:Arabidopsis Proteins; C489522:RAC1 protein, Arabidopsis