title: Patterns of Polymorphism at the Self-Incompatibility Locus in 1,083 Arabidopsis thaliana Genomes.
abstract: Although the transition to selfing in the model plant Arabidopsis thaliana involved the loss of the self-incompatibility (SI) system, it clearly did not occur due to the fixation of a single inactivating mutation at the locus determining the specificities of SI (the S-locus). At least three groups of divergent haplotypes (haplogroups), corresponding to ancient functional S-alleles, have been maintained at this locus, and extensive functional studies have shown that all three carry distinct inactivating mutations. However, the historical process of loss of SI is not well understood, in particular its relation with the last glaciation. Here, we took advantage of recently published genomic resequencing data in 1,083 Arabidopsis thaliana accessions that we combined with BAC sequencing to obtain polymorphism information for the whole S-locus region at a species-wide scale. The accessions differed by several major rearrangements including large deletions and interhaplogroup recombinations, forming a set of haplogroups that are widely distributed throughout the native range and largely overlap geographically. "Relict" A. thaliana accessions that directly derive from glacial refugia are polymorphic at the S-locus, suggesting that the three haplogroups were already present when glacial refugia from the last Ice Age became isolated. Interhaplogroup recombinant haplotypes were highly frequent, and detailed analysis of recombination breakpoints suggested multiple independent origins. These findings suggest that the complete loss of SI in A. thaliana involved independent self-compatible mutants that arose prior to the last Ice Age, and experienced further rearrangements during postglacial colonization.
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.|Department of Biology, Chiba University, Inage-ku, Chiba, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Tsuchimatsu
authors.affiliation: Université de Lille CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France.
authors.forename: Pauline M
authors.initials: PM
authors.lastname: Goubet
authors.affiliation: Université de Lille CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Gallina
authors.affiliation: Université de Lille CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France.
authors.forename: Anne-Catherine
authors.initials: AC
authors.lastname: Holl
authors.affiliation: Reproduction et Développement des Plantes, Univ. Lyon, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Claude Bernard Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Fobis-Loisy
authors.affiliation: Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Bergès
authors.affiliation: Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France.
authors.forename: William
authors.initials: W
authors.lastname: Marande
authors.affiliation: Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France.
authors.forename: Elisa
authors.initials: E
authors.lastname: Prat
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
authors.forename: Dazhe
authors.initials: D
authors.lastname: Meng
authors.affiliation: Department of Biochemistry and Molecular Biology & Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
authors.forename: Quan
authors.initials: Q
authors.lastname: Long
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
authors.forename: Alexander
authors.initials: A
authors.lastname: Platzer
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
authors.affiliation: Université de Lille CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Vekemans
authors.affiliation: Université de Lille CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Castric
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant / Q000235:genetics; D006239:Haplotypes / Q000235:genetics; D009154:Mutation; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D011110:Polymorphism, Genetic / Q000235:genetics; D057945:Self-Fertilization / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D010940:Plant Proteins
keywords: 1001 genomes project; Arabidopsis; evolution of selfing; evolutionary transition; self-incompatibility