title: Linkage Mapping Reveals Strong Chiasma Interference in Sockeye Salmon: Implications for Interpreting Genomic Data.
abstract: Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the rediploidization process of polyploid-origin genomes because crossovers between pairs of homeologous chromosomes retain duplicated regions. A better understanding of how recombination affects genome evolution is crucial for interpreting genomic data; unfortunately, current knowledge mainly originates from a few model species. Salmonid fishes provide a valuable system for studying the effects of recombination in nonmodel species. Salmonid females generally produce thousands of embryos, providing large families for conducting inheritance studies. Further, salmonid genomes are currently rediploidizing after a whole genome duplication and can serve as models for studying the role of homeologous crossovers on genome evolution. Here, we present a detailed interrogation of recombination patterns in sockeye salmon (Oncorhynchus nerka). First, we use RAD sequencing of haploid and diploid gynogenetic families to construct a dense linkage map that includes paralogous loci and location of centromeres. We find a nonrandom distribution of paralogs that mainly cluster in extended regions distally located on 11 different chromosomes, consistent with ongoing homeologous recombination in these regions. We also estimate the strength of interference across each chromosome; results reveal strong interference and crossovers are mostly limited to one per arm. Interference was further shown to continue across centromeres, but metacentric chromosomes generally had at least one crossover on each arm. We discuss the relevance of these findings for both mapping and population genomic studies.
authors.affiliation: School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195 National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, Silkeborg, Denmark morten.limborg@gmail.com.
authors.forename: Morten T
authors.identifier: http://orcid.org/0000-0002-7718-6531
authors.initials: MT
authors.lastname: Limborg
authors.affiliation: School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195.
authors.forename: Ryan K
authors.initials: RK
authors.lastname: Waples
authors.affiliation: Division of Biological Sciences, University of Montana, Missoula, Montana 59812.
authors.forename: Fred W
authors.initials: FW
authors.lastname: Allendorf
authors.affiliation: School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195.
authors.forename: James E
authors.initials: JE
authors.lastname: Seeb
mesh_terms: D000818:Animals; D002875:Chromosomes / Q000235:genetics*; D008040:Genetic Linkage; D016678:Genome; D011995:Recombination, Genetic; D012474:Salmon / Q000235:genetics*
keywords: genome data; gynogenesis; interference; meiosis; recombination