Data from: Linkage mapping reveals strong chiasma interference in sockeye salmon: implications for interpreting genomic data

Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the re-diploidization process of polyploid-origin genomes since 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 non-model species. Salmonid females generally produce thousands of embryos, providing large families to study meiotic recombination. Further, salmonid genomes are currently re-diploidizing 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 progeny to construct a dense linkage map which includes paralogous loci and location of centromeres. We find a non-random distribution of paralogs that mainly cluster in extended subtelomeric regions on 11 different chromosomes, consistent with ongoing homeologous recombination between 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.