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Research article - Peer-reviewed, 2020

Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)

Apuli, Rami-Petteri; Bernhardsson, Carolina; Schiffthaler, Bastian; Robinson, Kathryn M.; Jansson, Stefan; Street, Nathaniel R.; Ingvarsson, Paer K.


The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.


linkage disequilibrium; linkage map; linked selection; methylation; nucleotide diversity; recombination

Published in

2020, volume: 10, number: 1, pages: 299-309

Authors' information

Swedish University of Agricultural Sciences, Department of Plant Biology
Bernhardsson, Carolina
Swedish University of Agricultural Sciences, Department of Plant Biology
Bernhardsson, Carolina
Umeå University
Schiffthaler, Bastian
Umea University
Robinson, Kathryn M.
Umea University
Jansson, Stefan
Umea University
Street, Nathaniel R.
Umea University
Swedish University of Agricultural Sciences, Department of Plant Biology

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