Constructing a high-density linkage map to infer the genomic landscape of recombination rate variation in European Aspen(Populus tremula)

Abstract

The rate of meiotic recombination is one of the central factors determining levels of linkage disequilibrium and the efficiency of natural selection, and many organisms show a positive correlation between local rates of recombination and levels of nucleotide diversity indicating that linked selection is an important factor determining genome-wide levels of nucleotide diversity. Several methods for estimating recombination rates from segregating polymorphisms in natural populations have recently been developed. These methods have been extensively used in part because they are relatively simple to implement even in many non-model organisms, but also because they potentially offer higher resolution than traditional map-based methods. However, thorough comparisons of LD and map-based estimates of recombination are not readily available in plants. Here we present a new, highresolution linkage map for Populus tremula and use this to estimate variation in recombination rates across the P. tremula genome. We compare these results to recombination rates estimated based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with 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 identify a number of genomic regions with very high recombination rates that the map-based method fail 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.

Evidence for widespread selection in shaping the genomic landscape during speciation of Populus

“…To specifically test for the impact of positive and balancing selection on the genomic landscape during speciation of aspens, we first performed whole‐genome screening of selection using a cross‐population composite likelihood ratio test (XP‐CLR) that models likelihood of multilocus allele frequency differentiation between two populations. Following the method used in Booker, Ness, and Keightley (2017) and Apuli et al (2020), we first converted recombination rate estimates in units of ρ /bp from Ldhelmet results to centi‐Morgan (cM) in P. tremula . Genetic distance between adjacent SNPs were interpolated according to the centimorgan values calculated from the cumulative ρ at each analyzed SNP position after setting the total genetic map length for each chromosome to that estimated from Apuli et al (2020).…”

“…Following the method used in Booker, Ness, and Keightley (2017) and Apuli et al (2020), we first converted recombination rate estimates in units of ρ /bp from Ldhelmet results to centi‐Morgan (cM) in P. tremula . Genetic distance between adjacent SNPs were interpolated according to the centimorgan values calculated from the cumulative ρ at each analyzed SNP position after setting the total genetic map length for each chromosome to that estimated from Apuli et al (2020). The program XP‐CLR was run on all six comparisons of the three aspen species (for each comparison, using each species once as the objective and once as the reference population).…”

An Improved Chromosome-scale Genome Assembly and Population Genetics resource forPopulus tremula

“…We subsequently created an optical map of the genome in collaboration with BioNano genomics, which we utilized to further scaffold and orient our current assembly. Finally, we used the high-density genetic linkage map from Apuli et al (2019) as input to ALLMAPS (Tang et al, 2015) to place the scaffolds into chromosomes.…”