Inferring 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 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.

Keywords: linkage disequilibrium; linkage map; linked selection; methylation; nucleotide diversity; recombination.

Figure 1

Genetic maps and resulting physical map created by Allmaps for Chr1 and Chr5. The left panel shows the marker distribution (in cM) for the genetic maps and the anchored genomic region (in Mbp) for the physical map, while the right panel is showing the Marey maps, i.e., the correspondence between the physical (x-axis) and recombination-based (y-axis) position of markers. The female map is depicted in green and the male map is depicted in orange.

Figure 2

Recombination rates and genomic features calculated in 1 Mbp windows across chromosome 1 and 5 with a step size of 250kbp. A) Recombination rate estimated from the linkage map (cM/Mbp) B) Recombination rate estimated from sequence LD data (cM/Mbp) C) Nucleotide diversity (1/bp) D) Divergence (sites/Mbp) E) Gene density (percentage coding/Mbp) F) Repeat density (percentage repeats/Mbp) G) CpG methylation (percentage/Mbp).

Figure 3

Correlations between recombination rates and genomic features. All correlations are significant (P < 0.01) with the exception of those marked with * (P > 0.01).