Comparative recombination rates in the rat, mouse, and human genomes

Abstract

Levels of recombination vary among species, among chromosomes within species, and among regions within chromosomes in mammals. This heterogeneity may affect levels of diversity, efficiency of selection, and genome composition, as well as have practical consequences for the genetic mapping of traits. We compared the genetic maps to the genome sequence assemblies of rat, mouse, and human to estimate local recombination rates across these genomes. Humans have greater overall levels of recombination, as well as greater variance. In rat and mouse, the size of the chromosome and proximity to telomere have less effect on local recombination rate than in human. At the chromosome level, rat and mouse X chromosomes have the lowest recombination rates, whereas human chromosome X does not show the same pattern. In all species, local recombination rate is significantly correlated with several sequence variables, including GC%, CpG density, repetitive elements, and the neutral mutation rate, with some pronounced differences between species. Recombination rate in one species is not strongly correlated with the rate in another, when comparing homologous syntenic blocks of the genome. This comparative approach provides additional insight into the causes and consequences of genomic heterogeneity in recombination.

Figure 1

Plots of genetic position vs. physical position for all markers placed on the telocentric rat chromosome 10 (top), and recombination rate vs. physical position for rat chromosome 10 (bottom) after removing inconsistently placed markers. Similar plots for all chromosomes in all species are available as Supplemental Figures A–I.

Figure 2

Chromosomal recombination rate as a function of chromosome size. The regression slope is no longer significantly different than zero in mouse if the smallest chromosome (chr. 19) is removed. Similarly, in rat the regression is not significant if the three smallest chromosomes are removed. Note that the y-axis of the human graph is scaled differently than for the rodents.