Fuentes RR, de Ridder D, van Dijk ADJ, Peters SA.

Mol Biol Evol. 2022 Jan 7;39(1):msab287. doi: 10.1093/molbev/msab287.

Abstract

Meiotic recombination is a biological process of key importance in breeding, to generate genetic diversity and develop novel or agronomically relevant haplotypes. In crop tomato, recombination is curtailed as manifested by linkage disequilibrium decay over a longer distance and reduced diversity compared with wild relatives. Here, we compared domesticated and wild populations of tomato and found an overall conserved recombination landscape, with local changes in effective recombination rate in specific genomic regions. We also studied the dynamics of recombination hotspots resulting from domestication and found that loss of such hotspots is associated with selective sweeps, most notably in the pericentromeric heterochromatin. We detected footprints of genetic changes and structural variants, among them associated with transposable elements, linked with hotspot divergence during domestication, likely causing fine-scale alterations to recombination patterns and resulting in linkage drag.

See https://pubmed.ncbi.nlm.nih.gov/34597400/ 

Fig. 1.

Recombination landscape and transformation from wild to domesticated tomato. (A) Recombination landscape in chromosome 1 of wild (SP), early-domesticated (SLC), and vintage (SLL) tomato. This ρ/kb landscape is intended to show overall landscape only; r_e is used to compare populations in other analyses. Gray vertical lines mark heterochromatin boundaries. (B) Effective recombination rate (r_e) in 1-Mb windows of both wild and domesticated tomato. (C) Change in effective recombination rate in 50-kb regions during domestication (SLC r_e–SP r_e) and improvement (SLL r_e–SLC r_e). (D) Resulting change in r_e for chromosome 1 after the domestication process or between the wild and vintage population. Gray vertical lines mark the heterochromatin boundaries and the colors correspond to the colors in (C).