Samantha McConaughy, Keenan Amundsen, Qijian Song, Vince Pantalone, David Hyte

G3 (Bethesda). 2023 Jun 1;13(6):jkad075. doi: 10.1093/g3journal/jkad075.

Abstract

Recombination allows for the exchange of genetic material between two parents, which plant breeders exploit to make improved cultivars. This recombination is not distributed evenly across the chromosome. Recombination mostly occurs in euchromatic regions of the genome and even then, recombination is focused into clusters of crossovers termed recombination hotspots. Understanding the distribution of these hotspots along with the sequence motifs associated with them may lead to methods that enable breeders to better exploit recombination in breeding. To map recombination hotspots and identify sequence motifs associated with hotspots in soybean [Glycine max (L.) Merr.], two biparental recombinant inbred lines populations were genotyped with the SoySNP50k Illumina Infinium assay. A total of 451 recombination hotspots were identified in the two populations. Despite being half-sib populations, only 18 hotspots were in common between the two populations. While pericentromeric regions did exhibit extreme suppression of recombination, 27% of the detected hotspots were located in the pericentromeric regions of the chromosomes. Two genomic motifs associated with hotspots are similar to human, dog, rice, wheat, drosophila, and arabidopsis. These motifs were a CCN repeat motif and a poly-A motif. Genomic regions spanning other hotspots were significantly enriched with the tourist family of mini-inverted-repeat transposable elements that resides in <0.34% of the soybean genome. The characterization of recombination hotspots in these two large soybean biparental populations demonstrates that hotspots do occur throughout the soybean genome and are enriched for specific motifs, but their locations may not be conserved between different populations.

See https://pubmed.ncbi.nlm.nih.gov/36999557/

Fig. 1.

Genome wide recombination rates in two biparental populations and transposable elements associations. The outer ring represents the average biparental populations by physical distance along chromosomes for Williams 82 x PI479752 and Williams 82 x Essex. a) Directly under the physical distance, ring purple displays the recombination rates in cM/Mbp (y-axis). b) The next circle in orange represents a density plot of retrotransposon (class I). c) The circle in blue represents a density plot of transposable elements (class II). d) Transposable class II mite stowaway element frequencies are in green. e) TE Class type II MITE/Tourist element frequencies are in dark blue. f) The inner circle represents heterochromatic regions in black and euchromatic regions in white.