Recombination hotspots in soybean [Glycine max (L.) Merr.]

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 bi-parental 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, twenty-seven percent 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 less than 0.34% of the soybean genome. The characterization of recombination hotspots in these two large soybean bi-parental 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.

Effects of demographic history on recombination hotspots in soybean

“…Recombination rate is the average of recombination at a specific hotspot. In biparental soybean populations without selection or demographic effects, the recombination rate between different populations is not significantly different (McConaughy et al., 2023). Demographic effects like genetic bottlenecks and selection have the potential to influence the observed recombination rate.…”

“…In plant species, two common motifs have been identified within recombination hotspots, a poly‐A motif and a CCN repeat motif (Darrier et al., 2017; McConaughy et al., 2023; Shilo et al., 2015). In this study, among the 1381 shared recombination hotspots between the wild populations, landrace, and N.A.…”

“…Hotspots have been previously associated with gene regions and transposable elements (Choi et al., 2013; Darrier et al., 2017; McConaughy et al., 2023; Shilo et al., 2015). In the wild soybean population, landraces, and N.A.…”

“…Although not associated with PRDM9, some motifs linked to recombination hotspots have been associated with zinc finger domains in plants, suggesting a similar mechanism. Additionally, across plant species including potato, rice, tomato, soybean, and wheat, repetitive motifs, and transposable elements have been linked to recombination hotspots (Darrier et al, 2017;Fuentes et al, 2022;Marand et al, 2017Marand et al, , 2019McConaughy et al, 2023;Shilo et al, 2015).…”

Heterochromatin in plant meiosis

“…Pericentromeric COs are associated with premature separation of sister chromatids and lead to sporulation defects in S. cerevisiae [ 114 ]. Genome-wide sequencing has enabled high-resolution maps of meiotic recombination in Arabidopsis [ 95 , 97 , 102 , 109 ], rice [ 115 , 116 ], tomato [ 117 , 118 ], wheat [ 119–121 ], maize [ 122 , 123 ], barley [ 124 ] and soybean [ 125 , 126 ], confirming that centromeric and pericentromeric CO suppression is a common feature of plant species.…”