Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes

Abstract

During meiosis, chromosomes undergo DNA double-strand breaks (DSBs), which can be repaired using a homologous chromosome to produce crossovers. Meiotic recombination frequency is variable along chromosomes and tends to concentrate in narrow hotspots. We mapped crossover hotspots located in the Arabidopsis thaliana RAC1 and RPP13 disease resistance genes, using varying haplotypic combinations. We observed a negative non-linear relationship between interhomolog divergence and crossover frequency within the hotspots, consistent with polymorphism locally suppressing crossover repair of DSBs. The fancm, recq4a recq4b, figl1 and msh2 mutants, or lines with increased HEI10 dosage, are known to show increased crossovers throughout the genome. Surprisingly, RAC1 crossovers were either unchanged or decreased in these genetic backgrounds, showing that chromosome location and local chromatin environment are important for regulation of crossover activity. We employed deep sequencing of crossovers to examine recombination topology within RAC1, in wild type, fancm, recq4a recq4b and fancm recq4a recq4b backgrounds. The RAC1 recombination landscape was broadly conserved in the anti-crossover mutants and showed a negative relationship with interhomolog divergence. However, crossovers at the RAC1 5′-end were relatively suppressed in recq4a recq4b backgrounds, further indicating that local context may influence recombination outcomes. Our results demonstrate the importance of interhomolog divergence in shaping recombination within plant disease resistance genes and crossover hotspots.

Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley

“…2). As a consequence of this compartmentalization, differences in recombination rate might be caused by selection for elevated recombination rates in regions harboring defense response genes throughout barley’s domestication, as recombination hotspots tend to be found near disease resistance genes (Serra et al. 2018).…”

Population Genetics of the Highly Polymorphic RPP8 Gene Family

“…We explored the rate of RPP8 protein evolution by comparing the K a :K s ratio generated for comparisons of A. thaliana and A. lyrata alleles to the distribution of all genes shared between A. thaliana and A. lyrata [66,67]. Across the entire coding region, K a :K s ratios within paralogs varied between 0.53 and 0.61 (Table 4), higher than 91–94% of the K a :K s distribution in A. thaliana .…”

Preferential meiotic chromosome pairing among homologous chromosomes with cryptic sequence variation in tetraploid maize

“…It is well known that interhomologue sequence polymorphism can affect homologous recombination. Increased levels of sequence polymorphism were found to suppress homologous recombination (Opperman et al ., 2004; Li et al ., 2006; Serra et al ., 2018). However, the sequence‐polymorphism‐mediated suppression of crossovers is dependent on the chromosome location and local chromatin environment (Serra et al ., 2018).…”