Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination “hot spots”

Abstract

Crossover (CO) is a key process for the accurate segregation of homologous chromosomes during the first meiotic division. In most eukaryotes, meiotic recombination is not homogeneous along the chromosomes, suggesting a tight control of the location of recombination events. We genotyped 71 single nucleotide polymorphisms (SNPs) covering the entire chromosome 4 of Arabidopsis thaliana on 702 F2 plants, representing 1404 meioses and allowing the detection of 1171 COs, to study CO localization in a higher plant. The genetic recombination rates varied along the chromosome from 0 cM/Mb near the centromere to 20 cM/Mb on the short arm next to the NOR region, with a chromosome average of 4.6 cM/Mb. Principal component analysis showed that CO rates negatively correlate with the G+C content (P =3x10(-4)), in contrast to that reported in other eukaryotes. COs also significantly correlate with the density of single repeats and the CpG ratio, but not with genes, pseudogenes, transposable elements, or dispersed repeats. Chromosome 4 has, on average, 1.6 COs per meiosis, and these COs are subjected to interference. A detailed analysis of several regions having high CO rates revealed "hot spots" of meiotic recombination contained in small fragments of a few kilobases. Both the intensity and the density of these hot spots explain the variation of CO rates along the chromosome

Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis

“…In Arabidopsis, putative hot spots have been reported in short regions (a few kilobases) on Chr4 (Drouaud et al 2006). Here, one CO on Chr4 was in one of these regions (Supplemental Fig.…”

Detailed Recombination Studies Along Chromosome 3B Provide New Insights on Crossover Distribution in Wheat (Triticum aestivum L.)

“…Further, a recombination hotspot has been identified in a highly gene-rich region at the maize bz locus and characterized at a fine scale (Fu et al 2001). In contrast, in Arabidopsis (Drouaud et al 2006) fine-scale analysis failed to establish a correlation between recombination and gene density.…”

“…Their distribution can be analyzed by comparing physical and genetic maps or by studying linkage disequilibrium patterns. Studies performed in human, mouse, Arabidopsis, and rice (Wu et al 2003;Drouaud et al 2006;Arnheim et al 2007) provided insight into some of the major features of recombination distribution with the identification of hot and cold regions of recombination along the chromosomes as well as a general suppression of COs in centromeric and pericentromeric regions (for a review see Jones 1987). In some plants with large genomes such as maize [2.5 Gigabase (Gb)], barley (5 Gb), and wheat (17 Gb), recombination was shown to follow particular patterns with a gradual increase from the centromeres to the telomeres (Lukaszewski and Curtis 1993;Kunzel et al 2000;Tenaillon et al 2001;Anderson et al 2003).…”

GC Content and Recombination: Reassessing the Causal Effects for the Saccharomyces cerevisiae Genome

“…GC content represents perhaps the most prominent property for which strong correlations with recombination were reported for the genomes of many organisms including mammals, Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae (Gerton et al 2000;Marais et al 2001;Birdsell 2002;Kong et al 2002;Meunier and Duret 2004). On the other hand it was recently demonstrated that in Arabidopsis thaliana rate of crossover and GC content are not correlated (Drouaud et al 2006). However, despite these numerous results, it is not clear as yet (1) whether recombination drives GC content or the converse and (2) what are the length scales for the correlations between GC and recombination.…”