An ultra high-densityArabidopsis thalianacrossover map that refines the influences of structural variation and epigenetic features

Abstract

Many environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of over 17,000 COs between the Col-0 and Ler accessions of Arabidopsis thaliana . COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders, and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large and small-scale SVs, representing influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.

Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

“…In contrast, meiotic recombination in Arabidopsis was shown to be supressed by structural diversity 35 . To test if HOTs are indeed depleted for meiotic recombination, we overlapped rearranged regions with 15,683 crossover (CO) sites previously identified within Col-0/Ler F2 progenies 35,36 . Only 64 of them partially overlapped with non-syntenic regions while all other COs were found in syntenic regions ( Fig.…”

“…o f s a li c y li c a c id m e d ia t e d s ig n a li n g p a t h w a y S C F − d e p e n d e n t p r o t e in c a t a b o li c p r o c e s s S ig n a l t r a n s d u c t io n T e r p e n o id b io s y n t h e t ic p r o c e s s T r y p t o p h a n b io s y n t h e t ic p r o c e s The causes and consequences of hotspots of rearrangements. a Crossover (CO) breakpoints35,36 identified in Col-0 x Ler hybrids were checked for their overlaps in syntenic or rearranged regions. Only unique CO intervals smaller than 5 kb were used.…”

Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

“…In contrast, meiotic recombination in Arabidopsis was shown to be supressed by structural diversity 37 . To test if HRs are indeed depleted for meiotic recombination, we overlapped rearranged regions with 15,683 crossover (CO) sites previously identified within Col-0/Ler F2 progenies 37,38 . Only 64 of them partially overlapped with non-syntenic regions while all other COs were found in syntenic regions (Fig.…”

“… (a) Crossover (CO) breakpoints 37,38 identified in Col-0 x L er hybrids were checked for their overlaps in syntenic or rearranged regions. Only unique CO intervals smaller than 5kb were used.…”

Purging of deleterious mutations during domestication in the predominant selfing crop soybean

“…Interestingly, although correlation coefficients between historical recombination rates and other variables are relatively low with the highest value of 0.344 between recombination and indel density, our visual inspection indicated that the highest peak (hotspot) of historical recombination rates in each of half of the 20 chromosomes corresponded with the densest region of indels in each chromosome. A variety of genomic features such as gene density, CpG islands, and structural variants have been identified as being associated with regions of high recombination 17,18,22 . However, the association between high indel density and recombination hotspot has so far been poorly examined.…”