An Ultra High-Density<i>Arabidopsis thaliana</i>Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features

Rowan, Beth A.; Heavens, Darren; Feuerborn, Tatiana R.; Tock, Andrew J.; Henderson, Ian; Weigel, Detlef

doi:10.1534/genetics.119.302406

Cited by 103 publications

(115 citation statements)

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“…2C and Table 2). These data included: (i) nucleosome occupancy (MNase-seq) (Choi et al, 2016), (ii) markers of heterochromatin H3K9me2 (ChIP-seq), DNA methylation (BS-seq) and short interfering RNAs (siRNA-seq) (Lee et al, 2012;Stroud et al, 2013), (iii) histone marks enriched at euchromatic genes H3K4me3 (Choi et al, 2018), H3K4me2, H3K4me1 (ChIP-seq) and mRNA from flowers or male meiocytes (RNA-seq) (Walker et al, 2018), (iv) the Polycomb histone mark H3K27me3 (ChIP-seq) (Zhu et al, 2015), and (v) SPO11-1-oligos that mark meiotic DSBs (Choi et al, 2018) and crossovers mapped by sequencing Col×Ler F 2 plants (Serra et al, 2018;Rowan et al, 2019).…”

Section: Profiling the Genomic Landscape Of Rec8 Enrichment By Chip-seqmentioning

confidence: 99%

Interacting Genomic Landscapes of REC8-Cohesin, Chromatin, and Meiotic Recombination in Arabidopsis

et al. 2020

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Section: Profiling the Genomic Landscape Of Rec8 Enrichment By Chip-seqmentioning

confidence: 99%

Interacting Genomic Landscapes of REC8-Cohesin, Chromatin, and Meiotic Recombination in Arabidopsis

et al. 2020

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“…Several hypotheses may explain this pattern. For instance, SVs such as inversions or some categories of CNVs locally limit recombination (Rowan et al, 2019), thus reducing genome homogenization despite gene flow. Some…”

Section: Cnvs Reveal a Stronger Genetic Structure Than Snpsmentioning

confidence: 99%

“…SVs are pervasive variants that shape genome architecture and they can cover a larger proportion of genetic variation than SNPs (Redon et al, 2006;Wellenreuther et al, 2019;Catanach et al, 2019). They have functional consequences, notably impacting the regulation of gene expression (Gamazon & Stranger 2015) and recombination rate by diminishing the frequency of meiotic crossing-over, which can preserve the integrity of an adaptive haplotype (Rowan et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

Dorant

Cayuela

Wellband

et al. 2020

Preprint

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Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. Yet, our knowledge on genotypic variation and evolution is often limited to single nucleotide polymorphism (SNPs) and the role of CNVs has been overlooked in non-model species, partly due to their challenging identification until recently. Here, we document the usefulness of reducedrepresentation sequencing data (RAD-seq) to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (Homarus americanus) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs accounts for higher genetic differentiation than SNP markers. Contrary to SNPs for which no association was found, genetic-environment association revealed that 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal than SNPs.Our study provides the means to study CNVs in non-model species and underlines the importance to consider structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.

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“…Crossover and non-crossover formation events rely on single-end invasions and serve as synapsis initiation sites (Zhang et al, 2014); they are, however, spatiotemporally distinct and highly controlled. In the tribe of Triticeae (see Glossary), reciprocal exchange occurs within the sub-telomeres (Darrier et al, 2017), whereas in A. thaliana the highest rate of crossovers appears to be in the pericentromeric regions (Rowan et al, 2019). The decision whether to follow a crossover or non-crossover pathway for crossover processing is decided at an early stage of meiosis (Bishop and Zickler, 2004) and both structures play vital roles at meiosis.…”

Section: Emergence Of the Synaptonemal Complex Follows The Polarisedmentioning

confidence: 99%

Chromosome–nuclear envelope tethering – a process that orchestrates homologue pairing during plant meiosis?

Sepsi

Schwarzacher

2020

Journal of Cell Science

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During prophase I of meiosis, homologous chromosomes pair, synapse and exchange their genetic material through reciprocal homologous recombination, a phenomenon essential for faithful chromosome segregation. Partial sequence identity between non-homologous and heterologous chromosomes can also lead to recombination (ectopic recombination), a highly deleterious process that rapidly compromises genome integrity. To avoid ectopic exchange, homology recognition must be extended from the narrow position of a crossover-competent double-strand break to the entire chromosome. Here, we review advances on chromosome behaviour during meiotic prophase I in higher plants, by integrating centromere- and telomere dynamics driven by cytoskeletal motor proteins, into the processes of homologue pairing, synapsis and recombination. Centromere–centromere associations and the gathering of telomeres at the onset of meiosis at opposite nuclear poles create a spatially organised and restricted nuclear state in which homologous DNA interactions are favoured but ectopic interactions also occur. The release and dispersion of centromeres from the nuclear periphery increases the motility of chromosome arms, allowing meiosis-specific movements that disrupt ectopic interactions. Subsequent expansion of interstitial synapsis from numerous homologous interactions further corrects ectopic interactions. Movement and organisation of chromosomes, thus, evolved to facilitate the pairing process, and can be modulated by distinct stages of chromatin associations at the nuclear envelope and their collective release.

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An Ultra High-DensityArabidopsis thalianaCrossover Map That Refines the Influences of Structural Variation and Epigenetic Features

Abstract: Rowan et al. generated a dataset of over 17,000 meiotic crossovers (COs) from over 2000 F2 individuals from a single Arabidopsis thaliana cross. The unprecedented density of COs and the high-quality reference genomes of the two...

Cited by 103 publications

References 103 publications

Interacting Genomic Landscapes of REC8-Cohesin, Chromatin, and Meiotic Recombination in Arabidopsis

Interacting Genomic Landscapes of REC8-Cohesin, Chromatin, and Meiotic Recombination in Arabidopsis

Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

Chromosome–nuclear envelope tethering – a process that orchestrates homologue pairing during plant meiosis?

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