Quantifying Meiotic Crossover Recombination in Arabidopsis Lines Expressing Fluorescent Reporters in Seeds Using SeedScoring Pipeline for CellProfiler

Kbiri, Nadia; Dluzewska, Julia; Henderson, Ian; Ziolkowski, Piotr A

doi:10.1007/978-1-0716-2253-7_10

Cited by 4 publications

(3 citation statements)

References 23 publications

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“…The recombination within the obtained ESILs was measured using a seed-based system, which was already described 50 , 80 . First, the homozygous ESILs were crossed with the non-color accessions and the pictures of F 2 seeds, derived from the entire plant, were acquired using an epifluorescent stereomicroscope (Zeiss).…”

Section: Methodsmentioning

confidence: 99%

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The effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids

et al. 2023

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In hybrid organisms, genetically divergent homologous chromosomes pair and recombine during meiosis; however, the effect of specific types of polymorphisms on crossover is poorly understood. Here, to analyze this in Arabidopsis, we develop the seed-typing method that enables the massively parallel fine-mapping of crossovers by sequencing. We show that structural variants, observed in one of the generated intervals, do not change crossover frequency unless they are located directly within crossover hotspots. Both natural and Cas9-induced deletions result in lower hotspot activity but are not compensated by increases in immediately adjacent hotspots. To examine the effect of single nucleotide polymorphisms on crossover formation, we analyze hotspot activity in mismatch detection-deficient msh2 mutants. Surprisingly, polymorphic hotspots show reduced activity in msh2. In lines where only the hotspot-containing interval is heterozygous, crossover numbers increase above those in the inbred (homozygous). We conclude that MSH2 shapes crossover distribution by stimulating hotspot activity at polymorphic regions.

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Section: Methodsmentioning

confidence: 99%

“…Each set of seed pictures included pictures in brightfield, and ultraviolet through filters for red and green fluorescence. The number of seeds was counted using CellProfiler program according to the protocol 80 . Due to low recombination rates within ESILs, the number of single-color recombinants was detected manually.…”

Section: Methodsmentioning

confidence: 99%

The effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids

et al. 2023

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“…Recombination between the transgenes in a TL is useful if the goal is to study factors that influence recombination ( Melamed-Bessudo and Levy 2012 ; Ziolkowski et al 2015 , 2017 ; Saini et al 2020 ; Nageswaran et al 2021 ; Kbiri et al 2022 ). However, recombination is disadvantageous if the TL is being used to follow the segregation of an unmarked chromosome segment in trans to the TL because double recombination within the interval generates an unmarked chromosome that may be genetically different from the original unmarked chromosome.…”

Section: Introductionmentioning

confidence: 99%

Short-interval traffic lines: versatile tools for genetic analysis in Arabidopsis thaliana

Poethig

Cullina

Doody

et al. 2022

G3 Genes|Genomes|Genetics

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Traffic Lines (TLs) are transgenic stocks of Arabidopsis thaliana that contain a pair of linked seed-specific eGFP and DsRed markers. These stocks were originally developed for the purpose of studying recombination, but can also be used to follow the inheritance of unmarked chromosomes placed in trans to the marked chromosome. They are particularly useful for this latter purpose if the distance between markers is short, making double recombination within this interval relatively rare. We generated 163 TLs that cover the Arabidopsis genome in over-lapping intervals of approximately1.2 Mb (6.9 cM). These stocks make it possible to predict the genotype of a plant based on its seed fluorescence (or lack thereof) and facilitate many experiments in genetic analysis that are difficult, tedious, or expensive to perform using current techniques. Here we show how these lines enable phenotypic analysis of alleles with weak or variable phenotypes, genetic mapping of novel mutations, introducing transgenes into a lethal or sterile genetic background, and separating closely-linked mutations.

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MSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism

Dluzewska,

Dziegielewski,

Szymanska-Lejman

et al. 2023

Nat Commun

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Meiotic crossovers can be formed through the interfering pathway, in which one crossover prevents another from forming nearby, or by an independent non-interfering pathway. In Arabidopsis, local sequence polymorphism between homologs can stimulate interfering crossovers in a MSH2-dependent manner. To understand how MSH2 regulates crossovers formed by the two pathways, we combined Arabidopsis mutants that elevate non-interfering crossovers with msh2 mutants. We demonstrate that MSH2 blocks non-interfering crossovers at polymorphic loci, which is the opposite effect to interfering crossovers. We also observe MSH2-independent crossover inhibition at highly polymorphic sites. We measure recombination along the chromosome arms in lines differing in patterns of heterozygosity and observe a MSH2-dependent crossover increase at the boundaries between heterozygous and homozygous regions. Here, we show that MSH2 is a master regulator of meiotic DSB repair in Arabidopsis, with antagonistic effects on interfering and non-interfering crossovers, which shapes the crossover landscape in relation to interhomolog polymorphism.

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Quantifying Meiotic Crossover Recombination in Arabidopsis Lines Expressing Fluorescent Reporters in Seeds Using SeedScoring Pipeline for CellProfiler

Cited by 4 publications

References 23 publications

The effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids

The effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids

Short-interval traffic lines: versatile tools for genetic analysis in Arabidopsis thaliana

MSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism

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