Fluorescent In Situ Hybridization Using Oligonucleotide-Based Probes

Braz, Guilherme Tomaz; Fan, Yu; Martins, Lívia do Vale; Jiang, Jiming

doi:10.1007/978-1-0716-0623-0_4

Cited by 23 publications

(23 citation statements)

References 22 publications

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“…We then used the recently developed barcode FISH probes (Braz et al ., 2020a,b) to identify individual maize chromosomes in the 14 plants (Fig. 2a).…”

Section: Resultsmentioning

confidence: 99%

“…Root tips were harvested from plants and treated with N 2 O at a pressure of 160 psi ( c . 10.9 atm) for 2 h (Kato, 1999; Braz et al ., 2020a,b). The root tips were fixed in fixative solution (ethanol : acetic acid, 3 : 1) and kept at −20°C until use.…”

Section: Methodsmentioning

confidence: 99%

“…Combination of these two probes allowed identification of individual copies of chromosome 10 and their origination from either inbred B73 or H99. Probe labeling and hybridization to chromosomes were performed following published protocols (Cheng et al ., 2002; Braz et al ., 2020a,b). Biotin and digoxygenin‐labeled probes were detected by anti‐biotin fluorescein (Vector Laboratories, Burlingame, CA, USA) and anti‐digoxygenin rhodamine (Roche Diagnostics, Indianapolis, IN, USA), respectively.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2020

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Summary Meiotic chromosome pairing between homoeologous chromosomes was reported in many nascent allopolyploids. Homoeologous pairing is gradually eliminated and replaced by exclusive homologous pairing in well‐established allopolyploids, an evolutionary process referred to as the diploidization of allopolyploids. A fundamental question of the diploidization of allopolyploids is whether and to what extent the DNA sequence variation among homoeologous chromosomes contribute to the establishment of exclusive homologous chromosome pairing. We developed aneuploid tetraploid maize lines that contain three copies of chromosome 10 derived from inbred lines B73 and H99. We were able to identify the parental origin of each copy of chromosome 10 in the materials using oligonucleotide‐based haplotype‐specific chromosome painting. We demonstrate that the two identical copies of chromosome 10 from H99 pair preferentially over chromosome 10 from B73 in different stages of prophase I and metaphase I during meiosis. Thus, homologous chromosome pairing is favored to partners with the most similar DNA sequences and can be discriminated based on cryptic sequence variation. We propose that innate preference of homologous chromosome pairing exists in nascent allopolyploids and serves as the first layer that would eventually block all homoeologous chromosome pairing in allopolyploids.

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“…We then used the recently developed barcode FISH probes (Braz et al ., 2020a,b) to identify individual maize chromosomes in the 14 plants (Fig. 2a).…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

et al. 2020

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“…Freshly harvested root tips were treated with nitrous oxide under a pressure of 160 psi for 2 h and then fixed in a fixative solution (3 ethanol/1 acetic acid) until use. All chromosome painting probes were labeled by digoxigenin or biotin as described previously (Han et al ., 2015; Braz et al ., 2020b). FISH probes for the three satellite repeats, including the 5S rDNA, 45S rDNA and the 180‐bp repeat, were developed by labeling a single‐strand short oligo that is specific to each of these three satellite repeats.…”

Section: Methodsmentioning

confidence: 99%

Extraordinarily conserved chromosomal synteny ofCitrusspecies revealed by chromosome‐specific painting

Zhao

et al. 2020

The Plant Journal

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Summary Reliable identification of individual chromosomes in eukaryotic species is the foundation for comparative chromosome synteny and evolutionary studies. Unfortunately, chromosome identification has been a major challenge for plants with small chromosomes, such as the Citrus species. We developed oligonucleotide‐based chromosome painting probes for all nine chromosomes in Citrus maxima (Pummelo). We were able to identify all C. maxima chromosomes in the same metaphase cells using multiple rounds of sequential fluorescence in situ hybridization with the painting probes. We conducted comparative chromosome painting analysis in six different Citrus and related species. We found that each painting probe hybridized to only a single chromosome in all other five species, suggesting that the six species have maintained a complete chromosomal synteny after more than 9 million years of divergence. No interchromosomal rearrangement was identified in any species. These results support the hypothesis that karyotypes of woody species are more stable than herbaceous plants because woody plants need a longer period to fix chromosome structural variants in natural populations.

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“…We used oligonucleotide-based FISH probes (Oligo-FISH) (Han et al 2015) to specifically paint the chromosomes 7 and 8 of potato. Probe labeling and FISH were performed following published protocols (Braz et al 2018(Braz et al , 2020. Biotin and digoxygenin-labeled probes were detected by anti-biotin fluorescein (Vector Laboratories, Burlingame, CA, USA) and anti-digoxygenin rhodamine (Roche Diagnostics, Indianapolis, IN, USA), respectively.…”

Section: Oligo-fish Paintingmentioning

confidence: 99%

LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci

Comai

Amundson

Ordoñez

et al. 2021

Preprint

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Large scale structural variations, such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple and effective method aimed at identifying translocations using only the dosage of sequence reads mapped on the reference genome. We binned reads on genomic segments sized according to sequencing coverage and identified instances when copy number segregated in populations. For each dosage-polymorphic 1Mb bin, we tested linkage disequilibrium with other variable bins. In nine potato (Solanum tuberosum) dihaploid families translocations affecting pericentromeric regions were common and in two cases were due to genomic misassembly. In two populations, we found evidence for translocation affecting euchromatic arms. In cv. PI 310467, a non-reciprocal translocation between chromosome 7 and 8 resulted in a 5-3 copy number change affecting several Mb at the respective chromosome tips. In cv. Alca Tarma the terminal arm of chromosome 4 translocated to the tip of chromosome 1. Using oligonucleotide-based fluorescent in situ hybridization painting probes (oligo-FISH), we tested and confirmed the predicted arrangement in PI 310467. In 192 natural accessions of Arabidopsis thaliana, dosage haplotypes tended to vary continuously and resulted in higher noise, but we identified pericentromeric LD suggesting the effect of repeats. This method should be useful in species where translocations are suspected because it tests linkage without the need for genotyping.

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Fluorescent In Situ Hybridization Using Oligonucleotide-Based Probes

Cited by 23 publications

References 22 publications

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

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

Extraordinarily conserved chromosomal synteny ofCitrusspecies revealed by chromosome‐specific painting

LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci

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