Next Article in Journal
Nitrogen Use Efficiency in Oil Palm Seedlings: Unraveling the Untapped Potential of Elevated External Ammonium Supply
Next Article in Special Issue
Genome Analysis of Thinopyrum intermedium and Its Potential Progenitor Species Using Oligo-FISH
Previous Article in Journal
Camellia oleifera CoSWEET10 Is Crucial for Seed Development and Drought Resistance by Mediating Sugar Transport in Transgenic Arabidopsis
Previous Article in Special Issue
Cytogenetics and Consequences of Polyploidization on Different Biotic-Abiotic Stress Tolerance and the Potential Mechanisms Involved
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Plants
Volume 12
Issue 15
10.3390/plants12152816
plants-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Review

Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants

by
Arrashid Harun
1,2,3,†,
Hui Liu
3,†,
Shipeng Song
3,
Sumeera Asghar
2,3,
Xiaopeng Wen
2,
Zhongming Fang
1,* and
Chunli Chen
1,2,3,*
1
Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Rice Industry Technology Research, College of Agricultural Sciences, Guizhou University, Guiyang 550025, China
2
Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang 550025, China
3
National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Plants 2023, 12(15), 2816; https://doi.org/10.3390/plants12152816
Submission received: 19 June 2023 / Revised: 19 July 2023 / Accepted: 27 July 2023 / Published: 29 July 2023
(This article belongs to the Special Issue Plant Molecular Cytogenetics)
Browse Figures
Review Reports Versions Notes

Abstract

:
Fluorescence in situ hybridization (FISH) is an indispensable technique for studying chromosomes in plants. However, traditional FISH methods, such as BAC, rDNA, tandem repeats, and distributed repetitive sequence probe-based FISH, have certain limitations, including difficulties in probe synthesis, low sensitivity, cross-hybridization, and limited resolution. In contrast, oligo-based FISH represents a more efficient method for chromosomal studies in plants. Oligo probes are computationally designed and synthesized for any plant species with a sequenced genome and are suitable for single and repetitive DNA sequences, entire chromosomes, or chromosomal segments. Furthermore, oligo probes used in the FISH experiment provide high specificity, resolution, and multiplexing. Moreover, oligo probes made from one species are applicable for studying other genetically and taxonomically related species whose genome has not been sequenced yet, facilitating molecular cytogenetic studies of non-model plants. However, there are some limitations of oligo probes that should be considered, such as requiring prior knowledge of the probe design process and FISH signal issues with shorter probes of background noises during oligo-FISH experiments. This review comprehensively discusses de novo oligo probe synthesis with more focus on single-copy DNA sequences, preparation, improvement, and factors that affect oligo-FISH efficiency. Furthermore, this review highlights recent applications of oligo-FISH in a wide range of plant chromosomal studies.

1. Introduction

Fluorescence in situ hybridization (FISH) is a crucial technique in plant molecular cytogenetic research that allows the visualization of DNA or RNA sequence location on real chromosomes [1,2,3]. However, in situ hybridization (ISH) experiments using RNA labeled with radioactive tritium were first reported in 1969 [4] and the FISH method was first reported in the early 1980s [5]. FISH employs fluorophore-labeled DNA or RNA molecules as probes to produce a hybrid double-stranded molecule with signal in the genome that could be detected under a fluorescence microscope using a CCD (charge-coupled device) [6]. The success of FISH experiments largely depends on the probes used in the FISH experiment. While traditional cloned DNA probes, such as bacterial artificial chromosome (BAC), ribosomal DNA (rDNA), tandem repeats, and distributed repetitive sequences probes, have been used to construct karyotypes, identify chromosomes, and determine interspecies homoeologous relationships among various plant species [2,7,8,9,10], the reliability of traditional repetitive sequences in species with high percentages of repetitive sequences has been called into question due to the variability in available probes for a given species, as well as the complexity of preparing ordered BAC contigs covering the entire genome. Additionally, some species exhibit transposable elements within their repetitive sequences, further complicating the matter. As such, there is a need to reevaluate the use of traditional repetitive sequences in these cases. Recent advancements in next-generation sequencing (NGS) and DNA sequence synthesis technologies have led to the development of oligonucleotide fluorescence in situ hybridization (oligo-FISH), which uses synthetic oligonucleotides as probes [11,12,13].
Oligo probe synthesis is an important step of the oligo-FISH technique, which involves computational design yielding probe synthesis with fewer resources, saving time and improving the efficacy of chromosomal studies. Little work has been reported on the computational tools required to design the oligo probes, despite several advancements in these probes, and probe sets have been seen. However, previously, various tools were established for this purpose, including padlock probes [14], ribosomal RNA [15], and oligo pairs, but due to off-targeted and cross-hybridization effects, an incomplete sequential database, and limited experimental validation results, it is inevitable to combine experimental validations and computational predictions. The latest tools like ProbeDealer (MATLAB-based) [16], Chorus2 [17], and iFISH (Python-based) [18] undoubtedly reduce the required hyperparameters and configurations, but they still need advanced bioinformatic expertise. Therefore, it is recommended to merge the available computational predictions and experimental validations to overcome the above-mentioned constraints.
This review has extensively studied the major accomplishments in oligo probes. The recent applications are highlighted and well structured in the manuscript as oligo probe synthesis, preparation, and applications of oligo probes including chromosomal identification, karyotyping, and chromosomal rearrangements, with chromosomal translocations and fusion. The limitations and future perspectives are also highlighted.

2. De Novo Oligo Probe Synthesis

2.1. Brief Introduction of Oligo Probes

Oligonucleotides, which are small molecules composed of 20–50 nucleotides, have gained attention in the field of FISH experiments [1,19,20]. Currently, there are two types of oligo probes in plants: oligo probes based on single-copy sequences and oligo probes designed from repetitive DNA sequences. These probes consist of single-copy oligos or shorter sequences with repeated di-, tri-, or tetra-nucleotides, such as (AG)12 or (AGG)5, and are designed to target specific chromosomal segments or entire chromosomes. They can be used as a probe library and are easily synthesized, amplified, and labeled using PCR amplification, making them a cost-effective option. Shorter probes offer higher sensitivity, specificity, and ease of hybridization. Multiplex oligo probe designs are also available and are inspired by simple oligo probe design processes. The quality of the synthesis process depends on the synthesizer and the reagents used.

2.2. Comparison of Two Types of Oligo Probes

In plants, two types of oligo probes have their own advantages and disadvantages. Typically, single-copy oligo-based probes are used, which are synthesized from single-copy DNA sequences using a bioinformatics platform. These oligo sequences are labeled with fluorochrome, biotin-dUTP, or digoxigenin-dUTP through PCR amplification, generating oligo probes that have been used in FISH experiments [21]. Single-copy oligo probes provide flexibility for use on specific chromosome fragments or the entire chromosome as a library. It is easy to use for amplification via PCR for labeling, which reduces the cost of probe reuse. Single-copy oligo probes are valuable for studying chromosomal evolution, meiotic pairing, and recombination, which can distinguish homologous chromosomes and even homoeologous chromosomes from different cultivars [11]. However, the successful design of oligo probes needs to be achieved in plants that have completed genome sequencing. A lack of genome sequencing information hinders the application of single-copy oligo-based probes.
Unlike oligo probes based on single-copy sequences, designing probes from repetitive DNA sequences does not require genome sequencing information [1]. These oligo sequences consist of microsatellite repeats, satellite repeats, and tandem repeats, and can be end-labeled with biotin-dUTP or digoxigenin-dUTP [1,12]. Furthermore, repetitive DNA oligo probes are commonly used in FISH to produce unique signals for individual chromosomes. This technique is useful for karyotyping and phylogenetic analysis, as well as for non-denaturing FISH (ND-FISH) [22]. Although repetitive DNA oligo probes are easier to prepare, single-copy shorter probes are more specific and have higher sensitivity. Oligo probe design has multiple well-developed applications, making the design process easy.

2.3. The Procedure and Rules of Oligo Probe Preparations

De novo oligo probe synthesis is a combined approach that starts with a computational search of single-copy potential oligos in the genome, and then sequential steps are performed. A method for de novo single-copy oligo probe synthesis is described in Figure 1 and Figure 2, which represent combined approaches of computational and experimental techniques. In brief, the process involves selecting potential single-copy oligos, synthesizing them, and labeling them with fluorescent markers [7,23]. However, first, single-copy oligos are computationally searched in the target genome, repetitive sequences are filtered out, and potential bulked oligos are selected using the Chorus2 platform (Figure 1). Next, the selected potential DNA sequences are bound with a specific pair of primers to their 3’ and 5’ ends for PCR amplification for transcription or reverse transcription for making a double strand, and then fluorescent markers are added (Biotin, digoxigenin or fluorescence probe) in wet-lab experiments [24] (Figure 2). Obtaining genomic data for oligo selection is possible through the genomic database, and the process has been greatly facilitated using next-generation sequencing (NGS) technology [1]. Depending on the purpose of the experiment, single-copy oligo sequences can be made into ‘oligo pool’ probes specific to any region of the chromosome [12,20]. The specificity of the probe is crucial for a single-copy oligo probe to determine the quality of the FISH experiment with specific FISH signals [25]. Therefore, selecting a well-assembled reference genome and suitable software or a suitable platform is essential to design an efficient single-copy oligo probe. It is important to follow other rules as well, such as maintaining a minimum space of typically 10 bases between probes to minimize overlapping between adjacent probes, maximize PCR quality, and minimize the mismatch ratio between the probe and target sequence [20]. For more information, Liu and Zhang (2021) [26] published a review article summarizing the various attributes of single-copy oligonucleotides and discussing comprehensive probe design platforms. The preparation process of oligo probes based on repetitive sequences is similar to that for single-copy sequences, with the main distinction being the filtering process of target sequences.

2.4. Key Aspects (Characteristics) That Influence Single-Copy Oligo Probe Performance

In order to achieve a successful oligo-FISH experiment, it is crucial to design high-quality single-copy oligo probes. The process involves minimizing repetitive sequences in the target sequences [2,27,28,29] and taking into account factors such as probe density, length, temperature, and quality of the chromosome preparation, which are applicable to all types of cells [11,12,30]. Previous research has shown that successful oligo-FISH in plants has been achieved with varying densities of oligo probes, ranging from 0.1 to 0.5 oligo/kilobases [1]. The number of oligos in a probe pool is also important, as higher-density probes generate brighter signals but at a higher cost. However, repeat detection and filtering are essential for improving single-copy oligo probes, especially in large and complex plant genomes [17,31,32]. To ensure consistent separation of the two FISH signals, a distance of 5–10 Mb is necessary between the two spots, with each spot containing a minimum of ~1000 oligos to ensure a strong and punctuated signal of a smaller chromosomal region [1]. Earlier studies on various plant species have indicated that a density of 0.1–0.5 oligos/kb is the most effective way to obtain a high-quality signal on condensed metaphase chromosomes. However, to achieve a strong signal, a higher density of approximately 2 oligos/kb is required for pachytene chromosomes, which are known to be extended 10–20 times more than metaphase chromosomes [1]. This was demonstrated in rice (Oryza sativa) where a probe with a density of 2 oligos/kb produced an excellent signal on pachytene chromosomes for specific chromosome identification [33], and cucumber (Cucumis sativus) produced stronger signals with 7.3 oligos/kb than 3.2 oligos/kb for megabase-size chromosome painting [12].
Both single and repetitive sequences oligo probes can be designed for plant species with sequenced genomes using various platforms such as Chorus2, iFISH, and Oligopaint [17,18,34]. These techniques offer several potential advantages in plant cytogenetic research, including the ability to design probes for plants without reference genomes. Researchers can use either chromosome-level or single-copy sequences in the target plant species or other genetically related plants to design oligo probes [11,12,30,35]. Oligo-FISH can also be used to design chromosome-level probes for detecting polyploid plant species, which demonstrate multiple-genome hybridization with varying levels of homology. The cross-hybridization of homologous or homoeologous chromosomes during probe design can be accounted for by designing each oligo from homoeologous chromosomes with a similar level of sequence similarity. This allows for a similar level of signal to be produced from each oligo, which can be useful in revealing the polyploid genomes [35]. However, oligo-FISH is a useful technique that can be applied to a wide range of plant species which provide valuable insights into their genome structure and organization, including polyploid species such as corn (Zea perennis) [11] and Saccharum [36,37].

3. Applications of Oligo-FISH in Plants

Oligo-FISH has become a widely used technique in various molecular cytogenetic applications in plant species in recent years. Like traditional FISH, chromosome identification through chromosome painting is the key application of oligo-FISH, which is more powerful than traditional probes. However, chromosome painting is one of the most successful applications of this technique, and it has been reported in many plant species. Other applications of oligo-FISH in various plants have been systematically summarized in Table 1, Table 2 and Table 3. These include chromosome identification, karyotyping, and the determination of chromosome rearrangements, which allow for the construction of detailed chromosomal maps of plant species. These maps are important tools for understanding genome structural organization and evolution analysis in plants. Figure 3 illustrates the versatility of this technique and its potential to contribute to a wide range of research areas in plant molecular cytogenetics. The continued development and refinement of oligo-FISH techniques are likely to play increasingly important roles in advancing our understanding of plants’ chromosomal identification and their evolutionary history.

3.1. Chromosome Identification with Chromosomal Arms, Segments, and Centromere Sequence Markers

The oligo-FISH technique is a highly effective method for identifying and mapping chromosomes in various plant species, including those without reference genomes. It involves the use of specific single-copy DNA sequences for probes to identify whole chromosomes, chromosomal segments, and the long and short arms of chromosomes. This technique has been successfully applied in various plant species, such as sweet orange (Citrus sinensis) [77], calamondin (C. microcarpa) [78], cucumber (Cucumis sativus) [12], maize (Zea mays) [46], sorghum (Sorghum bicolor) [52], sugarcane (Tripidium arundinaceum) [52], wheat (Triticum boeoticum) [44], banana (Musa spp.) [56], potato (Solanum tuberosum) [35,48], tomato (Solanum lycopersicum) [35], and barley (Hordeum vulgare) [50]. The use of specific oligo probes has been allowed for the separation of Ab- and A-genome chromosomes in wheat (Triticum boeoticum) [44]. In addition, oligo-FISH has been used to identify all ten Erianthus rufipilus (Saccharum complex) centromeres, using satellite CEN137 monomers as probes [79]. Overall, the oligo-FISH technique is a powerful tool for chromosome identification with chromosome painting using any markers as probes, applicable for both model and non-model plants.

3.2. Karyotyping and Evolution

Oligo-FISH is an important molecular cytogenetic technique that not only enables the identification of chromosomes via painting but also gives valuable insights for the karyotyping of plant species [80] and evolution of plant chromosomes across different species with repetitive and single-copy oligo sequences, respectively [1]. While comparative genetic linkage mapping has traditionally been used to study the syntenic and evolutionary relationships of homoeologous chromosomes among species [81], repetitive oligo probes have emerged as a more effective, flexible, and easy-to-use tool for such analyses. Many plant species have already successfully adopted this technique for karyotyping and identifying evolutionary relationships among them [11,38,39], as shown in Table 1. For example, Zhang et al. (2023) [82] recently used oligo-FISH to reveal the evolutionary effects of stable meiotic pairing behavior in different clones of cultivated sugarcane (Saccharum spontaneum). He et al. (2020) [63] revealed the extraordinarily conserved chromosomal synteny of Citrus species via oligo-FISH. Furthermore, oligo-FISH played an important role in the construction of ancestral chromosome karyotypes in Cucumis [83]. Overall, oligo-FISH is a valuable tool for studying the evolutionary relationships among related plant species with specific single-copy DNA sequences.

3.3. Chromosomal Rearrangement through Chromosomal Translocations and Fusion

Oligo-FISH mapping is a useful technique for identifying chromosomal translocations in various plant species with low-copy oligo probes. For example, it has been used to identify translocations between chromosome 9 and chromosome 11 in the indica rice (Oryza sativa) variety Zhongxian 3037 [33], as well as to measure the breakpoints of the 5B and 7B chromosomes during translocation in the wheat (Triticum aestivum) variety CM62 [41]. The oligo-GISH technique has also been used with a specific DNA probe to identify chromosome transmission in BC4 progenies during intergeneric hybrids between sugarcane (Saccharum spp.) and the saccharum complex (Erianthus arundinaceus) (Retz.) Jeswiet [59]. Recent research on oligo-FISH using a subgenome-specific interspersed repeat (IR) oligo probe revealed that four chromosomal translocations occurred between the A and B subgenomes during peanut (Arachis hypogaea) variety FS2020-2-1 polyploidization [58]. Overall, oligo-FISH is an important technique for chromosomal painting, mapping, evolution analysis, and the detection of chromosomal translocations in plants with specific probes.

4. Discussion

Oligo-FISH has emerged as a promising alternative to traditional FISH in plant molecular cytogenetic research, overcoming many of the limitations of traditional FISH methods [12,35,40,45,46,65,84,85,86]. This technique has proven useful in chromosomal identification, karyotyping, and the detection of chromosomal rearrangements through chromosomal fusion or segment translocation. Oligo-FISH has also contributed significantly to genomic and evolution analyses in both diploid and polyploid plants, as well as in studying chromosome pairing during meiosis [12,13,37,48]. Recent advancements in next-generation sequencing technology and probe designing tools have enabled the use of oligo probes for single and repetitive sequences, chromosomal segments, and entire chromosomes with all types of genomes, expanding the range of applications of oligo-FISH in plants. In summary, the combination of modern sequencing technologies, oligo probe designing tools, and the oligo-FISH technique provide researchers with a powerful arrangement for studying the molecular cytogenetics and genetic mechanisms underlying plant chromosome identification, karyotyping, and evolution analysis for the development of plants.

4.1. Advantages of Oligo-FISH

Oligo probes which utilize both single-copy and repetitive DNA sequences offer several advantages over traditional probes, including a higher probe density, lower probe cost, stronger probe availability, and greater flexibility in probe designing, targeting both the single-copy and repetitive-copy basis of experimental needs. Furthermore, oligo-FISH can visualize multiple targets within a cell, such as mRNA (RNA FISH discussed later), using “probe sets” as well as single targets, using target-specific oligo probes [87].

4.2. Efficient Use of Oligo-FISH

In order to improve the efficiency and experimental results of oligo-FISH, it is necessary to pay attention to several aspects in the design of oligo probes. Firstly, different types of oligo probes need to be designed according to the purpose of the experiment. For example, the probes designed for the chromosomal segment may not be suitable for identifying chromosomal variations among plants, which require numerous oligos covering all individual chromosomes. Meanwhile, when designing probes and preparing chromosomes for oligo-FISH, it is crucial to also take into consideration the thermodynamic properties of the sample DNA, which can vary depending on the plant cells. Unfavorable conditions may result in failed probe and target hybridization, ultimately affecting the success of the oligo-FISH experiment [88]. Furthermore, plants with large genomes and big chromosome numbers often have a high proportion of repetitive sequences, making it challenging to obtain efficient single-copy oligo probes with low background noises. To address this challenge, a combination of sequence alignment and k-mer-based analysis can be applied during probe design to identify single-copy oligos. Repetitive sequences may not be effectively eliminated using sequence alignment alone [17]. To address this issue, the genomic shotgun sequencing method can be used to filter out repetitive sequences from the low-quality sequencing data of these genomes. The above approaches will be helpful to improve the efficiency of oligo-FISH for plants.

4.3. Limitation of Oligo-FISH

Although we can design oligo probes of both repetitive and single sequences for target species with the help of NGS and probe designing software, many plant species still face obstacles in adopting oligo-FISH for chromosomal analysis due to their big and diverse chromosome numbers and lack of genomic information, despite the potential benefits of this technique for improving crops cytogenetically [1]. For example, tropical fruit crops such as mango (Mangifera indica), pitaya (Hylocereus undatus), and cactus (Selenicerus grandiflorus) species currently lack the necessary resources for oligo probe design for chromosomal analyses with oligo-FISH. However, there is hope for the future, as the oligo-FISH technique has already been utilized for more complex and polyploid genomes such as wheat (Triticum aestivum) [39], sugarcane (Saccharum officinarum) [37,88], and potato (Solanum tuberosum) [35,48]. With advancements in next-generation sequencing technology and oligo probe design software, it is hoped that more crops will be able to take advantage of genomic and cytogenetic studies in the future.

5. Conclusions and Future Perspectives

FISH has been considered to be the most fundamental technique in plant cytogenetic research since 1969. However, the lack of robust DNA probes in many plant species has been a major challenge. With the development of next-generation sequencing technologies and bioinformatics tools, the design and synthesis processes of oligo probes for oligo-FISH have greatly improved, resulting in a more flexible and target-specific oligo probe designing, which has led to the achievement of target site determination in the genome. This has expanded its applications in the molecular cytogenetic field in plants, particularly in the areas of molecular identification of chromosomal variations, chromosomal rearrangement, and evolution detection. Moreover, oligo probes have alleviated the previous dilemma of the lack of universal DNA probes for many genetically related plant species, which was a limitation of traditional probes, making the oligo probe an important tool in plant molecular cytogenetic research. It also provides a good understanding of plants’ genomic structures, opening up new avenues for exploring the genetic mechanisms underlying plants’ development and evolution [1]. However, several advanced FISH techniques have gained popularity in the field of biology, significantly impacting research in molecular cytogenetics.
π-FISH is a highly efficient and robust fluorescence in situ hybridization (FISH) method called the π-FISH rainbow for detecting diverse biomolecules, including DNA, RNA, proteins, and neurotransmitters, with high sensitivity and specificity. The π-FISH rainbow method involves the use of target probes containing 2–4 complementary base pairs in the middle region, followed by secondary and tertiary U-shaped amplification probes, and a fluorescence signal probe. The versatility of the π-FISH rainbow was demonstrated by applying it to diverse species in frozen, paraffin, and whole-mount samples, and by combining it with other imaging technologies, such as vascular labeling. Additionally, the π-FISH rainbow was utilized to determine the spatial landscape of cells in intact tissue and to detect small genomic indels and breakpoints. The π-FISH rainbow was combined with the hybridization chain reaction (HCR) to detect short nucleic acid fragments, such as microRNA and the prostate cancer anti-androgen therapy-resistant marker ARV7 splicing variant [89].
Three-dimensional (3D) FISH has been used to construct the 3D structure of plant interphase nuclei, meiotic nuclei, and the nuclear disposition of hybrids [90,91]. With the increasing availability of plant genome sequencing and the design flexibility of oligo painting probes, 3D-FISH using oligo probes will become more diverse in studying the three-dimensional spatial structure of plant chromosomes and chromatin with immunolabeling and high-resolution microscopy approaches in the future.
RNA-FISH is another type of oligo-FISH that uses oligonucleotide probes to detect mRNAs with single-molecule resolution and sRNA [92]. By combining single-copy oligonucleotide probes, RNA FISH can be used to detect any kind of RNA, including tRNA. RNA imaging in live cells and 3D combined with immunofluorescence may become a new direction of plant cytogenetic research, providing researchers with a powerful tool to study the spatial and temporal regulation of gene expression in plants. This will expand our understanding of plant gene regulation and development at the molecular level, opening up new avenues for exploring the genetic mechanisms underlying plant growth and adaptation in changing environments.
Live imaging is a novel FISH technique called LiveFISH, which uses oligo probes to target genomic sequences in living cells, and has been developed for imaging telomeric sequences in tobacco (Nicotiana benthamiana) [93,94,95]. By combining CRISPR-mediated LiveFISH with fusion fluorescent protein transgenic approaches, it will be possible to trace defined DNA sequences and proteins in living plant cells simultaneously. This has potential applications to study the dynamics of chromatin during special cell activities such as cell fusion, mitosis, and meiosis. However, oligo-FISH based on chromosome and oligonucleotide synthetic probes remains the cornerstone of many types of FISH. Combined with the above diversified FISH technologies, oligo-FISH will be widely used in plants in the future.

Author Contributions

The topic was conceived and outlined by C.C. and Z.F. The original draft was written by A.H. and H.L., while A.H., H.L., S.S., S.A. and X.W. contributed to writing, reviewing, and editing the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Natural Science Foundation of China (31970525, 32060663), the Opening Foundation of the Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Regions (Ministry of Education) (Guizhou Education Technology 2022-428), and the Cultivating Fund Project of Hubei Hongshan Laboratory (2022hspy002).

Data Availability Statement

This review article does not contain any original data or analyses. All data used in this article were obtained from previously published sources, which are cited appropriately.

Acknowledgments

Our gratitude goes to the two anonymous reviewers who provided critical feedback and valuable suggestions for improving the manuscript.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Jiang, J. Fluorescence in situ hybridization in plants: Recent developments and future applications. Chromosom. Res. 2019, 27, 153–165. [Google Scholar] [CrossRef]
  2. Jiang, J.; Gill, B.S. Nonisotopic in situ hybridization and plant genome mapping: The first 10 years. Genome 1994, 37, 717–725. [Google Scholar] [CrossRef] [PubMed]
  3. Levsky, J.M.; Singer, R.H. Fluorescence in situ hybridization: Past, present and future. J. Cell Sci. 2003, 116, 2833–2838. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  4. Gall, J.G.; Pardue, M.L. Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc. Natl. Acad. Sci. USA 1969, 63, 378–383. [Google Scholar] [CrossRef]
  5. Langer-Safer, P.R.; Levine, M.; Ward, D.C. Immunological method for mapping genes on Drosophila polytene chromosomes (biotin-labeled DNA/anti-biotin/fluorescence microscopy/immunoperoxidase localization). Genetics 1982, 79, 4381–4385. [Google Scholar]
  6. Speicher, M.R.; Carter, N.P. The new cytogenetics: Blurring the boundaries with molecular biology. Nat. Rev. Genet. 2005, 6, 782–792. [Google Scholar] [CrossRef] [PubMed]
  7. Danilova, T.V.; Friebe, B.; Gill, B.S. Single-copy gene Fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat. Chromosoma 2012, 121, 597–611. [Google Scholar] [CrossRef] [Green Version]
  8. Danilova, T.V.; Friebe, B.; Gill, B.S. Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae. Theor. Appl. Genet. 2014, 127, 715–730. [Google Scholar] [CrossRef] [Green Version]
  9. Jiang, J.; Gill, B.S. Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 2006, 49, 1057–1068. [Google Scholar] [CrossRef]
  10. Lysak, M.A.; Fransz, P.F.; Ali, H.B.M.; Schubert, I. Chromosome painting in Arabidopsis thaliana. Plant J. 2001, 28, 689–697. [Google Scholar] [CrossRef]
  11. Braz, G.T.; do Vale Martins, L.; Zhang, T.; Albert, P.S.; Birchler, J.A.; Jiang, J. A universal chromosome identification system for maize and wild Zea species. Chromosom. Res. 2020, 28, 183–194. [Google Scholar] [CrossRef] [PubMed]
  12. Han, Y.; Zhang, T.; Thammapichai, P.; Weng, Y.; Jiang, J. Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics 2015, 200, 771–779. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  13. do Vale Martins, L.; Yu, F.; Zhao, H.; Dennison, T.; Lauter, N.; Wang, H.; Deng, Z.; Thompson, A.; Semrau, K.; Rouillard, J.M.; et al. Meiotic crossovers characterized by haplotype-specific chromosome painting in maize. Nat. Commun. 2019, 10, 4604. [Google Scholar] [CrossRef] [Green Version]
  14. Stenberg, J.; Nilsson, M.; Landegren, U. ProbeMaker: An extensible framework for design of sets of oligonucleotide probes. BMC Bioinform. 2005, 6, 229. [Google Scholar] [CrossRef] [Green Version]
  15. Yilmaz, L.S.; Parnerkar, S.; Noguera, D.R. MathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization. Appl. Environ. Microbiol. 2011, 77, 1118–1122. [Google Scholar] [CrossRef] [Green Version]
  16. Hu, M.; Yang, B.; Cheng, Y.; Radda, J.S.D.; Chen, Y.; Liu, M.; Wang, S. ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization. Sci. Rep. 2020, 10, 22031. [Google Scholar] [CrossRef]
  17. Zhang, T.; Liu, G.; Zhao, H.; Braz, G.T.; Jiang, J. Chorus2: Design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization. Plant Biotechnol. J. 2021, 19, 1967–1978. [Google Scholar] [CrossRef] [PubMed]
  18. Gelali, E.; Girelli, G.; Matsumoto, M.; Wernersson, E.; Custodio, J.; Mota, A.; Schweitzer, M.; Ferenc, K.; Li, X.; Mirzazadeh, R.; et al. iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture. Nat. Commun. 2019, 10, 1636. [Google Scholar] [CrossRef] [Green Version]
  19. Lakhia, R.; Mishra, A.; Patel, V. Manipulation of Renal Gene Expression Using Oligonucleotides. In Methods in Cell Biology; Academic Press: Cambridge, MA, USA, 2019; Volume 154, ISBN 9780128203354. [Google Scholar]
  20. Beliveau, B.J.; Joyce, E.F.; Apostolopoulos, N.; Yilmaz, F.; Fonseka, C.Y.; McCole, R.B.; Chang, Y.; Li, J.B.; Senaratne, T.N.; Williams, B.R.; et al. Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc. Natl. Acad. Sci. USA 2012, 109, 21301–21306. [Google Scholar] [CrossRef]
  21. Yamada, N.A.; Rector, L.S.; Tsang, P.; Carr, E.; Scheffer, A.; Sederberg, M.C.; Aston, M.E.; Ach, R.A.; Tsalenko, A.; Sampas, N.; et al. Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH. Cytogenet. Genome Res. 2011, 132, 248–254. [Google Scholar] [CrossRef] [PubMed]
  22. Tang, S.; Qiu, L.; Xiao, Z.; Fu, S.; Tang, Z. New oligonucleotide probes for ND-FISH analysis to identify barley chromosomes and to investigate polymorphisms of wheat chromosomes. Genes 2016, 7, 118. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  23. Tang, Z.; Yang, Z.; Fu, S. Oligonucleotides replacing the roles of repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 for FISH analysis. J. Appl. Genet. 2014, 55, 313–318. [Google Scholar] [CrossRef] [PubMed]
  24. Bi, Y.; Zhao, Q.; Yan, W.; Li, M.; Liu, Y.; Cheng, C.; Zhang, L.; Yu, X.; Li, J.; Qian, C.; et al. Flexible chromosome painting based on multiplex PCR of oligonucleotides and its application for comparative chromosome analyses in Cucumis. Plant J. 2020, 102, 178–186. [Google Scholar] [CrossRef]
  25. Li, G.; Zhang, T.; Yu, Z.; Wang, H.; Yang, E.; Yang, Z. An efficient Oligo-FISH painting system for revealing chromosome rearrangements and polyploidization in Triticeae. Plant J. 2021, 105, 978–993. [Google Scholar] [CrossRef]
  26. Liu, G.; Zhang, T. Single copy oligonucleotide fluorescence in situ hybridization probe design platforms: Development, application and evaluation. Int. J. Mol. Sci. 2021, 22, 7124. [Google Scholar] [CrossRef]
  27. Thumjamras, S.; Iamtham, S.; Prammanee, S.; de Jong, H. Meiotic analysis and FISH with rDNA and rice BAC probes of the Thai KPS 01-01-25 sugarcane cultivar. Plant Syst. Evol. 2016, 302, 305–317. [Google Scholar] [CrossRef] [Green Version]
  28. Grüning, B.; Dale, R.; Sjamp, A.; Chapman, B.A.; Rowe, J.; Tomkins-Tinch, C.H.; Valieris, R.; Kamp, J. Bioconda: Sustainable and comprehensive software distribution for the life sciences. Nat. Methods 2018, 15, 475–476. [Google Scholar] [CrossRef]
  29. Yu, F.; Huang, Y.; Luo, L.; Li, X.; Wu, J.; Chen, R.; Zhang, M.; Deng, Z. An improved suppression subtractive hybridization technique to develop species-specific repetitive sequences from Erianthus arundinaceus (Saccharum complex). BMC Plant Biol. 2018, 18, 269. [Google Scholar] [CrossRef]
  30. Swigoňová, Z.; Lai, J.; Ma, J.; Ramakrishna, W.; Llaca, V.; Bennetzen, J.L.; Messing, J. Close split of sorghum and maize genome progenitors. Genome Res. 2004, 14, 1916–1923. [Google Scholar] [CrossRef] [Green Version]
  31. Novák, P.; Neumann, P.; Pech, J.; Steinhaisl, J.; MacAs, J. RepeatExplorer: A Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 2013, 29, 792–793. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  32. Beier, S.; Ulpinnis, C.; Schwalbe, M.; Münch, T.; Hoffie, R.; Koeppel, I.; Hertig, C.; Budhagatapalli, N.; Hiekel, S.; Pathi, K.M.; et al. Kmasker plants—A tool for assessing complex sequence space in plant species. Plant J. 2020, 102, 631–642. [Google Scholar] [CrossRef] [Green Version]
  33. Hou, L.; Xu, M.; Zhang, T.; Xu, Z.; Wang, W.; Zhang, J.; Yu, M.; Ji, W.; Zhu, C.; Gong, Z.; et al. Chromosome painting and its applications in cultivated and wild rice. BMC Plant Biol. 2018, 18, 110. [Google Scholar] [CrossRef] [Green Version]
  34. Beliveau, B.J.; Joyce, E.F.; Apostolopoulosa, N.; Yilmaza, F.; Fonseka, C.Y.; McCole, R.B.; Chang, Y.; Li, J.B.; Senaratne, T.N.; Williams, B.R.; et al. Oligopaints: Highly efficient, bioinformatically designed probes for fluorescence in situ hybridization. Epigenetics Chromatin 2013, 6, P5. [Google Scholar] [CrossRef]
  35. Braz, G.T.; He, L.; Zhao, H.; Zhang, T.; Semrau, K.; Rouillard, J.M.; Torres, G.A.; Jiang, J. Comparative oligo-FISH mapping: An efficient and powerful methodology to reveal karyotypic and chromosomal evolution. Genetics 2018, 208, 513–523. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  36. Meng, Z.; Han, J.; Lin, Y.; Zhao, Y.; Lin, Q.; Ma, X.; Wang, J.; Zhang, M.; Zhang, L.; Yang, Q.; et al. Characterization of a Saccharum spontaneum with a basic chromosome number of x = 10 provides new insights on genome evolution in genus Saccharum. Theor. Appl. Genet. 2020, 133, 187–199. [Google Scholar] [CrossRef]
  37. Piperidis, N.; D’Hont, A. Sugarcane genome architecture decrypted with chromosome-specific oligo probes. Plant J. 2020, 103, 2039–2051. [Google Scholar] [CrossRef] [PubMed]
  38. Liu, X.; Sun, S.; Wu, Y.; Zhou, Y.; Gu, S.; Yu, H.; Yi, C.; Gu, M.; Jiang, J.; Liu, B.; et al. Dual-color oligo-FISH can reveal chromosomal variations and evolution in Oryza species. Plant J. 2020, 101, 112–121. [Google Scholar] [CrossRef] [PubMed]
  39. Zou, Y.; Wan, L.; Luo, J.; Tang, Z.; Fu, S. FISH landmarks reflecting meiotic recombination and structural alterations of chromosomes in wheat (Triticum aestivum L.). BMC Plant Biol. 2021, 21, 167. [Google Scholar] [CrossRef] [PubMed]
  40. Song, X.; Song, R.; Zhou, J.; Yan, W.; Zhang, T.; Sun, H.; Xiao, J.; Wu, Y.; Xi, M.; Lou, Q.; et al. Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L. Chromosom. Res. 2020, 28, 171–182. [Google Scholar] [CrossRef] [PubMed]
  41. Lang, T.; Li, G.; Wang, H.; Yu, Z.; Chen, Q.; Yang, E.; Fu, S.; Tang, Z.; Yang, Z. Physical location of tandem repeats in the wheat genome and application for chromosome identification. Planta 2019, 249, 663–675. [Google Scholar] [CrossRef]
  42. Tang, S.; Tang, Z.; Qiu, L.; Yang, Z.; Li, G.; Lang, T.; Zhu, W.; Zhang, J.; Fu, S. Developing new oligo probes to distinguish specific chromosomal segments and the A, B, D genomes of wheat (Triticum aestivum L.) using ND-FISH. Front. Plant Sci. 2018, 9, 01104. [Google Scholar] [CrossRef]
  43. Xiao, Z.; Tang, S.; Qiu, L.; Tang, Z.; Fu, S. Oligonucleotides and ND-fish displaying different arrangements of tandem repeats and identification of dasypyrum villosum chromosomes in wheat backgrounds. Molecules 2017, 22, 973. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  44. Feng, Z.; Zhang, M.; Liu, X.; Liang, D.; Liu, X.; Hao, M.; Liu, D.; Ning, S.; Yuan, Z.; Jiang, B.; et al. FISH karyotype comparison between Ab- and A-genome chromosomes using oligonucleotide probes. J. Appl. Genet. 2020, 61, 313–322. [Google Scholar] [CrossRef]
  45. Xi, W.; Tang, Z.; Tang, S.; Yang, Z.; Luo, J.; Fu, S. New ND-FISH-positive oligo probes for identifying thinopyrum chromosomes in wheat backgrounds. Int. J. Mol. Sci. 2019, 20, 2031. [Google Scholar] [CrossRef] [Green Version]
  46. Albert, P.S.; Zhang, T.; Semrau, K.; Rouillard, J.M.; Kao, Y.H.; Wang, C.J.R.; Danilova, T.V.; Jiang, J.; Birchler, J.A. Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. Proc. Natl. Acad. Sci. USA 2019, 116, 1679–1685. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  47. Kato, A.; Lamb, J.C.; Birchler, J.A. Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc. Natl. Acad. Sci. USA 2004, 101, 13554–13559. [Google Scholar] [CrossRef] [PubMed]
  48. He, L.; Braz, G.T.; Torres, G.A.; Jiang, J. Chromosome painting in meiosis reveals pairing of specific chromosomes in polyploid Solanum species. Chromosoma 2018, 127, 505–513. [Google Scholar] [CrossRef]
  49. Fu, S.; Chen, L.; Wang, Y.; Li, M.; Yang, Z.; Qiu, L.; Yan, B.; Ren, Z.; Tang, Z. Oligonucleotide probes for ND-FISH analysis to identify rye and wheat chromosomes. Sci. Rep. 2015, 5, 10552. [Google Scholar] [CrossRef] [Green Version]
  50. Aliyeva-Schnorr, L.; Stein, N.; Houben, A. Collinearity of homoeologous group 3 chromosomes in the genus Hordeum and Secale cereale as revealed by 3H-derived FISH analysis. Chromosom. Res. 2016, 24, 231–242. [Google Scholar] [CrossRef]
  51. He, Q.; Cai, Z.; Hu, T.; Liu, H.; Bao, C.; Mao, W.; Jin, W. Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.). BMC Plant Biol. 2015, 15, 105. [Google Scholar] [CrossRef] [Green Version]
  52. Yu, F.; Chai, J.; Li, X.; Yu, Z.; Yang, R.; Ding, X.; Wang, Q.; Wu, J.; Yang, X.; Deng, Z. Chromosomal characterization of tripidium arundinaceum revealed by oligo-fish. Int. J. Mol. Sci. 2021, 22, 8539. [Google Scholar] [CrossRef]
  53. Yu, F.; Zhao, X.; Chai, J.; Ding, X.; Li, X.; Huang, Y.; Wang, X.; Wu, J.; Zhang, M.; Yang, Q.; et al. Chromosome-specific painting unveils chromosomal fusions and distinct allopolyploid species in the Saccharum complex. New Phytol. 2022, 233, 1953–1965. [Google Scholar] [CrossRef] [PubMed]
  54. Han, Y.; Qu, M.; Li, K.; Han, Y.; Chen, L.; Li, Z. Integrated Karyotyping of Woodland Strawberry (Fragaria vesca) with Oligopaint FISH Probes. Cytogenet. Genome Res. 2018, 153, 158–164. [Google Scholar] [CrossRef]
  55. Qu, M.; Zhang, L.; Li, K.; Sun, J.; Li, Z.; Han, Y. Karyotypic stability of Fragaria (strawberry) species revealed by cross-species chromosome painting. Chromosom. Res. 2021, 29, 285–300. [Google Scholar] [CrossRef] [PubMed]
  56. Šimoníková, D.; Němečková, A.; Karafiátová, M.; Uwimana, B.; Swennen, R.; Doležel, J.; Hřibová, E. Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana (Musa Spp.). Front. Plant Sci. 2019, 10, 01503. [Google Scholar] [CrossRef] [Green Version]
  57. do Vale Martins, L.; de Oliveira Bustamante, F.; da Silva Oliveira, A.R.; da Costa, A.F.; de Lima Feitoza, L.; Liang, Q.; Zhao, H.; Benko-Iseppon, A.M.; Muñoz-Amatriaín, M.; Pedrosa-Harand, A.; et al. BAC- and oligo-FISH mapping reveals chromosome evolution among Vigna angularis, V. unguiculata, and Phaseolus vulgaris. Chromosoma 2021, 130, 133–147. [Google Scholar] [CrossRef]
  58. Du, P.; Fu, L.; Wang, Q.; Lang, T.; Liu, H.; Han, S.; Li, C.; Huang, B.; Qin, L.; Dai, X.; et al. Development of Oligo-GISH kits for efficient detection of chromosomal variants in peanut. Crop J. 2023, 11, 238–246. [Google Scholar] [CrossRef]
  59. Yang, S.; Zeng, K.; Chen, K.; Wu, J.; Wang, Q.; Li, X.; Deng, Z.; Huang, Y.; Huang, F.; Chen, R.; et al. Chromosome transmission in BC 4 progenies of intergeneric hybrids between Saccharum spp. and Erianthus arundinaceus (Retz.) Jeswiet. Sci. Rep. 2019, 9, 2528. [Google Scholar] [CrossRef] [Green Version]
  60. Luo, X.; He, Z.; Liu, J.; Wu, H.; Gong, X. FISH Mapping of Telomeric and Non-Telomeric (AG3T3)3 Reveal the Chromosome Numbers and Chromosome Rearrangements of 41 Woody Plants. Genes 2022, 13, 1239. [Google Scholar] [CrossRef]
  61. Wang, L.; Wang, Y.; Zhang, J.; Feng, Y.; Chen, Q.; Liu, Z.S.; Liu, C.L.; He, W.; Wang, H.; Yang, S.F.; et al. Comparative Analysis of Transposable Elements and the Identification of Candidate Centromeric Elements in the Prunus Subgenus Cerasus and Its Relatives. Genes 2022, 13, 641. [Google Scholar] [CrossRef]
  62. He, Z.; Zhang, W.; Luo, X.; Huan, J. Five Fabaceae Karyotype and Phylogenetic Relationship Analysis Based on Oligo-FISH for 5S rDNA and (AG3T3)3. Genes 2022, 13, 768. [Google Scholar] [CrossRef] [PubMed]
  63. He, L.; Zhao, H.; He, J.; Yang, Z.; Guan, B.; Chen, K.; Hong, Q.; Wang, J.; Liu, J.; Jiang, J. Extraordinarily conserved chromosomal synteny of Citrus species revealed by chromosome-specific painting. Plant J. 2020, 103, 2225–2235. [Google Scholar] [CrossRef]
  64. Chen, L.; Su, D.; Sun, J.; Li, Z.; Han, Y. Development of a set of chromosome-specific oligonucleotide markers and karyotype analysis in the Japanese morning glory Ipomoea nil. Sci. Hortic. 2020, 273, 109633. [Google Scholar] [CrossRef]
  65. Xin, H.; Zhang, T.; Han, Y.; Wu, Y.; Shi, J.; Xi, M.; Jiang, J. Chromosome painting and comparative physical mapping of the sex chromosomes in Populus tomentosa and Populus deltoides. Chromosoma 2018, 127, 313–321. [Google Scholar] [CrossRef] [PubMed]
  66. Xin, H.; Zhang, T.; Wu, Y.; Zhang, W.; Zhang, P.; Xi, M.; Jiang, J. An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting. Plant J. 2020, 101, 253–264. [Google Scholar] [CrossRef] [PubMed]
  67. Bielski, W.; Książkiewicz, M.; Šimoníková, D.; Hřibová, E.; Susek, K.; Naganowska, B. The puzzling fate of a lupin chromosome revealed by reciprocal oligo-fish and bac-fish mapping. Genes 2020, 11, 1489. [Google Scholar] [CrossRef]
  68. He, J.; Zhao, Y.; Zhang, S.; He, Y.; Jiang, J.; Chen, S.; Fang, W.; Guan, Z.; Liao, Y.; Wang, Z.; et al. Uneven Levels of 5S and 45S rDNA Site Number and Loci Variations across Wild Chrysanthemum Accessions. Genes 2022, 13, 894. [Google Scholar] [CrossRef]
  69. Song, Z.; Dai, S.; Bao, T.; Zuo, Y.; Xiang, Q.; Li, J.; Liu, G.; Yan, Z. Analysis of Structural Genomic Diversity in Aegilops umbellulata, Ae. markgrafii, Ae. comosa, and Ae. uniaristata by Fluorescence In Situ Hybridization Karyotyping. Front. Plant Sci. 2020, 11, 710. [Google Scholar] [CrossRef]
  70. Yu, Z.; Wang, H.; Xu, Y.; Li, Y.; Lang, T.; Yang, Z.; Li, G. Characterization of chromosomal rearrangement in new wheat—Thinopyrum intermedium addition lines carrying thinopyrum—Specific grain hardness genes. Agronomy 2019, 9, 18. [Google Scholar] [CrossRef] [Green Version]
  71. Xie, J.; Zhao, Y.; Yu, L.; Liu, R.; Dou, Q. Molecular karyotyping of Siberian wild rye (Elymus sibiricus L.) with oligonucleotide fluorescence in situ hybridization (FISH) probes. PLoS ONE 2020, 15, e0227208. [Google Scholar] [CrossRef]
  72. Meng, Z.; Zhang, Z.; Yan, T.; Lin, Q.; Wang, Y.; Huang, W.; Huang, Y.; Li, Z.; Yu, Q.; Wang, J.; et al. Comprehensively characterizing the cytological features of saccharum spontaneum by the development of a complete set of chromosome-specific oligo probes. Front. Plant Sci. 2018, 871, 01624. [Google Scholar] [CrossRef] [Green Version]
  73. Amosova, A.V.; Bolsheva, N.L.; Samatadze, T.E.; Twardovska, M.O.; Zoshchuk, S.A.; Andreev, I.O.; Badaeva, E.D.; Kunakh, V.A.; Muravenko, O.V. Molecular cytogenetic analysis of Deschampsia antarctica Desv. (Poaceae), Maritime Antarctic. PLoS ONE 2015, 10, e0138878. [Google Scholar] [CrossRef] [PubMed]
  74. Cheng, M.; Li, X.; Cui, H.; Sun, H.; Deng, T.; Song, X.; Song, R.; Wang, T.; Wang, Z.; Wang, H.; et al. FISH-based “pan” and “core” karyotypes reveal genetic diversification of Roegneria ciliaris. J. Genet. Genom. 2023, 50, 135–138. [Google Scholar] [CrossRef] [PubMed]
  75. Zhou, H.C.; Pellerin, R.J.; Waminal, N.E.; Yang, T.J.; Kim, H.H. Pre-labelled oligo probe-FISH karyotype analyses of four Araliaceae species using rDNA and telomeric repeat. Genes Genom. 2019, 41, 839–847. [Google Scholar] [CrossRef] [PubMed]
  76. Hoang, P.T.N.; Rouillard, J.M.; Macas, J.; Kubalová, I.; Schubert, V.; Schubert, I. Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds. Chromosoma 2021, 130, 15–25. [Google Scholar] [CrossRef]
  77. Song, S.; Liu, H.; Miao, L.; He, L.; Xie, W.; Lan, H.; Yu, C.; Yan, W.; Wu, Y.; Wen, X.P.; et al. Molecular cytogenetic map visualizes the heterozygotic genome and identifies translocation chromosomes in Citrus sinensis. J. Genet. Genom. 2023, 50, 410–421. [Google Scholar] [CrossRef]
  78. Song, S.; He, L.; You, X.; Zheng, D.; Tang, Y.; Chen, C. Molecular cytogenetic maps provide new insights into the differences between hybrid Citrus microcarpa and lemons. Sci. Hortic. 2023, 321, 112307. [Google Scholar] [CrossRef]
  79. Wang, T.; Wang, B.; Hua, X.; Tang, H.; Zhang, Z.; Gao, R.; Qi, Y.; Zhang, Q.; Wang, G.; Yu, Z.; et al. A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus. Nat. Plants 2023, 9, 554–571. [Google Scholar] [CrossRef]
  80. Badaeva, E.D.; Amosova, A.V.; Muravenko, O.V.; Samatadze, T.E.; Chikida, N.N.; Zelenin, A.V.; Friebe, B.; Gill, B.S. Genome differentiation in Aegilops. 3. Evolution of the D-genome cluster. Plant Syst. Evol. 2002, 231, 163–190. [Google Scholar] [CrossRef]
  81. Paterson, A.H.; Bowers, J.E.; Burow, M.D.; Draye, X.; Elsik, C.G.; Jiang, C.X.; Katsar, C.S.; Lan, T.H.; Lin, Y.R.; Ming, R.; et al. Comparative genomics of plant chromosomes. Plant Cell 2000, 12, 1523–1539. [Google Scholar] [CrossRef]
  82. Zhang, X.; Meng, Z.; Han, J.; Khurshid, H.; Esh, A.; Hasterok, R.; Wang, K. Characterization of meiotic chromosome behavior in the autopolyploid Saccharum spontaneum reveals preferential chromosome pairing without distinct DNA sequence variation. Crop J. 2023; in press. [Google Scholar] [CrossRef]
  83. Zhao, Q.; Meng, Y.; Wang, P.; Qin, X.; Cheng, C.; Zhou, J.; Yu, X.; Li, J.; Lou, Q.; Jahn, M.; et al. Reconstruction of ancestral karyotype illuminates chromosome evolution in the genus Cucumis. Plant J. 2021, 107, 1243–1259. [Google Scholar] [CrossRef] [PubMed]
  84. Beliveau, B.J.; Boettiger, A.N.; Avendaño, M.S.; Jungmann, R.; McCole, R.B.; Joyce, E.F.; Kim-Kiselak, C.; Bantignies, F.; Fonseka, C.Y.; Erceg, J.; et al. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat. Commun. 2015, 6, 8147. [Google Scholar] [CrossRef]
  85. Boettiger, A.; Murphy, S. Advances in Chromatin Imaging at Kilobase-Scale Resolution. Trends Genet. 2020, 36, 273–287. [Google Scholar] [CrossRef] [PubMed]
  86. Nir, G.; Farabella, I.; Pérez Estrada, C.; Ebeling, C.G.; Beliveau, B.J.; Sasaki, H.M.; Lee, S.H.; Nguyen, S.C.; McCole, R.B.; Chattoraj, S.; et al. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet. 2018, 14, 1007872. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  87. Boyle, S.; Rodesch, M.J.; Halvensleben, H.A.; Jeddeloh, J.A.; Bickmore, W.A. Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis. Chromosom. Res. 2011, 19, 901–909. [Google Scholar] [CrossRef] [Green Version]
  88. D’Hont, A. Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana. Cytogenet. Genome Res. 2005, 109, 27–33. [Google Scholar] [CrossRef]
  89. Tao, Y.; Zhou, X.; Sun, L.; Lin, D.; Cai, H.; Chen, X.; Zhou, W.; Yang, B.; Hu, Z.; Yu, J.; et al. Highly efficient and robust π-FISH rainbow for multiplexed in situ detection of diverse biomolecules. Nat. Commun. 2023, 14, 443. [Google Scholar] [CrossRef]
  90. Howe, E.S.; Murphy, S.P.; Bass, H.W. Three-dimensional acrylamide fluorescence in situ hybridization for plant cells. In Plant Meiosis: Methods and Protocols; Springer: Berlin/Heidelberg, Germany, 2013; Volume 990, ISBN 9781627033329. [Google Scholar]
  91. Koláčková, V.; Perničková, K.; Vrána, J.; Duchoslav, M.; Jenkins, G.; Phillips, D.; Turkosi, E.; Šamajová, O.; Sedlářová, M.; Šamaj, J.; et al. Nuclear disposition of alien chromosome introgressions into wheat and rye using 3D-FISH. Int. J. Mol. Sci. 2019, 20, 4143. [Google Scholar] [CrossRef] [Green Version]
  92. Huang, J.; Wang, C.; Wang, H.; Lu, P.; Zheng, B.; Ma, H.; Copenhaver, G.P.; Wanga, Y. Meiocyte-specific and at SPO11-1-dependent small RNAs and their association with meiotic gene expression and recombination. Plant Cell 2019, 31, 444–464. [Google Scholar] [CrossRef] [Green Version]
  93. Huang, X.; Huang, S.; Han, B.; Li, J. The integrated genomics of crop domestication and breeding. Cell 2022, 185, 2828–2839. [Google Scholar] [CrossRef]
  94. Geng, Y.; Pertsinidis, A. Simple and versatile imaging of genomic loci in live mammalian cells and early pre-implantation embryos using CAS-LiveFISH. Sci. Rep. 2021, 11, 12220. [Google Scholar] [CrossRef] [PubMed]
  95. Wang, H.; Wang, H.; Nakamura, M.; Abbott, T.R.; Zhao, D.; Luo, K.; Yu, C.; Cindy, M.; Lo, A.; Daley, T.P.; et al. CRISPR-mediated live imaging of genome editing and transcription. Science 2019, 365, 1301–1305. [Google Scholar] [CrossRef] [PubMed]
Plants 12 02816 g001 550
Figure 1. The oligo search, filtering, and selecting of potential oligos in the genome using the Chorus2 pipeline.
Figure 1. The oligo search, filtering, and selecting of potential oligos in the genome using the Chorus2 pipeline.
Plants 12 02816 g001
Plants 12 02816 g002 550
Figure 2. The schematic diagram represents oligo probe library enrichment, PCR amplification for primer binding, fluorophore labeling for de novo probe synthesis, and FISH experiment being performed with developed oligo probes.
Figure 2. The schematic diagram represents oligo probe library enrichment, PCR amplification for primer binding, fluorophore labeling for de novo probe synthesis, and FISH experiment being performed with developed oligo probes.
Plants 12 02816 g002
Plants 12 02816 g003 550
Figure 3. Applications of oligo-FISH in plants.
Figure 3. Applications of oligo-FISH in plants.
Plants 12 02816 g003
Table
Table 1. The applications of both oligo-FISH and traditional FISH techniques on economical plants are summarized.
Table 1. The applications of both oligo-FISH and traditional FISH techniques on economical plants are summarized.
Serial No.SpeciesFISH-ProbeApplicationSignal EffectCellRef.
1.Rice
(Oryza sativa)		Two specific oligo and 5S-rDNA-based probesKaryotyping, detection of chromosomal variations, and chromosome translocation, mainly transpositionStrongMetaphase and pachytene[38]
Chromosome-9-specific oligo pools, CentO repetitive, and 45S-rDNA-based probesChromosome identification and translocation detectionStrongInterphase, prometaphase, premeiotic interphase, zygotene, pachytene, and microspore[33]
2.Wheat
(Triticum aestivum)		Specific oligo probes, named pTa-535, oligo-18, pTa-275, pSc119.2, SC5A-479, and SC5A-527, derived from both single-copy and tandem repeatsKaryotyping, detection of meiotic recombination, and structural alterationsMixedMetaphase[39]
Synthesized oligo probe library contains 27,392 oligo poolsChromosome identification and detection of chromosomal rearrangementsMixedMetaphase[40]
Twenty specific oligo probes with lengths of 20–60bpChromosome identification, karyotyping, and chromosomal translocation detectionMixedMetaphase[41]
One hundred and twenty specific oligo probes based on new tandem repeatsChromosomal mapping and distinguishing A-, B-, and D-genome chromosomesMixedMetaphase[42]
Repetitive oligo probesChromosomal mapping and distinguishing chromosomes of wheat (T. aestivum)-D. villosum amphiploidMixedMetaphase[43]
3.Wheat
(Triticum boeoticum)		Specific oligo probes, named Oligo-pTa535-HM, Oligo-pSc119.2-HM, (ACT)7, (CTT)7, (GAA)7, Oligo-pTa713,,(CAG)7, and (CAC)7Chromosome identification and comparison between Ab- and A-genome chromosomesMixedMetaphase[44]
4.Wheat
(Triticum aestivum L.)-Th. Ponticum, Th. intermedium partial amphiploid lines		Two specific oligo probes, named oligo-B11 and oligo-pThp3.93Chromosome mapping, discrimination of chromosomes of Th. elongatum, Th. intermedium, and Th. ponticum in wheat backgrounds and chromosomal translocation detectionMixedMetaphase[45]
5.Maize
(Zea mays)		Two oligo bar codesChromosome identification, karyotyping, and chromosomal translocation detectionMixedMetaphase[11]
Chromosome-1-to-10-specific unique-sequence-based oligo pools and repetitive-sequence-based probe named CentC Chromosome identification and rearrangement analysesMixedMetaphase, pachytene, and interphase[46]
Oligo probes specific to chromosome 10 haplotypeChromosome painting and visualization of COs (cross overs)MixedMetaphase[13]
Microsatellite, subtelomeric, 5S rRNA, Cent4, CentC, knob, NOR, pMTY9ER-telomere-associated sequence, and tandem-repeated DNA sequence 1(TR-1)-based repetitive probesChromosome identification, mapping, karyotyping, chromosomal structure, and behavior analysesMixedPachytene, late prophase I, and metaphase I[47]
6.Potato
(Solanum tuberosum)		Single-copy DNA sequence-based oligo probesIdentification of individual chromosomes, both diploid and polyploid of potato, homologous chromosomes of tomato (S. lycopersicum) and eggplant (S. melongena), karyotyping and translocation detectionMixedMetaphase[35]
Four chromosome-specific oligo probesKaryotyping, meiotic pairing, and translocation detectionMixedMetaphase, early metaphase, early leptotene, late leptotene, zygotene, pachytene, diplotene, and diakinesis[48]
7.Rye
(Secale cereale)		Oligo probes, named Oligo-1162, pSc200, and pSc250Detection of rye chromosomes from wheat (Triticum aestivum) backgroundStrongMetaphase[49]
8.Wheat×rye hybrid (Triticum aestivum × Secale cereale)Nine oligo probes with specific repeat sequencesIdentification of individual chromosomes and karyotypingStrongMetaphase[23]
9.Barely
(Hordeum vulgare)		Seven chromosome-specific oligo poolsChromosomal mapping of wheat and barley, karyotyping of other Triticeae, homologous and non-homologous chromosomal rearrangements in Triticeae, and wheat–barley synteny identificationStrongMetaphase[25]
BAC and 5S rDNA probesIdentification of individual chromosomes and karyotypingStrongMetaphase and pachytene[50]
10.Brassica
(Brassica rapa)		Three satellite repeat sequences from radish (R. sativus)-based probesChromosomal mappingWeakMetaphase[51]
11.Radish
(Raphanus sativus)		Three satellite repeat sequences, and 45S- and 5S-rDNA-based probesKaryotypingMixedMetaphase[51]
12.Cucumis
(Cucumis sativus)		Chromosome-1-and-4-specific oligo probesChromosome identification,
homoeologous relationship detection among cucumber, C. hystrix, and C. melo chromosomes		StrongMetaphase and pachytene[24]
Chromosomal segments and arm-specific oligo poolsChromosome identification, chromosomal pairing, rearrangement, and evolution analysesStrongMetaphase, zygotene, and pachytene[12]
13.Sugarcane
(Tripidium arundinaceum)		Maize chromosome painting probes (MCPs), 5S rDNA, and 35S rDNAIdentification of chromosome and karyotypingMixedMetaphase[52]
14Sugarcane
(Saccharum officinarum)		Chromosome-1-to-10-specific oligo poolsIdentification of chromosomes, novel cytotypes, and chromosomal rearrangement analysesMixedMetaphase[53]
Chromosome-specific oligo probesChromosomal rearrangements, karyotyping, and translocation detectionStrongMetaphase[37]
15.Strawberry
(Fragaria vesca)		Chromosome-specific
bulked oligo probes, and 45S and 5S rDNA probes		Identification of chromosomes,
chromosomal mapping, and karyotyping		MixedMetaphase[54,55]
16.Banana
(Musa spp.)		Nineteen chromosomes/chromosome-arm-specific oligo
pools and 45S rDNA probes		Identification of chromosomes,
molecular karyotyping, and evolution analyses		MixedMetaphase and pachytene[56]
17.Beans
(Phaseolus vulgaris,
Vigna angularis,
Vigna unguiculata)		Two oligo probes named Pv2 and Pv3, BAC and 35S rDNA probesIdentification of chromosomes, karyotyping, chromosomal rearrangements, evolution, cytogenetics maps, and syntonic relationship analysesMixedMetaphase[57]
18.Peanut
(Arachis hypogaea)		Subgenome-specific interspersed repeat (IR) oligo probesIdentification of chromosomes, genomic relationships, and chromosomal variant analysesStrongMetaphase[58]
19.Saccharum spp. ×
Erianthus arundinaceus hybrid		EaHN92 and HN92-105 (E. arundinaceus) genomic DNA sequence-based oligo probesIdentification of chromosomes and chromosome transmission detectionStrongMetaphase[59]
20.Buckthorn
(Hippophaë rhamnoides)		Oligo probes specific to (AG3T3)3 repetitive sequences, 5S rDNA, and (TTG)6 repetitive-sequence-based probesChromosome identification and karyotypingStrongMetaphase and anaphase[60]
21.Sour cherry
(Prunus
Cerasus)		Oligo probes from Arabidopsis telomere repetitive sequence, and centromere repetitive-sequence-basedChromosomal mapping and
karyotyping		MixedMetaphase[61]
22.Fabaceae
(Robinia pseudoacacia,
R. pseudoacacia, R. pseudoacacia,
Styphnolobium japonicum,
Amorpha fruticose)		Two specific oligo probes,
repeat sequence (AG3T3)3, and 5S rDNA-based probes		Chromosome identification and karyotypingStrongMetaphase[62]
Table
Table 2. The applications of both oligo-FISH and traditional FISH techniques on horticultural plants are summarized.
Table 2. The applications of both oligo-FISH and traditional FISH techniques on horticultural plants are summarized.
Serial No.SpeciesFISH-ProbeApplicationSignal EffectCellRef.
1.Citrus (Citrus maxima)Nine chromosome-specific oligo probes, repeats, and 45s- and 5S-rDNA-based probesIdentification of chromosomes, karyotyping, and chromosomal syntonic relationship analysesMixedMetaphase[63]
2.Japanese morning glory (Ipomoea nil)Four specific oligo probes, 45s- and 5S-rDNA-based probesIdentification of chromosomes, pseudochromosomes, karyotyping, chromosomal variation, and evolution analysesMixedMetaphase[64]
3.Poplar
(Populus trichocarpa)		Oligo probes specific to chromosome 19Chromosome painting, mapping, and chromosomal pairing detectionMixedMetaphase and pachytene[65]
Complete set of 19 chromosome painting probesIdentification of chromosomes, karyotyping, chromosome pairing, collinearity, and evolution analysesMixedMetaphase and pachytene[66]
4.Lupin
(Lupinus)		Oligo probes based on chromosome-arm-specific and BAC probesKaryotyping, chromosome evolution, and translocation detectionMixedMetaphase[67]
5.Chrysanthemum
(Chrysanthemum nankingense, C. lavandulifolium, C. dichrum, C. indicum cv. Henan, C. indicum cv. Fujian,
C. indicum cv. Hubei, C. potentilloides, and C. rhombifolium)		Specific oligo probes, and 5S- and 45S-rDNA-based probesChromosomal mapping and
karyotyping		StrongInterphase nuclei and metaphase[68]
Table
Table 3. The applications of both oligo-FISH and traditional FISH techniques on flowering plants and grass species are summarized.
Table 3. The applications of both oligo-FISH and traditional FISH techniques on flowering plants and grass species are summarized.
Serial No.SpeciesFISH-ProbeApplicationSignal EffectCellRef.
1.Aegilops
(Aegilops
umbellulata,
Aegilops markgrafii,
Aegilops comosa,
Aegilops uniaristata)		Oligo probes, named pSc119.2 and pTa71, in combination with (AAC)5, (ACT)7, and (CTT)12 repetitive sequencesChromosomal variation and karyotypingMixedMetaphase[69]
2.Wheatgrasses
(Thinopyrum intermedium)		Specific oligo probes and 5S rDNAIdentification of chromosomes and karyotypingStrongMetaphase[70]
3.Siberian wild rye (Elymus sibiricus)Two specific oligo probes, repeats, and rDNA probesIdentification of chromosomes,
Karyotyping, and ideogram constructing		MixedMetaphase[71]
4.Wild sugarcane
(Saccharum spontaneum)		Chromosome-specific oligo barcodeChromosome distinguishing, karyotyping, and rearrangement analysesStrongMetaphase[36]
Seventeen oligo barcodes, sorghum-derived oligo probes, 45S- and 5S-rDNA-based probesChromosome identification,
Karyotyping, and chromosomal rearrangement analyses		StrongMetaphase[72]
5.Antarctic hairgrass
(Deschampsia antarctica Desv.)		Repeated DNA, 45s- and 5S-rDNA-based probesIdentification of chromosomes and karyotypingStrongMetaphase[73]
6.Grass
(Roegneria ciliaris)		Oligo multiplexing probesChromosome identification and identification of pan and core karyotypingStrongMetaphase[74]
7.Araliaceae5S-, 45S-rDNA-, and
telomeric-repeat-based probes		Identification of chromosomes and karyotypingStrongMetaphase[75]
8.Duckweeds (Lemnaceae)Chromosome-specific oligo probes and BAC probesIdentification of chromosomes, chromosomal rearrangement, and evolution analysesMixedMetaphase[76]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Harun, A.; Liu, H.; Song, S.; Asghar, S.; Wen, X.; Fang, Z.; Chen, C. Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants. Plants 2023, 12, 2816. https://doi.org/10.3390/plants12152816

AMA Style

Harun A, Liu H, Song S, Asghar S, Wen X, Fang Z, Chen C. Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants. Plants. 2023; 12(15):2816. https://doi.org/10.3390/plants12152816

Chicago/Turabian Style

Harun, Arrashid, Hui Liu, Shipeng Song, Sumeera Asghar, Xiaopeng Wen, Zhongming Fang, and Chunli Chen. 2023. "Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants" Plants 12, no. 15: 2816. https://doi.org/10.3390/plants12152816

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop