Chromosome painting and its applications in cultivated and wild rice

Hou, Lili; Xu, Meng; Tao, Zhang; Xu, Zhihao; Wang, Weiyun; Zhang, Jianxiang; Yu, Meimei; Ji, Wen T.; Zhu, Cenwen; Gong, Zhiyun; Gu, Minghong; Jiang, Jiming; Yu, Hengxiu

doi:10.1186/s12870-018-1325-2

Cited by 48 publications

(32 citation statements)

References 58 publications

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“…Chromosome painting allows the identification and tracking of the target chromosome at different stages of mitosis and meiosis (Han et al, 2015). Oligo-based chromosome painting probes have been developed in an increasing number of plant species (Han et al, 2015;Qu et al, 2017;Braz et al, 2018;He et al, 2018;Hou et al, 2018;Meng et al, 2018;Albert et al, 2019), and have been used in various cytogenetic and genome studies (Jiang, 2019).…”

Section: Introductionmentioning

confidence: 99%

An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting

Xin

Zhang

et al. 2019

The Plant Journal

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Summary The karyotype represents the basic genetic make‐up of a eukaryotic species. Comparative cytogenetic analysis of related species based on individually identified chromosomes has been conducted in only a few plant groups and not yet in woody plants. We have developed a complete set of 19 chromosome painting probes based on the reference genome of the model woody plant Populus trichocarpa. Using sequential fluorescence in situ hybridization we were able to identify all poplar chromosomes in the same metaphase cells, which led to the development of poplar karyotypes based on individually identified chromosomes. We demonstrate that five Populus species, belonging to five different sections within Populus, have maintained a remarkably conserved karyotype. No inter‐chromosomal structural rearrangements were observed on any of the 19 chromosomes among the five species. Thus, the chromosomal synteny in Populus has been remarkably maintained after nearly 14 million years of divergence. We propose that the karyotypes of woody species are more stable than those of herbaceous plants since it may take a longer period of time for woody plants to fix chromosome number or structural variants in natural populations.

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Section: Introductionmentioning

confidence: 99%

An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting

Xin

Zhang

et al. 2019

The Plant Journal

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“…One of the main concerns in chromosome painting is to produce a sufficiently complex pool of probe sequences, which results in a suitable painting along the entire length of the target chromosome (Christian et al, 1999;Yang et al, 2016). For a long time, chromosome painting through CISS hybridization with probes obtained by microdissection was not achievable in plant species (Fuchs et al, 1996;Lysak and Mandáková, 2013;Hou et al, 2018). The main constraint to the success in this technique was the inefficient blocking of dispersed repetitive sequences, which are characteristic of plant genomes (Fuchs et al, 1996).…”

Section: Discussionmentioning

confidence: 99%

“…In addition, the painting technique involved the application of a pool of BAC clones as probe, allowing to enrich the probe with low-copy sequences (Lysak et al, 2001(Lysak et al, , 2003. Nonetheless, chromosome painting using DNA probes from flow-sorted or microdissected chromosomes, even associated to the CISS hybridization, has still failed to yield satisfactory results in plant species (Hou et al, 2018). Thus, it is mainly restricted to B or Y chromosomes, most likely due to the presence of chromosome-specific repetitive sequences in these chromosomes, rather than low-or single-copy sequences (Houben et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

Plant Chromosome-Specific Probes by Microdissection of a Single Chromosome: Is That a Reality?

et al. 2020

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Painting plant chromosomes through chromosomal in situ suppression (CISS) hybridization has long been considered impracticable. Seeking to build specific and complex probes from a single microdissected chromosome, we employed human chromosomes as models to standardize all the necessary steps for application in plants. Human metaphases were used to define the adequate conditions for microdissection, chromosome DNA amplification and labeling through degenerate oligonucleotideprimed PCR, and in situ hybridization stringency. Subsequently, these methodologies were applied in the plant species Zea mays (chromosome 1) and Capsicum annuum (chromosome 7 or 8). The high quality of human and plant cytogenetic preparations and the meticulous standardization of each step, especially the most critical onesmicrodissection and first round of DNA amplification -were crucial to eliminate the signs of non-specific hybridization and for direct application in plants. By overcoming these challenges, we obtained chromosome-specific probes, which allowed to achieve a clear and uniform painting of the entire target chromosomes with little or no background, evidencing their complexity and specificity. Despite the high amount of ubiquitous repetitive sequences in plant genomes, the main drawback for chromosome painting, we successfully employed our methodology on two plant species. Both have more than 80% repetitive sequences, which is compared to the human genome (66-69%). This is the first time that plant chromosome-specific probes were successfully obtained from a single A mitotic or meiotic microdissected chromosome. Thereby, we assume that chromosome painting through microdissection and CISS hybridization can now be considered a reality in the field of plant cytogenetics.

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“…If the genomic sequence is available from a target species, oligos, typically 40-50 bp long, specific to a chromosomal region or to an entire chromosome can be synthesized in parallel and labeled as a FISH probe (Han et al 2015). Oligo-FISH probes have been successfully developed in several plant species for various types of cytogenetic studies (Albert et al 2019;Bi et al 2020;He et al 2018;Hou et al 2018;Martins et al 2019;Meng et al 2018;Qu et al 2017;Simonikova et al 2019;Song et al 2020;Xin et al 2018;Xin et al 2020).…”

Section: Introductionmentioning

confidence: 99%

A universal chromosome identification system for maize and wildZeaspecies

Braz

Martins

Zhang

et al. 2020

Preprint

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Maize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the oldest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species remains a challenge. We developed a new technique for maize chromosome identification based on fluorescence in situ hybridization (FISH). We developed two oligonucleotide-based probes that hybridize to 24 chromosomal regions. Individual maize chromosomes show distinct FISH signal patterns, which allow universal identification of all chromosomes from different Zea species. We developed karyotypes from three Zea mays subspecies and two additional wild Zea species based on individually identified chromosomes. A paracentric inversion was discovered on the long arm of chromosome 4 in Z. nicaraguensis and Z. luxurians based on modifications of the FISH signal patterns. Chromosomes from these two species also showed distinct distribution patterns of terminal knobs compared to other Zea species. These results support that Z. nicaraguensis and Z. luxurians are closely related species. ReferencesAdawy SSM, Stupar RM, Jiang J (2004) Fluorescence in situ hybridization of knob-associated DNA elements analysis reveals multiple loci in one-knob and knobless maize lines. J (2019) Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. P Natl Acad Sci USA 116:1679-1685 Amarillo FIE, Bass HW (2007) A transgenomic cytogenetic sorghum (Sorghum propinquum) bacterial artificial chromosome fluorescence in situ hybridization map of maize (Zea mays L.) pachytene chromosome 9, evidence for regions of genome hyperexpansion.

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Chromosome painting and its applications in cultivated and wild rice

Cited by 48 publications

References 58 publications

An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting

An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting

Plant Chromosome-Specific Probes by Microdissection of a Single Chromosome: Is That a Reality?

A universal chromosome identification system for maize and wildZeaspecies

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