Chromosome genomics uncovers plant genome organization and function

Zwyrtková, Jana; Šimková, Hana; Doležel, Jaroslav

doi:10.1016/j.biotechadv.2020.107659

Cited by 20 publications

(21 citation statements)

References 146 publications

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“…Molecular markers based on DNA have been developed, both at the chromosome and the DNA sequence level. Polymorphisms were identified at the level of chromosome banding, through cytofluorometry [ 66 , 67 ]. The analysis of 58 varieties and landraces demonstrated a remarkable reproducibility and sensitivity of flow cytometry for the detection of numerical and structural chromosome changes [ 68 ].…”

Section: Exploration Of Genetic Diversity and Population Structurementioning

confidence: 99%

Importance of Landraces in Cereal Breeding for Stress Tolerance

Marone

Russo

et al. 2021

Plants

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The renewed focus on cereal landraces is a response to some negative consequences of modern agriculture and conventional breeding which led to a reduction of genetic diversity. Cereal landraces are still cultivated on marginal lands due to their adaptability to unfavourable conditions, constituting an important source of genetic diversity usable in modern plant breeding to improve the adaptation to abiotic or biotic stresses, yield performance and quality traits in limiting environments. Traditional agricultural production systems have played an important role in the evolution and conservation of wide variability in gene pools within species. Today, on-farm and ex situ conservation in gene bank collections, together with data sharing among researchers and breeders, will greatly benefit cereal improvement. Many efforts are usually made to collect, organize and phenotypically and genotypically analyse cereal landrace collections, which also utilize genomic approaches. Their use in breeding programs based on genomic selection, and the discovery of beneficial untapped QTL/genes/alleles which could be introgressed into modern varieties by MAS, pyramiding or biotechnological tools, increase the potential for their better deployment and exploitation in breeding for a more sustainable agricultural production, particularly enhancing adaptation and productivity in stress-prone environments to cope with current climate changes.

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Section: Exploration Of Genetic Diversity and Population Structurementioning

confidence: 99%

Importance of Landraces in Cereal Breeding for Stress Tolerance

Marone

Russo

et al. 2021

Plants

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“…Ideally, the studies should be done on purified mitotic chromosomes as this helps to discriminate the “genuine” and functionally significant chromosomal proteins from those isolated from interphase nuclei, which escaped synchronization, and cytoplasmic proteins. However, any preparation of pure fractions of mitotic chromosomes is challenging in plants ( Doležel et al, 2012 ; Zwyrtková et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Proteome Analysis of Condensed Barley Mitotic Chromosomes

et al. 2021

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Proteins play a major role in the three-dimensional organization of nuclear genome and its function. While histones arrange DNA into a nucleosome fiber, other proteins contribute to higher-order chromatin structures in interphase nuclei, and mitotic/meiotic chromosomes. Despite the key role of proteins in maintaining genome integrity and transferring hereditary information to daughter cells and progenies, the knowledge about their function remains fragmentary. This is particularly true for the proteins of condensed chromosomes and, in particular, chromosomes of plants. Here, we purified barley mitotic metaphase chromosomes by a flow cytometric sorting and characterized their proteins. Peptides from tryptic protein digests were fractionated either on a cation exchanger or reversed-phase microgradient system before liquid chromatography coupled to tandem mass spectrometry. Chromosomal proteins comprising almost 900 identifications were classified based on a combination of software prediction, available database localization information, sequence homology, and domain representation. A biological context evaluation indicated the presence of several groups of abundant proteins including histones, topoisomerase 2, POLYMERASE 2, condensin subunits, and many proteins with chromatin-related functions. Proteins involved in processes related to DNA replication, transcription, and repair as well as nucleolar proteins were found. We have experimentally validated the presence of FIBRILLARIN 1, one of the nucleolar proteins, on metaphase chromosomes, suggesting that plant chromosomes are coated with proteins during mitosis, similar to those of human and animals. These results improve significantly the knowledge of plant chromosomal proteins and provide a basis for their functional characterization and comparative phylogenetic analyses.

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“…It is also possible to grow vegetative organs, such as bulbs or stem cuttings, using hydroponic systems to initiate root formation and growth [32, 33]. Due to these advantages, almost all experiments on chromosome analysis and sorting in plants reported so far have utilized samples prepared from synchronized root tip meristems [34–36]. The subsequent parts of this paper will deal with this type of source tissue.…”

Section: Sample Preparationmentioning

confidence: 99%

“…Plant chromosomes sorted by flow cytometry have been used in a variety of applications, including molecular cytogenetics, molecular biology, genome sequencing, and gene cloning, and proteomics [36]. The way chromosomes are sorted for each application may differ as outlined below.…”

Section: Chromosome Sorting For Various Applicationsmentioning

confidence: 99%

Chromosome analysis and sorting

et al. 2021

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Flow cytometric analysis and sorting of plant mitotic chromosomes has been mastered by only a few laboratories worldwide. Yet, it has been contributing significantly to progress in plant genetics, including the production of genome assemblies and the cloning of important genes. The dissection of complex genomes by flow sorting into the individual chromosomes that represent small parts of the genome reduces DNA sample complexity and streamlines projects relying on molecular and genomic techniques. Whereas flow cytometric analysis, that is, chromosome classification according to fluorescence and light scatter properties, is an integral part of any chromosome sorting project, it has rarely been used on its own due to lower resolution and sensitivity as compared to other cytogenetic methods. To perform chromosome analysis and sorting, commercially available electrostatic droplet sorters are suitable. However, in order to resolve and purify chromosomes of interest the instrument must offer high resolution of optical signals as well as stability during long runs. The challenge is thus not the instrumentation, but the adequate sample preparation. The sample must be a suspension of intact mitotic metaphase chromosomes and the protocol, which includes the induction of cell cycle synchrony, accumulation of dividing cells at metaphase, and release of undamaged chromosomes, is time consuming and laborious and needs to be performed very carefully. Moreover, in addition to fluorescent staining chromosomal DNA, the protocol may include specific labelling of DNA repeats to facilitate discrimination of particular chromosomes. This review introduces the applications of chromosome sorting in plants, and discusses in detail sample preparation, chromosome analysis and sorting to achieve the highest purity in flowsorted fractions, and their suitability for downstream applications.

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Chromosome genomics uncovers plant genome organization and function

Cited by 20 publications

References 146 publications

Importance of Landraces in Cereal Breeding for Stress Tolerance

Importance of Landraces in Cereal Breeding for Stress Tolerance

Proteome Analysis of Condensed Barley Mitotic Chromosomes

Chromosome analysis and sorting

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