Cytogenetics and Agronomic Traits of Crops

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Cell Biology".

Deadline for manuscript submissions: closed (15 September 2023) | Viewed by 9086

Special Issue Editors


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Guest Editor
All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
Interests: molecular biology; genetics; plant biology; plant physiology; genomics; PCR; cloning; plant biotechnology; electrophoresis; DNA; in situ hybridization; FISH; GISH; chromosome rearrangements; marker assisted breeding; repetitive DNA; cytogenetic markers; PCR markers; whole genome sequencing; chromosome markers; tandem repeats; satellite repeats; intergeneric hybridization; distant hybridization

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Guest Editor
All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
Interests: wheat; triticale; triticeae; wild wheat related species; wide hybridization; intergeneric hybridization; distant hybridization; wheat-wheatgrass hybrids; dwarfing genes; sequencing; repetitive DNA; cytogenetic markers; PCR markers; whole genome sequencing; chromosome markers; tandem repeats; satellite repeats; agronomic value traits; Rht; della; gibberellin sensitivity; pseudoroegneria; dasypyrum; thinopyrum; elytrigia; agropyron; elymus; in situ hybridization; FISH; GISH; chromosome rearrangements; marker assisted breeding; marker assisted selection; recombinant inbred lines

Special Issue Information

Dear Colleagues,

During the breeding process, new forms of plants with higher adaptability, productivity and quality arise, which is associated with significant changes at various levels of chromatin. Chromosome engineering is a method that makes it possible to carry out prebreeding of the initial material, monitor the inheritance of chromosomal rearrangements, determine the probability of transferring valuable chromatin into the genome of a cultivated species, and control the dosage of alien chromatin introgressions. Thanks to the development of Next Generation Sequencing technologies and associated bioinformatics analysis, the improvement of non-denaturing FISH methods and the use of oligo- and multi-oilgo probes and cytogenetic approaches have made significant progress in recent years and are in demand in the breeding improvement of crops. A Special Issue of the MDPI journal Plants entitled “Cytogenetics and Agronomic Traits of Crops” is dedicated to achievements in the field of chromosomal engineering of cultivated plants, the study of the influence of the state of chromosomes and chromatin on agronomically valuable traits, as well as the development of tools for the cytogenetic characterization of crop plants.

We also invite you to publish papers with negative results of studies in which, subject to all the rules of the experiment, the method gives a consistently reproducible lack of the expected result. This is especially true during the transition from vegetative experiment to field conditions when previously established relationships and correlations are violated and lose reproducibility. Usually dismissed, these results, in our opinion, can be useful so that future researchers can use your negative experience.

You are welcome to submit your experimental studies and critical reviews if they contain, but are not limited to the following topics:

  • Development of new more advanced protocols and their modifications for the preparation of chromosome preparations, banding and/or in situ hybridization procedures for the study of chromosomes in crops;
  • Development and localization of new chromosomal markers (including using NGS-data and bioinformatics) for the study of agricultural crops;
  • Study of the initial breeding material at the stage of prebreeding and its evolutionary and population characteristics;
  • Karyotyping and karyotype diversity of agricultural crops;
  • Cytogenetic characterization of valuable breeding forms, including those obtained by distant hybridization;
  • Studying the influence of chromosomal rearrangements and epigenetic changes in chromatin on economically valuable traits of agricultural crops;
  • Cytogenetic study of polyploidy of cultivated plants and their wild relatives in the context of breeding improvement of agricultural crops;
  • Microdissection and sequencing of individual chromosomes associated with valuable economic traits.

Dr. Mikhail Divashuk
Dr. Pavel Yu. Kroupin
Guest Editors

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Published Papers (5 papers)

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Research

21 pages, 9588 KiB  
Article
Comparative Cytogenetics and Fluorescent Chromosome Banding in Five Indian Species of Dipcadi Medik
by Tundra Samanta, Timir B. Jha, Sudipta Ray and Sumita Jha
Plants 2023, 12(13), 2534; https://doi.org/10.3390/plants12132534 - 3 Jul 2023
Viewed by 1463
Abstract
The genus Dipcadi Medik. (Subfamily: Scilloideae) has a narrow distribution in India and several overlapping morphological traits make the genus taxonomically challenging at the species level. Cytogenetic characterization can provide additional taxonomic data and can be used to evaluate genetic diversity at the [...] Read more.
The genus Dipcadi Medik. (Subfamily: Scilloideae) has a narrow distribution in India and several overlapping morphological traits make the genus taxonomically challenging at the species level. Cytogenetic characterization can provide additional taxonomic data and can be used to evaluate genetic diversity at the species level. We have accomplished comparative karyotype analysis and fluorescence banding patterns using 4′-6-Diamidino-2-phenylindole (DAPI) and Chromomycin A3 (CMA) in five Indian species for the first time. The karyotypes of D. concanense and D. goaense exhibited similar fluorochrome banding profiles. However, D. montanum, D. ursulae and D. erythraeum differ distinctly in their karyotypes. In all taxa, CMA+ve/DAPI−ve or DAPI0 (GC-rich) constitutive heterochromatin was located at the constriction region or terminal satellite of the nucleolar chromosome. DAPI+ve/CMA−ve or CMA0 (AT-rich) heterochromatin dominates in D. montanum, D. ursulae and D. erythraeum. However, D. erythraeum shows a distinct variation in fluorochrome banding pattern from all other species. The distribution of CMA and DAPI bands is a reflection of heterochromatin composition and variations acquired by different species. This characterization can be used to assess phylogenetic relationships in the understudied genus Dipcadi and may serve as a basis for other genomic analyses and evolutionary studies. Full article
(This article belongs to the Special Issue Cytogenetics and Agronomic Traits of Crops)
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11 pages, 1641 KiB  
Article
Permanent Spreading of 1RS.1AL and 1RS.1BL Translocations in Modern Wheat Breeding
by Varvara A. Korobkova, Ludmila A. Bespalova, Aleksey S. Yanovsky, Anastasiya G. Chernook, Pavel Yu. Kroupin, Andrey V. Arkhipov, Anna I. Yurkina, Lubov A. Nazarova, Aleksandra A. Mudrova, Anastasiya D. Voropaeva, Olga Yu. Puzyrnaya, Elena V. Agaeva, Gennady I. Karlov and Mikhail G. Divashuk
Plants 2023, 12(6), 1205; https://doi.org/10.3390/plants12061205 - 7 Mar 2023
Cited by 2 | Viewed by 1829
Abstract
Wheat-rye translocations 1RS.1BL and 1RS.1AL are used in bread wheat breeding worldwide because a short arm of rye chromosome 1 (1RS) when introgressed into the wheat genome confers resistance to diseases, pests and better performance under drought-stress conditions. However, in durum wheat genotypes, [...] Read more.
Wheat-rye translocations 1RS.1BL and 1RS.1AL are used in bread wheat breeding worldwide because a short arm of rye chromosome 1 (1RS) when introgressed into the wheat genome confers resistance to diseases, pests and better performance under drought-stress conditions. However, in durum wheat genotypes, these translocations occur only in experimental lines, although their advantages could enhance the potential of this crop. P.P. Lukyanenko National Grain Centre (NGC) has successfully developed commercially competitive cultivars of bread and durum wheat demanded by many agricultural producers in the South of Russia for decades. Here, 94 accessions of bread and 343 accessions of durum wheat, representing lines and cultivars from collection, competitive variety trials and breeding nursery developed at NGC were screened for 1RS using PCR markers and genomic in situ hybridization. The 1RS.1BL and 1RS.1AL translocations were detected in 38 and 6 bread wheat accessions, respectively. None of the durum wheat accessions showed translocation, despite the fact that some of them had 1RS.1BL donors in their pedigree. The absence of translocations in the studied durum wheat germplasm can be caused by the negative selection of 1RS carriers at different stages of the breeding process due to low quality and difficulties in transferring rye chromatin through wheat gametes. Full article
(This article belongs to the Special Issue Cytogenetics and Agronomic Traits of Crops)
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18 pages, 29193 KiB  
Article
qPCR as a Selective Tool for Cytogenetics
by Mikhail G. Divashuk, Ekaterina A. Nikitina, Victoria M. Sokolova, Anna I. Yurkina, Alina A. Kocheshkova, Olga V. Razumova, Gennady I. Karlov and Pavel Yu. Kroupin
Plants 2023, 12(1), 80; https://doi.org/10.3390/plants12010080 - 23 Dec 2022
Cited by 2 | Viewed by 1786
Abstract
qPCR is widely used in quantitative studies of plant genomes and transcriptomes. In this article, this method is considered as an auxiliary step in the preparation and selection of markers for FISH analysis. Several cases from the authors’ research on populations of the [...] Read more.
qPCR is widely used in quantitative studies of plant genomes and transcriptomes. In this article, this method is considered as an auxiliary step in the preparation and selection of markers for FISH analysis. Several cases from the authors’ research on populations of the same species were reviewed, and a comparison of the closely related species, as well as the adaptation of the markers, based on satellite tandem repeats (TRs) using quantitative qPCR data was conducted. In the selected cases, TRs with contrast abundance were identified in the cases of the Dasypyrum, Thinopyrum and Aegilops species, and the transfer of TRs between the wheat and related species was demonstrated. TRs with intraspecific copy number variation were revealed in Thinopyrum ponticum and wheat-wheatgrass partial amphidiploids, and the TR showing predominant hybridization to the sea buckthorn Y chromosome was identified. Additionally, problems such as the absence of a reference gene for qPCR, and low-efficiency and self-complementary primers, were illustrated. In the cases considered here, the qPCR results clearly show high correlation with the subsequent results of the FISH analysis, which confirms the value of this method for cytogenetic studies. Full article
(This article belongs to the Special Issue Cytogenetics and Agronomic Traits of Crops)
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17 pages, 3541 KiB  
Article
Agro-Morphological and Cytogenetic Characterization of Colchicine-Induced Tetraploid Plants of Polemonium caeruleum L. (Polemoniaceae)
by Tatiana E. Samatadze, Olga Yu. Yurkevich, Firdaus M. Khazieva, Irina V. Basalaeva, Elena A. Konyaeva, Alla E. Burova, Svyatoslav A. Zoshchuk, Alexander I. Morozov, Alexandra V. Amosova and Olga V. Muravenko
Plants 2022, 11(19), 2585; https://doi.org/10.3390/plants11192585 - 30 Sep 2022
Cited by 4 | Viewed by 1934
Abstract
Polemonium caeruleum L. (Polemoniaceae) is a valuable medicinal herb with a wide spectrum of biological activities. Under natural conditions, the productivity of this species is rather low. In this study, colchicine-induced tetraploid plants (2n = 4x = 36) of P. caeruleum were obtained, [...] Read more.
Polemonium caeruleum L. (Polemoniaceae) is a valuable medicinal herb with a wide spectrum of biological activities. Under natural conditions, the productivity of this species is rather low. In this study, colchicine-induced tetraploid plants (2n = 4x = 36) of P. caeruleum were obtained, and for the first time, their morphological and cytogenetic characterization was performed. In the tetraploid plants, raw material productivity and also the content of triterpene saponins were significantly higher than in the control diploids. The analysis of chromosome behavior at meiosis and FISH chromosome mapping of 45S and 5S rDNA generally demonstrated stability of both genomes in the tetraploid plants. Based on chromosome morphology and distribution patterns of the studied molecular cytogenetic markers, all chromosome pairs in karyotypes were identified, and chromosome karyograms and idiograms of P. caeruleum were constructed. The revealed specific microdiagnostic characteristics of P. caeruleum (strongly sinuous cells and anomocytic stomata of the leaf epidermis, and also glandular hairs along the veins) could be useful for raw material identification. In the obtained tetraploids, the predominance of large stomata on the lower leaf epidermis was determined. The studied tetraploids can be used in various breeding programs to obtain high-quality pharmaceutical raw materials of P. caeruleum. Full article
(This article belongs to the Special Issue Cytogenetics and Agronomic Traits of Crops)
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7 pages, 730 KiB  
Communication
Developing Oligo Probes for Chromosomes Identification in Hemp (Cannabis sativa L.)
by Dmitry V. Romanov, Gennady I. Karlov and Mikhail G. Divashuk
Plants 2022, 11(15), 1900; https://doi.org/10.3390/plants11151900 - 22 Jul 2022
Cited by 1 | Viewed by 1554
Abstract
Hemp (Cannabis sativa L., 2n = 20) is a valuable crop that is successfully used as a food, technical and medicinal crop. It is a dioecious plant with an XX\XY sex determination system. Some chromosomes of C. sativa have almost the same [...] Read more.
Hemp (Cannabis sativa L., 2n = 20) is a valuable crop that is successfully used as a food, technical and medicinal crop. It is a dioecious plant with an XX\XY sex determination system. Some chromosomes of C. sativa have almost the same lengths and centromeric indexes. Cytogenetic markers help to distinguish similar plant chromosomes, including sex chromosomes, which is important for the breeding process. Two repeats (CS-1 and CS-237) were used to develop labeled oligo-probes for rapid and low-cost oligo-FISH. These oligos can be recommended for use as cytological markers to distinguish sex chromosomes (X and Y) and somatic chromosome pairs 3, 6, and 8 by rapid oligo-FISH in a short time. Full article
(This article belongs to the Special Issue Cytogenetics and Agronomic Traits of Crops)
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