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Miroshnichenko D, Timerbaev V, Divashuk M, Pushin A, Alekseeva V, Kroupin P, Bazhenov M, Samarina M, Ermolaev A, Karlov G, Dolgov S. CRISPR/Cas9-mediated мultiplexed multi-allelic mutagenesis of genes located on A, B and R subgenomes of hexaploid triticale. Plant Cell Rep 2024; 43:59. [PMID: 38329578 DOI: 10.1007/s00299-023-03139-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 12/29/2023] [Indexed: 02/09/2024]
Abstract
KEY MESSAGE The first-time generation of hexaploid triticale plants harbouring variable panels of novel mutations in gene families involved in starch biosynthesis has been achieved by the subgenome-independent multiplexed CRISPR/Cas9-mediated editing.
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Affiliation(s)
- Dmitry Miroshnichenko
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia.
- Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Pushchino, Russia.
| | - Vadim Timerbaev
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Pushchino, Russia
| | - Mikhail Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Alexander Pushin
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Pushchino, Russia
| | - Valeria Alekseeva
- Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Pushchino, Russia
| | - Pavel Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Mikhail Bazhenov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Mariya Samarina
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Aleksey Ermolaev
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Gennady Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Sergey Dolgov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Pushchino, Russia
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Divashuk M, Chernook A, Kroupina A, Vukovic M, Karlov G, Ermolaev A, Shirnin S, Avdeev S, Igonin V, Pylnev V, Kroupin P. TaGRF3-2A Improves Some Agronomically Valuable Traits in Semi-Dwarf Spring Triticale. Plants (Basel) 2021; 10:2012. [PMID: 34685820 PMCID: PMC8537337 DOI: 10.3390/plants10102012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022]
Abstract
The breeding improvement of triticale is tightly associated with the introgression of dwarfing genes, in particular, gibberellin (GA)-insensitive Ddw1 from rye. Despite the increase in harvest index and resistance to lodging, this gene adversely affects grain weight and size. Growth regulation factor (GRF) genes are plant-specific transcription factors that play an important role in plant growth, including GA-induced stem elongation. This study presents the results of a two-year field experiment to assess the effect of alleles of the TaGRF3-2A gene in interaction with DDW1 on economically valuable traits of spring triticale plants grown in the Non-Chernozem zone. Our results show that, depending on the allelic state, the TaGRF3-2A gene in semi-dwarf spring triticale plants influences the thousand grain weight and the grain weight of the main spike in spring triticale, which makes it possible to use it to compensate for the negative effects of the dwarfing allele Ddw1. The identified allelic variants of the TaGRF3-2A gene can be included in marker-assisted breeding for triticale to improve traits.
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Affiliation(s)
- Mikhail Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.C.); (A.K.); (M.V.); (G.K.); (A.E.); (S.S.); (V.I.); (P.K.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 49, 127550 Moscow, Russia; (S.A.); (V.P.)
| | - Anastasiya Chernook
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.C.); (A.K.); (M.V.); (G.K.); (A.E.); (S.S.); (V.I.); (P.K.)
| | - Aleksandra Kroupina
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.C.); (A.K.); (M.V.); (G.K.); (A.E.); (S.S.); (V.I.); (P.K.)
| | - Milena Vukovic
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.C.); (A.K.); (M.V.); (G.K.); (A.E.); (S.S.); (V.I.); (P.K.)
| | - Gennady Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.C.); (A.K.); (M.V.); (G.K.); (A.E.); (S.S.); (V.I.); (P.K.)
| | - Aleksey Ermolaev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.C.); (A.K.); (M.V.); (G.K.); (A.E.); (S.S.); (V.I.); (P.K.)
| | - Sergey Shirnin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.C.); (A.K.); (M.V.); (G.K.); (A.E.); (S.S.); (V.I.); (P.K.)
| | - Sergey Avdeev
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 49, 127550 Moscow, Russia; (S.A.); (V.P.)
| | - Vladimir Igonin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.C.); (A.K.); (M.V.); (G.K.); (A.E.); (S.S.); (V.I.); (P.K.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 49, 127550 Moscow, Russia; (S.A.); (V.P.)
| | - Vladimir Pylnev
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 49, 127550 Moscow, Russia; (S.A.); (V.P.)
| | - Pavel Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.C.); (A.K.); (M.V.); (G.K.); (A.E.); (S.S.); (V.I.); (P.K.)
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Nikitina E, Kuznetsova V, Kroupin P, Karlov GI, Divashuk MG. Development of Specific Thinopyrum Cytogenetic Markers for Wheat-Wheatgrass Hybrids Using Sequencing and qPCR Data. Int J Mol Sci 2020; 21:E4495. [PMID: 32599865 PMCID: PMC7349979 DOI: 10.3390/ijms21124495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/15/2020] [Accepted: 06/21/2020] [Indexed: 01/19/2023] Open
Abstract
The cytogenetic study of wide hybrids of wheat has both practical and fundamental values. Partial wheat-wheatgrass hybrids (WWGHs) are interesting as a breeding bridge to confer valuable genes to wheat genome, as well as a model object that contains related genomes of Triticeae. The development of cytogenetic markers is a process that requires long and laborious fluorescence in situ hybridization (FISH) testing of various probes before a suitable probe is found. In this study, we aimed to find an approach that allows to facilitate this process. Based on the data sequencing of Thinopyrum ponticum, we selected six tandem repeat (TR) clusters using RepeatExplorer2 pipeline and designed primers for each of them. We estimated the found TRs' abundance in the genomes of Triticum aestivum, Thinopyrum ponticum, Thinopyrum intermedium and four different WWGH accessions using real-time qPCR, and localized them on the chromosomes of the studied WWGHs using fluorescence in situ hybridization. As a result, we obtained three tandem repeat cytogenetic markers that specifically labeled wheatgrass chromosomes in the presence of bread wheat chromosomes. Moreover, we designed and tested primers for these repeats, and demonstrated that they can be used as qPCR markers for quick and cheap monitoring of the presence of certain chromosomes of wheatgrass in breeding programs.
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Affiliation(s)
- Ekaterina Nikitina
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Victoria Kuznetsova
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Pavel Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Gennady I. Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Mikhail G. Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
- Kurchatov Genomics Center—ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia
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Bazhenov M, Chernook A, Kroupin P, Karlov G, Divashuk M. Molecular Characterization of the Dwarf53 Gene Homolog in Dasypyrum villosum. Plants (Basel) 2020; 9:plants9020186. [PMID: 32028730 PMCID: PMC7076371 DOI: 10.3390/plants9020186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/24/2020] [Accepted: 02/01/2020] [Indexed: 11/16/2022]
Abstract
The Dwarf53 (D53) gene, first studied in rice, encodes a protein that acts as a repressor of the physiological response of plants to strigolactones—substances that regulate the activity of axillary buds, stem growth, branching of roots and other physiological processes. In this work, we isolated and sequenced the homolog of the D53 gene in several accessions of the wild grass Dasypyrum villosum of different geographical origins, resulting in the discovery of large allelic variety. A molecular marker was also created that allows us to differentiate the D. villosum D53 gene from common wheat genes. Using this marker and monosomic addition, substitution and translocation wheat lines carrying the known D. villosum chromosomes, the D53 gene was localized on the long arm of the 5V chromosome.
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Affiliation(s)
- Mikhail Bazhenov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya street, 42, 127550 Moscow, Russia; (A.C.); (P.K.); (G.K.); (M.D.)
- Correspondence:
| | - Anastasiya Chernook
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya street, 42, 127550 Moscow, Russia; (A.C.); (P.K.); (G.K.); (M.D.)
- Kurchatov Genomics Center of All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, 127550 Moscow, Russia
| | - Pavel Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya street, 42, 127550 Moscow, Russia; (A.C.); (P.K.); (G.K.); (M.D.)
- Kurchatov Genomics Center of All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, 127550 Moscow, Russia
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya street, 42, 127550 Moscow, Russia; (A.C.); (P.K.); (G.K.); (M.D.)
| | - Mikhail Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya street, 42, 127550 Moscow, Russia; (A.C.); (P.K.); (G.K.); (M.D.)
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Kroupin P, Chernook A, Karlov G, Soloviev A, Divashuk M. Effect of Dwarfing Gene Ddw1 on Height and Agronomic Traits in Spring Triticale in Greenhouse and Field Experiments in a Non-Black Earth Region of Russia. Plants (Basel) 2019; 8:plants8050131. [PMID: 31100890 PMCID: PMC6571949 DOI: 10.3390/plants8050131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/09/2019] [Accepted: 05/14/2019] [Indexed: 01/17/2023]
Abstract
Triticale is a relatively new crop which still possesses serious drawbacks that can be significantly improved by breeding. The dwarfing genes proved to be very useful in the development of new lodging resistant and productive cultivars of winter triticale. The aim of our research was to assess the effect of the Ddw1 dwarfing gene from rye on the agronomic valuable traits in spring triticale. The Ddw1 effect was studied in the greenhouse experiment in segregating the F2:3 population and in the field of F3:4 and F4:5 families derived from crossing winter triticale ‘Hongor’ (Ddw1Ddw1) and spring triticale ‘Dublet’ (ddw1ddw1). As a result, in all three generations, a strong decrease in plant height was demonstrated that was accompanied by a decrease in grain weight per spike and 1000-grain weight. In field experiments, a decrease in spike length and increase in spike density and delay in flowering and heading were observed. As a result of decrease in culm vegetative weight due to Ddw1, the harvest index measured in F4:5 increased. The spike fertility and number of grains were not affected by Ddw1. The comparison of Ddw1 in rye, winter, and spring triticale, and the possible role of Ddw1 in improving spring triticale are discussed.
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Affiliation(s)
- Pavel Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Centre for Molecular Biotechnology, Russian State Agrarian University ⁻ Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow 127550, Russia.
| | - Anastasiya Chernook
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Centre for Molecular Biotechnology, Russian State Agrarian University ⁻ Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow 127550, Russia.
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Centre for Molecular Biotechnology, Russian State Agrarian University ⁻ Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow 127550, Russia.
| | - Alexander Soloviev
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Department of Distant Hybridization, N.V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, Botanicheskaya str., 4, Moscow 127276, Russia.
| | - Mikhail Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Centre for Molecular Biotechnology, Russian State Agrarian University ⁻ Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow 127550, Russia.
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Kroupin P, Kuznetsova V, Romanov D, Kocheshkova A, Karlov G, Dang TX, Khuat TML, Kirov I, Alexandrov O, Polkhovskiy A, Razumova O, Divashuk M. Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species. Genes (Basel) 2019; 10:E113. [PMID: 30717300 PMCID: PMC6409974 DOI: 10.3390/genes10020113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 11/19/2022] Open
Abstract
Repetitive DNA including tandem repeats (TRs) is a significant part of most eukaryotic genomes. TRs include rapidly evolving satellite DNA (satDNA) that can be shared by closely related species, their abundance may be associated with evolutionary divergence, and they have been widely used for chromosome karyotyping using fluorescence in situ hybridization (FISH). The recent progress in the development of whole-genome sequencing and bioinformatics tools enables rapid and cost-effective searches for TRs including satDNA that can be converted into molecular cytogenetic markers. In the case of closely related taxa, the genome sequence of one species (donor) can be used as a base for the development of chromosome markers for related species or genomes (target). Here, we present a pipeline for rapid and high-throughput screening for new satDNA TRs in whole-genome sequencing of the donor genome and the development of chromosome markers based on them that can be applied in the target genome. One of the main peculiarities of the developed pipeline is that preliminary estimation of TR abundance using qPCR and ranking found TRs according to their copy number in the target genome; it facilitates the selection of the most prospective (most abundant) TRs that can be converted into cytogenetic markers. Another feature of our pipeline is the probe preparation for FISH using PCR with primers designed on the aligned TR unit sequences and the genomic DNA of a target species as a template that enables amplification of a whole pool of monomers inherent in the chromosomes of the target species. We demonstrate the efficiency of the developed pipeline by the example of FISH probes developed for A, B, and R subgenome chromosomes of hexaploid triticale (BBAARR) based on a bioinformatics analysis of the D genome of Aegilops tauschii (DD) whole-genome sequence. Our pipeline can be used to develop chromosome markers in closely related species for comparative cytogenetics in evolutionary and breeding studies.
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Affiliation(s)
- Pavel Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Victoria Kuznetsova
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Dmitry Romanov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Alina Kocheshkova
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Thi Xuan Dang
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Thi Mai L Khuat
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Ilya Kirov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Oleg Alexandrov
- Laboratory of Plant Cell Engineering, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Alexander Polkhovskiy
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Olga Razumova
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Mikhail Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
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