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Gubaev R, Karzhaev D, Grigoreva E, Lytkin K, Safronycheva E, Volkov V, Nesterchuk V, Vetchinnikova L, Zhigunov A, Potokina E. Dissection of figured wood trait in curly birch (Betula pendula Roth var. carelica (Mercklin) Hämet-Ahti) using high-throughput genotyping. Sci Rep 2024; 14:5058. [PMID: 38424163 PMCID: PMC10904815 DOI: 10.1038/s41598-024-55404-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Curly (Karelian) birch is a special variety of Betula pendula Roth distributed in the northwestern part of Europe. Karelian birch is well-known for its valuable figured curly wood also known as "wooden marble". The genetic basis underlying curly wood formation has been debated since last century, however, there was no data about loci responsible for the curly wood trait. In the present study, we analyzed two full-sibs populations derived from experimental crosses of curly birches and segregating for the trait. RADseq genotyping was applied to reveal how many loci are involved in 'curliness' formation and to search for genetic variants associated with this trait. One single interval on chromosome 10 was detected containing possible candidate genes. InDel marker BpCW1 was suggested for the first time for marker-assisted selection of trees with curly wood at their earliest stages of development.
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Affiliation(s)
- Rim Gubaev
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
| | - Dmitry Karzhaev
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
- Research Laboratory, Saint Petersburg Forest Research Institute, St. Petersburg, Russia
| | - Elizaveta Grigoreva
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Kirill Lytkin
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
| | - Elizaveta Safronycheva
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
- Research Laboratory, Saint Petersburg Forest Research Institute, St. Petersburg, Russia
| | - Vladimir Volkov
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
- Research Laboratory, Saint Petersburg Forest Research Institute, St. Petersburg, Russia
| | - Veronika Nesterchuk
- Research Laboratory, Saint Petersburg Forest Research Institute, St. Petersburg, Russia
| | - Lidiia Vetchinnikova
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
- Forest Research Institute of Karelian Research Centre Russian Academy of Sciences, Petrozavodsk, Russia
| | - Anatoly Zhigunov
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
| | - Elena Potokina
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia.
- Skolkovo Institute of Science and Technology, Moscow, Russia.
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Lytkin K, Nosulchak V, Agakhanov M, Matveikina E, Lushchay E, Karzhaev D, Raines E, Vasylyk I, Rybachenko N, Grigoreva E, Volkov V, Volynkin V, Gentzbittel L, Potokina E. Development of a High-Density Genetic Map for Muscadine Grape Using a Mapping Population from Selfing of the Perfect-Flowered Vine 'Dixie'. Plants (Basel) 2022; 11:3231. [PMID: 36501271 PMCID: PMC9738875 DOI: 10.3390/plants11233231] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Intraspecific diversity of the immune grape Muscadinia rotundifolia Michaux. can serve as a rich source of valuable resistance loci to the most widespread pathogens and pests of grapevine. While only one Run1/Rpg1 resistance locus has been introgressed from M. rotundifolia to the Vitis vinifera gene pool, a number of other genes conferring resistance to powdery mildew and downy mildew have been identified in various Muscadinia cultivars. A larger introduction of Muscadinia varieties to the European continent would greatly facilitate experiments of interspecific crosses as well as stimulate biotechnological efforts to overcome the main barrier to F1 fertility caused by the differences in chromosome number. For the successful introduction of Muscadinia into the new European environment, it is necessary to overcome the difficulties associated with the physiological characteristics of the species, such as insufficient cold tolerance and very late fruit ripening. To facilitate the further discovery of valuable loci in Muscadinia and their transfer to grapevine breeding programs, we constructed a high-density linkage map using an S1 mapping population obtained from the self-pollination of M. rotundifolia cv. Dixie maintained on the southern coast of Crimea. Using ddRADseq, 3730 SNPs were ordered across 20 linkage groups spanning 2753.6 cM of the total map length. No segregation in resistance to diseases and pests was observed among the 'Dixie' S1 population, suggesting the presence of homozygous non-segregating resistant loci in the genetic background of 'Dixie'. Markers with high segregation distortion showed a bias towards chromosomal intervals on linkage groups 10 and 20, where loci affecting the survival of 'Dixie' S1 progeny may be localized. QTLs with significant additive and dominance effects were discovered on LG14 and LG18, affecting the morphological traits associated with the vigor of growth and adaptability of young Muscadinia vines in the conditions of Crimea.
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Affiliation(s)
- Kirill Lytkin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Vasily Nosulchak
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg 190031, Russia
| | - Magamedgusein Agakhanov
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg 190031, Russia
| | - Elena Matveikina
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Ekaterina Lushchay
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Dmitry Karzhaev
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Evgenii Raines
- Information Technologies and Programming Faculty, ITMO University, St. Petersburg 197101, Russia
| | - Irina Vasylyk
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Nataliya Rybachenko
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Elizaveta Grigoreva
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Vladimir Volkov
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Vladimir Volynkin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | | | - Elena Potokina
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
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Grigoreva E, Tkachenko A, Arkhimandritova S, Beatovic A, Ulianich P, Volkov V, Karzhaev D, Ben C, Gentzbittel L, Potokina E. Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar ( Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis. Genes (Basel) 2021; 12:genes12070952. [PMID: 34206279 PMCID: PMC8303896 DOI: 10.3390/genes12070952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/08/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 01/08/2023] Open
Abstract
Guar (Cyamopsis tetragonoloba (L.) Taub.) is an annual legume crop native to India and Pakistan. Seeds of the plant serve as a source of galactomannan polysaccharide (guar gum) used in the food industry as a stabilizer (E412) and as a gelling agent in oil and gas fracturing fluids. There were several attempts to introduce this crop to countries of more northern latitudes. However, guar is a plant of a short photoperiod, therefore, its introduction, for example, to Russia is complicated by a long day length during the growing season. Breeding of new guar varieties insensitive to photoperiod slowed down due to the lack of information on functional molecular markers, which, in turn, requires information on guar genome. Modern breeding strategies, e.g., genomic predictions, benefit from integration of multi-omics approaches such as transcriptome, proteome and metabolome assays. Here we present an attempt to use transcriptome-metabolome integration to understand the genetic determination of flowering time variation among guar plants that differ in their photoperiod sensitivity. This study was performed on nine early- and six delayed-flowering guar varieties with the goal to find a connection between 63 metabolites and 1,067 differentially expressed transcripts using Shiny GAM approach. For the key biomarker of flowering in guar myo-inositol we also evaluated the KEGG biochemical pathway maps available for Arabidopsis thaliana. We found that the phosphatidylinositol signaling pathway is initiated in guar plants that are ready for flowering through the activation of the phospholipase C (PLC) gene, resulting in an exponential increase in the amount of myo-inositol in its free form observed on GC-MS chromatograms. The signaling pathway is performed by suppression of myo-inositol phosphate kinases (phosphorylation) and alternative overexpression of phosphatases (dephosphorylation). Our study suggests that metabolome and transcriptome information taken together, provide valuable information about biomarkers that can be used as a tool for marker-assisted breeding, metabolomics and functional genomics of this important legume crop.
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Affiliation(s)
- Elizaveta Grigoreva
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia; (E.G.); (A.B.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia; (V.V.); (E.P.)
- Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Alexander Tkachenko
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia; (E.G.); (A.B.)
- Correspondence: ; Tel.: +7-9217634039
| | | | - Aleksandar Beatovic
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia; (E.G.); (A.B.)
| | - Pavel Ulianich
- All-Russian Research Institute of Agricultural Microbiology, 196608 St. Petersburg, Russia;
| | - Vladimir Volkov
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia; (V.V.); (E.P.)
- Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Dmitry Karzhaev
- Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Cécile Ben
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (C.B.); (L.G.)
| | - Laurent Gentzbittel
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (C.B.); (L.G.)
| | - Elena Potokina
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia; (V.V.); (E.P.)
- Sirius University of Science and Technology, 354340 Sochi, Russia;
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Volynkin V, Vasylyk I, Volodin V, Grigoreva E, Karzhaev D, Lushchay E, Ulianich P, Volkov V, Risovannaya V, Blinova S, Alekseev J, Gorislavets S, Likhovskoi V, Beatovic A, Potokina E. The Assessment of Agrobiological and Disease Resistance Traits of Grapevine Hybrid Populations ( Vitis vinifera L. × Muscadinia rotundifolia Michx.) in the Climatic Conditions of Crimea. Plants (Basel) 2021; 10:plants10061215. [PMID: 34203712 PMCID: PMC8232157 DOI: 10.3390/plants10061215] [Citation(s) in RCA: 3] [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: 04/30/2021] [Revised: 06/06/2021] [Accepted: 06/11/2021] [Indexed: 11/24/2022]
Abstract
The Crimean autochthonous grape varieties are unique by their origin and serve as a valuable source for breeding new cultivars with increased salt and frost resistance, as well as high-quality berries. However, they suffer from fungal pathogens, as the dry and hot summer months contribute to the epiphytotic course of diseases. An increase in the resistance of Crimean grape varieties is currently achieved through interspecific hybridization. In this study, we describe the genetic and agrobiological diversity of three hybrid populations obtained using the Vitis interspecific hybrid ‘Magarach 31-77-10′ as a female parent and Muscadinia rotundifolia × Vitis vinifera BC5 hybrid plants as male parents. The hybrid nature of the populations was assessed using RADseq high-throughput genotyping. We discovered 12,734 SNPs, which were common to all three hybrid populations. We also proved with the SSR markers that the strong powdery and downy mildew resistance of the paternal genotypes is determined by the dominant Run1/Rpv1 locus inherited from M. rotundifolia. As a result, the disease development score (R, %) for both mildew diseases in the female parent ‘Magarach 31-77-10’ was three times higher than in male parents 2000-305-143 and 2000-305-163 over two years of phytopathological assessment. The highest values of yield-contributing traits (average bunch weight ~197 g and 1.3 kg as yield per plant) were detected in the population 4-11 (♀M. No. 31-77-10 × 2000-305-163). Despite the epiphytotic development of PM, the spread of oidium to the vegetative organs of hybrids 4-11 did not exceed 20%. Some hybrid genotypes with high productivity and resistance to pathogens were selected for further assessment as promising candidates for new varieties.
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Affiliation(s)
- Vladimir Volynkin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Irina Vasylyk
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Vitalii Volodin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Elizaveta Grigoreva
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia;
| | - Dmitry Karzhaev
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
| | - Ekaterina Lushchay
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Pavel Ulianich
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- All-Russian Research Institute of Agricultural Microbiology, 196608 St. Petersburg, Russia
| | - Vladimir Volkov
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
| | - Valentina Risovannaya
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Sofiya Blinova
- Syntol, 127434 Moscow, Russia;
- All-Russian Research Institute of Agricultural Biotechnology, 127434 Moscow, Russia
| | - Jakov Alekseev
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Syntol, 127434 Moscow, Russia;
| | - Svetlana Gorislavets
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Vladimir Likhovskoi
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Aleksandar Beatovic
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia;
| | - Elena Potokina
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-911-084-1422
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Grigoreva E, Ulianich P, Ben C, Gentzbittel L, Potokina E. First Insights into the Guar (Cyamopsis tetragonoloba (L.) Taub.) Genome of the ‘Vavilovskij 130’ Accession, Using Second and Third-Generation Sequencing Technologies. RUSS J GENET+ 2019. [DOI: 10.1134/s102279541911005x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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