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Rozentsvet O, Bogdanova E, Nesterov V, Bakunov A, Milekhin A, Rubtsov S, Rozentsvet V. Phenotyping of Potato Plants Using Morphological and Physiological Tools. PLANTS (BASEL, SWITZERLAND) 2024; 13:647. [PMID: 38475492 DOI: 10.3390/plants13050647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
Potato (Solanum tuberosum L.) is one of the main non-grain agricultural crops and one of the main sources of food for humanity. Currently, growing potatoes requires new approaches and methods for cultivation and breeding. Phenotyping is one of the important tools for assessing the characteristics of a potato variety. In this work, 29 potato varieties of different ripeness groups were studied. Linear leaf dimensions, leaf mass area, number of stems, number of tubers per plant, average tuber weight, signs of virus infection, dry weight, pigment content, and number of stomata per unit leaf area were used as phenotyping tools. The strongest positive relationship was found between yield and bush area in the stage of full shoots (R = 0.77, p = 0.001), linear dimensions of a complex leaf (R = 0.44, p = 0.002; R = 0.40, p = 0.003), number of stems (R = 0.36, p = 0.05), and resistance to viruses X (R = 0.42, p = 0.03) and S (R = 0.43, p = 0.02). An inverse relationship was found between growth dynamics and yield (R = -0.29, p = 0.05). Thus, the use of morphological and physiological phenotyping tools in the field is informative for predicting key agricultural characteristics such as yield and/or stress resistance.
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Affiliation(s)
- Olga Rozentsvet
- Samara Federal Research Scientific Center RAS, Institute of Ecology of the Volga Basin RAS, 10, Komzina, Togliatti 445003, Russia
| | - Elena Bogdanova
- Samara Federal Research Scientific Center RAS, Institute of Ecology of the Volga Basin RAS, 10, Komzina, Togliatti 445003, Russia
| | - Viktor Nesterov
- Samara Federal Research Scientific Center RAS, Institute of Ecology of the Volga Basin RAS, 10, Komzina, Togliatti 445003, Russia
| | - Alexey Bakunov
- Samara Federal Research Scientific Center RAS, Samara Scientific Research Agriculture Institute Named after N.M. Tulaykov, Bezenchuk 446254, Russia
| | - Alexey Milekhin
- Samara Federal Research Scientific Center RAS, Samara Scientific Research Agriculture Institute Named after N.M. Tulaykov, Bezenchuk 446254, Russia
| | - Sergei Rubtsov
- Samara Federal Research Scientific Center RAS, Samara Scientific Research Agriculture Institute Named after N.M. Tulaykov, Bezenchuk 446254, Russia
| | - Victor Rozentsvet
- Samara Federal Research Scientific Center RAS, Institute of Ecology of the Volga Basin RAS, 10, Komzina, Togliatti 445003, Russia
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Mäkinen K, Aspelin W, Pollari M, Wang L. How do they do it? The infection biology of potyviruses. Adv Virus Res 2023; 117:1-79. [PMID: 37832990 DOI: 10.1016/bs.aivir.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Affiliation(s)
- Kristiina Mäkinen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
| | - William Aspelin
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Maija Pollari
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Linping Wang
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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3
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Ghosh D, Chakraborty S, Kodamana H, Chakraborty S. Application of machine learning in understanding plant virus pathogenesis: trends and perspectives on emergence, diagnosis, host-virus interplay and management. Virol J 2022; 19:42. [PMID: 35264189 PMCID: PMC8905280 DOI: 10.1186/s12985-022-01767-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/27/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Inclusion of high throughput technologies in the field of biology has generated massive amounts of data in the recent years. Now, transforming these huge volumes of data into knowledge is the primary challenge in computational biology. The traditional methods of data analysis have failed to carry out the task. Hence, researchers are turning to machine learning based approaches for the analysis of high-dimensional big data. In machine learning, once a model is trained with a training dataset, it can be applied on a testing dataset which is independent. In current times, deep learning algorithms further promote the application of machine learning in several field of biology including plant virology. MAIN BODY Plant viruses have emerged as one of the principal global threats to food security due to their devastating impact on crops and vegetables. The emergence of new viral strains and species help viruses to evade the concurrent preventive methods. According to a survey conducted in 2014, plant viruses are anticipated to cause a global yield loss of more than thirty billion USD per year. In order to design effective, durable and broad-spectrum management protocols, it is very important to understand the mechanistic details of viral pathogenesis. The application of machine learning enables precise diagnosis of plant viral diseases at an early stage. Furthermore, the development of several machine learning-guided bioinformatics platforms has primed plant virologists to understand the host-virus interplay better. In addition, machine learning has tremendous potential in deciphering the pattern of plant virus evolution and emergence as well as in developing viable control options. CONCLUSIONS Considering a significant progress in the application of machine learning in understanding plant virology, this review highlights an introductory note on machine learning and comprehensively discusses the trends and prospects of machine learning in the diagnosis of viral diseases, understanding host-virus interplay and emergence of plant viruses.
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Affiliation(s)
- Dibyendu Ghosh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Srija Chakraborty
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016 India
| | - Hariprasad Kodamana
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016 India
- School of Artificial Intelligence, Indian Institute of Technology Delhi, New Delhi, 110016 India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
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Tiwari JK, Buckseth T, Zinta R, Bhatia N, Dalamu D, Naik S, Poonia AK, Kardile HB, Challam C, Singh RK, Luthra SK, Kumar V, Kumar M. Germplasm, Breeding, and Genomics in Potato Improvement of Biotic and Abiotic Stresses Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:805671. [PMID: 35197996 PMCID: PMC8859313 DOI: 10.3389/fpls.2022.805671] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/17/2022] [Indexed: 05/23/2023]
Abstract
Potato is one of the most important food crops in the world. Late blight, viruses, soil and tuber-borne diseases, insect-pests mainly aphids, whiteflies, and potato tuber moths are the major biotic stresses affecting potato production. Potato is an irrigated and highly fertilizer-responsive crop, and therefore, heat, drought, and nutrient stresses are the key abiotic stresses. The genus Solanum is a reservoir of genetic diversity, however, a little fraction of total diversity has been utilized in potato breeding. The conventional breeding has contributed significantly to the development of potato varieties. In recent years, a tremendous progress has been achieved in the sequencing technologies from short-reads to long-reads sequence data, genomes of Solanum species (i.e., pan-genomics), bioinformatics and multi-omics platforms such as genomics, transcriptomics, proteomics, metabolomics, ionomics, and phenomics. As such, genome editing has been extensively explored as a next-generation breeding tool. With the available high-throughput genotyping facilities and tetraploid allele calling softwares, genomic selection would be a reality in potato in the near future. This mini-review covers an update on germplasm, breeding, and genomics in potato improvement for biotic and abiotic stress tolerance.
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Affiliation(s)
| | | | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, India
| | - Nisha Bhatia
- ICAR-Central Potato Research Institute, Shimla, India
- School of Biotechnology, Shoolini University, Solan, India
| | - Dalamu Dalamu
- ICAR-Central Potato Research Institute, Shimla, India
| | - Sharmistha Naik
- ICAR-Central Potato Research Institute, Shimla, India
- ICAR-National Research Centre for Grapes, Pune, India
| | - Anuj K. Poonia
- School of Biotechnology, Shoolini University, Solan, India
| | - Hemant B. Kardile
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Clarissa Challam
- ICAR-Central Potato Research Institute, Regional Station, Shillong, India
| | | | - Satish K. Luthra
- ICAR-Central Potato Research Institute, Regional Station, Meerut, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Regional Station, Meerut, India
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Kachaev ZM, Ivashchenko SD, Kozlov EN, Lebedeva LA, Shidlovskii YV. Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus. Cells 2021; 10:3239. [PMID: 34831461 PMCID: PMC8623629 DOI: 10.3390/cells10113239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.
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Affiliation(s)
- Zaur M. Kachaev
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Sergey D. Ivashchenko
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Eugene N. Kozlov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Lyubov A. Lebedeva
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
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Ayash M, Abukhalaf M, Thieme D, Proksch C, Heilmann M, Schattat MH, Hoehenwarter W. LC-MS Based Draft Map of the Arabidopsis thaliana Nuclear Proteome and Protein Import in Pattern Triggered Immunity. FRONTIERS IN PLANT SCIENCE 2021; 12:744103. [PMID: 34858452 PMCID: PMC8630587 DOI: 10.3389/fpls.2021.744103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Despite its central role as the ark of genetic information and gene expression the plant nucleus is surprisingly understudied. We isolated nuclei from the Arabidopsis thaliana dark grown cell culture left untreated and treated with flg22 and nlp20, two elicitors of pattern triggered immunity (PTI) in plants, respectively. An liquid chromatography mass spectrometry (LC-MS) based discovery proteomics approach was used to measure the nuclear proteome fractions. An enrichment score based on the relative abundance of cytoplasmic, mitochondrial and Golgi markers in the nuclear protein fraction allowed us to curate the nuclear proteome producing high quality catalogs of around 3,000 nuclear proteins under untreated and both PTI conditions. The measurements also covered low abundant proteins including more than 100 transcription factors and transcriptional co-activators. We disclose a list of several hundred potentially dual targeted proteins including proteins not yet found before for further study. Protein import into the nucleus in plant immunity is known. Here we sought to gain a broader impression of this phenomenon employing our proteomics data and found 157 and 73 proteins to possibly be imported into the nucleus upon stimulus with flg22 and nlp20, respectively. Furthermore, the abundance of 93 proteins changed significantly in the nucleus following elicitation of immunity. These results suggest promiscuous ribosome assembly and a role of prohibitins and cytochrome C in the nucleus in PTI.
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Affiliation(s)
- Mohamed Ayash
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Mohammad Abukhalaf
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Domenika Thieme
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Carsten Proksch
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Mareike Heilmann
- Institute for Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | | | - Wolfgang Hoehenwarter
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Halle, Germany
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Heenan-Daly D, Coughlan S, Dillane E, Doyle Prestwich B. Volatile Compounds From Bacillus, Serratia, and Pseudomonas Promote Growth and Alter the Transcriptional Landscape of Solanum tuberosum in a Passively Ventilated Growth System. Front Microbiol 2021; 12:628437. [PMID: 34367077 PMCID: PMC8333284 DOI: 10.3389/fmicb.2021.628437] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/07/2021] [Indexed: 11/15/2022] Open
Abstract
The interaction of an array of volatile organic compounds (VOCs) termed bacterial volatile compounds (BVCs) with plants is now a major area of study under the umbrella of plant-microbe interactions. Many growth systems have been developed to determine the nature of these interactions in vitro. However, each of these systems have their benefits and drawbacks with respect to one another and can greatly influence the end-point interpretation of the BVC effect on plant physiology. To address the need for novel growth systems in BVC-plant interactions, our study investigated the use of a passively ventilated growth system, made possible via Microbox® growth chambers, to determine the effect of BVCs emitted by six bacterial isolates from the genera Bacillus, Serratia, and Pseudomonas. Solid-phase microextraction GC/MS was utilized to determine the BVC profile of each bacterial isolate when cultured in three different growth media each with varying carbon content. 66 BVCs were identified in total, with alcohols and alkanes being the most abundant. When cultured in tryptic soy broth, all six isolates were capable of producing 2,5-dimethylpyrazine, however BVC emission associated with this media were deemed to have negative effects on plant growth. The two remaining media types, namely Methyl Red-Voges Proskeur (MR-VP) and Murashige and Skoog (M + S), were selected for bacterial growth in co-cultivation experiments with Solanum tuberosum L. cv. ‘Golden Wonder.’ The BVC emissions of Bacillus and Serratia isolates cultured on MR-VP induced alterations in the transcriptional landscape of potato across all treatments with 956 significantly differentially expressed genes. This study has yielded interesting results which indicate that BVCs may not always broadly upregulate expression of defense genes and this may be due to choice of plant-bacteria co-cultivation apparatus, bacterial growth media and/or strain, or likely, a complex interaction between these factors. The multifactorial complexities of observed effects of BVCs on target organisms, while intensely studied in recent years, need to be further elucidated before the translation of lab to open-field applications can be fully realized.
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Affiliation(s)
- Darren Heenan-Daly
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Simone Coughlan
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Eileen Dillane
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Barbara Doyle Prestwich
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
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