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Zinta R, Tiwari JK, Buckseth T, Goutam U, Singh RK, Kumar V, Thakur AK. Transcriptome profiling and characterization of genes associated with tuberization under high temperature in aeroponics in potato cv. Kufri Anand. Genes Genomics 2024; 46:409-421. [PMID: 38381322 DOI: 10.1007/s13258-024-01503-z] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/02/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND High temperature stress is an important abiotic factor, which affects tuberization and ultimately causes heavy yield reduction in potato. OBJECTIVES Identification and characterization of genes associated with tuberization under high temperature stress is essential for future management through biotechnology. METHODOLOGY Two contrasting potato varieties Kufri Anand (profuse tuber-bearing) versus Kufri Frysona (very less/scanty tuber-bearing, control) were cultivated in aeroponics under high temperature stress, and transcriptomes were analyzed. RESULTS Potato cv. Kufri Anand was found superior over control (Kufri Frysona) for tuber yield and its component traits along with root morphology under aeroponics. Transcriptomes of tuber and leaf tissues were analyzed. Statistically significant (p < 0.05) differentially expressed genes (DEGs) were categorised into up-regulated (> 2 log2 fold change, FC) and down-regulated (< -2 log2 FC) genes. DEGs were annotated by gene ontology and KEGG pathways. A few selected up-regulated genes of both tissues were identified, and phylogeny tree and motif analysis were analysed based on 36 peptide sequences representing 15 selected DEGs in this study. Further, gene expression markers were developed and validated by real time qPCR analysis for the identification of high temperature tolerant genotypes. CONCLUSION A few key genes associated in tuberization under high temperature conditions were heat shock proteins (e.g. 18.5 kDa class I heat shock protein), sugar metabolism (e.g. glucosyltransferase), transcription factor (e.g. WRKY), and phytohormones (e.g. auxin-induced beta-glucosidase). Our study provides an overview of key genes involved in tuberization under high temperature stress in potato cv. Kufri Anand under aeroponics.
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Affiliation(s)
- Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
- ICAR-Indian Institute of Vegetable Research Institute, Varanasi, Uttar Pradesh, India.
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Umesh Goutam
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay Kumar Thakur
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Bhatia N, Tiwari JK, Kumari C, Zinta R, Sharma S, Thakur AK, Buckseth T, Dalamu D, Singh RK, Kumar V. Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato. Front Plant Sci 2023; 14:1212135. [PMID: 37502703 PMCID: PMC10368984 DOI: 10.3389/fpls.2023.1212135] [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: 04/25/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023]
Abstract
Late blight (Phytophthora infestans) is a serious disease of potatoes. The aim of this study was to screen wild potato species and identify differentially expressed genes (DEGs) associated with late blight resistance. Wild potato species such as PIN45 (Solanum pinnatisectum), CPH62 (Solanum cardiophyllum), JAM07 (Solanum jamesii), MCD24 (Solanum microdontum), PLD47 (Solanum polyadenium), and cv. Kufri Bahar (control) were tested by artificial inoculation of P. infestans under controlled conditions. Transcriptomes of the leaf tissues (96 h post-inoculation) were sequenced using the Illumina platform. Statistically significant (p < 0.05) DEGs were analyzed in wild species by comparison with the control, and upregulated (>2 log2 fold change, FC) and downregulated (<-2 log2 FC) genes were identified. DEGs were functionally characterized with Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Selected genes were validated by real-time PCR analysis to confirm RNA-seq results. We identified some upregulated genes associated with late blight resistance in wild species such as cytochrome P450, proline-rich protein, MYB transcription factor MYB139, ankyrin repeat-containing protein, and LRR receptor-like serine/threonine-protein kinase in PIN45; glucosyltransferase, fructose-bisphosphate aldolase, and phytophthora-inhibited protease 1 in CPH62; steroid binding protein and cysteine proteinase 3 in JAM07; glycine-rich cell wall structural protein 1 and RING finger protein in MCD24; and cysteine proteinase 3 and major latex protein in PLD47. On the other hand, downregulated genes in these species were snakin-2 and WRKY transcription factor 3 in PIN45; lichenase and phenylalanine ammonia-lyase 1 in CPH62; metallothionein and LRR receptor-like serine/threonine-protein kinase in JAM07; UDP-glucoronosyl/UDP-glucosyl transferase family protein and steroid binding protein in MCD24; and cytoplasmic small heat shock protein class I and phosphatase PLD47. Our study identified highly resistant wild potato species and underlying genes such as disease resistance, stress response, phytohormones, and transcription factors (e.g., MYB, WRKY, AP2/ERF, and AN1) associated with late blight resistance in wild potato species.
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Affiliation(s)
- Nisha Bhatia
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Jagesh Kumar Tiwari
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Division of Vegetable Improvement, Indian Council of Agricultural Research—Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Chandresh Kumari
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Rasna Zinta
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Sanjeev Sharma
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay Kumar Thakur
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Tanuja Buckseth
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Dalamu Dalamu
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajesh Kumar Singh
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Division of Vegetable Improvement, Indian Council of Agricultural Research—Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Vinod Kumar
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Singh DP, Bisen MS, Prabha R, Maurya S, Yerasu SR, Shukla R, Tiwari JK, Chaturvedi KK, Farooqi MS, Srivastava S, Rai A, Sarma BK, Rai N, Singh PM, Behera TK, Farag MA. Untargeted Metabolomics of Alternaria solani-Challenged Wild Tomato Species Solanum cheesmaniae Revealed Key Metabolite Biomarkers and Insight into Altered Metabolic Pathways. Metabolites 2023; 13:metabo13050585. [PMID: 37233626 DOI: 10.3390/metabo13050585] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 05/27/2023] Open
Abstract
Untargeted metabolomics of moderately resistant wild tomato species Solanum cheesmaniae revealed an altered metabolite profile in plant leaves in response to Alternaria solani pathogen. Leaf metabolites were significantly differentiated in non-stressed versus stressed plants. The samples were discriminated not only by the presence/absence of specific metabolites as distinguished markers of infection, but also on the basis of their relative abundance as important concluding factors. Annotation of metabolite features using the Arabidopsis thaliana (KEGG) database revealed 3371 compounds with KEGG identifiers belonging to biosynthetic pathways including secondary metabolites, cofactors, steroids, brassinosteroids, terpernoids, and fatty acids. Annotation using the Solanum lycopersicum database in PLANTCYC PMN revealed significantly upregulated (541) and downregulated (485) features distributed in metabolite classes that appeared to play a crucial role in defense, infection prevention, signaling, plant growth, and plant homeostasis to survive under stress conditions. The orthogonal partial least squares discriminant analysis (OPLS-DA), comprising a significant fold change (≥2.0) with VIP score (≥1.0), showed 34 upregulated biomarker metabolites including 5-phosphoribosylamine, kaur-16-en-18-oic acid, pantothenate, and O-acetyl-L-homoserine, along with 41 downregulated biomarkers. Downregulated metabolite biomarkers were mapped with pathways specifically known for plant defense, suggesting their prominent role in pathogen resistance. These results hold promise for identifying key biomarker metabolites that contribute to disease resistive metabolic traits/biosynthetic routes. This approach can assist in mQTL development for the stress breeding program in tomato against pathogen interactions.
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Affiliation(s)
| | | | - Ratna Prabha
- ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
| | - Sudarshan Maurya
- ICAR-Indian Institute of Vegetable Research, Varanasi 221305, India
| | | | - Renu Shukla
- Indian Council of Agricultural Research, New Delhi 110012, India
| | | | | | - Md Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
| | - Birinchi Kumar Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Nagendra Rai
- ICAR-Indian Institute of Vegetable Research, Varanasi 221305, India
| | | | | | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Cairo 11562, Egypt
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Tiwari JK, Singh AK, Behera TK. CRISPR/Cas genome editing in tomato improvement: Advances and applications. Front Plant Sci 2023; 14:1121209. [PMID: 36909403 PMCID: PMC9995852 DOI: 10.3389/fpls.2023.1121209] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/02/2023] [Indexed: 06/12/2023]
Abstract
The narrow genetic base of tomato poses serious challenges in breeding. Hence, with the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (CRISPR/Cas9) genome editing, fast and efficient breeding has become possible in tomato breeding. Many traits have been edited and functionally characterized using CRISPR/Cas9 in tomato such as plant architecture and flower characters (e.g. leaf, stem, flower, male sterility, fruit, parthenocarpy), fruit ripening, quality and nutrition (e.g., lycopene, carotenoid, GABA, TSS, anthocyanin, shelf-life), disease resistance (e.g. TYLCV, powdery mildew, late blight), abiotic stress tolerance (e.g. heat, drought, salinity), C-N metabolism, and herbicide resistance. CRISPR/Cas9 has been proven in introgression of de novo domestication of elite traits from wild relatives to the cultivated tomato and vice versa. Innovations in CRISPR/Cas allow the use of online tools for single guide RNA design and multiplexing, cloning (e.g. Golden Gate cloning, GoldenBraid, and BioBrick technology), robust CRISPR/Cas constructs, efficient transformation protocols such as Agrobacterium, and DNA-free protoplast method for Cas9-gRNAs ribonucleoproteins (RNPs) complex, Cas9 variants like PAM-free Cas12a, and Cas9-NG/XNG-Cas9, homologous recombination (HR)-based gene knock-in (HKI) by geminivirus replicon, and base/prime editing (Target-AID technology). This mini-review highlights the current research advances in CRISPR/Cas for fast and efficient breeding of tomato.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Division of Vegetable Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Anand Kumar Singh
- Division of Horticulture, Indian Council of Agricultural Research, Krishi Anusandhan Bhawan - II, Pusa, New Delhi, India
| | - Tusar Kanti Behera
- Division of Vegetable Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
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Zinta R, Tiwari JK, Buckseth T, Thakur K, Goutam U, Kumar D, Challam C, Bhatia N, Poonia AK, Naik S, Singh RK, Thakur AK, Dalamu D, Luthra SK, Kumar V, Kumar M. Root system architecture for abiotic stress tolerance in potato: Lessons from plants. Front Plant Sci 2022; 13:926214. [PMID: 36212284 PMCID: PMC9539750 DOI: 10.3389/fpls.2022.926214] [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] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
The root is an important plant organ, which uptakes nutrients and water from the soil, and provides anchorage for the plant. Abiotic stresses like heat, drought, nutrients, salinity, and cold are the major problems of potato cultivation. Substantial research advances have been achieved in cereals and model plants on root system architecture (RSA), and so root ideotype (e.g., maize) have been developed for efficient nutrient capture to enhance nutrient use efficiency along with genes regulating root architecture in plants. However, limited work is available on potatoes, with a few illustrations on root morphology in drought and nitrogen stress. The role of root architecture in potatoes has been investigated to some extent under heat, drought, and nitrogen stresses. Hence, this mini-review aims to update knowledge and prospects of strengthening RSA research by applying multi-disciplinary physiological, biochemical, and molecular approaches to abiotic stress tolerance to potatoes with lessons learned from model plants, cereals, and other plants.
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Affiliation(s)
- Rasna Zinta
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Lovely Professional University, Phagwada, Punjab, India
| | - Jagesh Kumar Tiwari
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Tanuja Buckseth
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Kanika Thakur
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Umesh Goutam
- Lovely Professional University, Phagwada, Punjab, India
| | - Devendra Kumar
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Regional Station, Meerut, India
| | - Clarissa Challam
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Regional Station, Shillong, India
| | - Nisha Bhatia
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Anuj K. Poonia
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Sharmistha Naik
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Indian Council of Agricultural Research (ICAR)-National Research Centre for Grapes, Pune, Maharashtra, India
| | - Rajesh K. Singh
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay K. Thakur
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Dalamu Dalamu
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Satish K. Luthra
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Regional Station, Meerut, India
| | - Vinod Kumar
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Manoj Kumar
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Regional Station, Meerut, India
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Tiwari JK, A J, Tuteja N, Khurana SMP. Genome editing (CRISPR-Cas)-mediated virus resistance in potato (Solanum tuberosum L.). Mol Biol Rep 2022; 49:12109-12119. [PMID: 35764748 DOI: 10.1007/s11033-022-07704-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 06/14/2022] [Indexed: 11/26/2022]
Abstract
Plant viruses are the major pathogens that cause heavy yield loss in potato. The important viruses are potato virus X, potato virus Y and potato leaf roll virus around the world. Besides these three viruses, a novel tomato leaf curl New Delhi virus is serious in India. Conventional cum molecular breeding and transgenics approaches have been applied to develop virus resistant potato genotypes. But progress is slow in developing resistant varieties due to lack of host genes and long breeding process, and biosafety concern with transgenics. Hence, CRISPR-Cas mediated genome editing has emerged as a powerful technology to address these issues. CRISPR-Cas technology has been deployed in potato for several important traits. We highlight here CRISPR-Cas approaches of virus resistance through targeting viral genome (DNA or RNA), host factor gene and multiplexing of target genes simultaneously. Further, advancement in CRISPR-Cas research is presented in the area of DNA-free genome editing, virus-induced genome editing, and base editing. CRISPR-Cas delivery, transformation methods, and challenges in tetraploid potato and possible methods are also discussed.
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Affiliation(s)
- Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
| | - Jeevalatha A
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi, 110067, India
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7
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Tiwari JK, Buckseth T, Challam C, Zinta R, Bhatia N, Dalamu D, Naik S, Poonia AK, Singh RK, Luthra SK, Kumar V, Kumar M. CRISPR/Cas Genome Editing in Potato: Current Status and Future Perspectives. Front Genet 2022; 13:827808. [PMID: 35186041 PMCID: PMC8849127 DOI: 10.3389/fgene.2022.827808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, India.,School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, 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
| | | | | | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Meerut, 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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Tiwari JK, Rawat S, Luthra SK, Zinta R, Sahu S, Varshney S, Kumar V, Dalamu D, Mandadi N, Kumar M, Chakrabarti SK, Rao AR, Rai A. Genome sequence analysis provides insights on genomic variation and late blight resistance genes in potato somatic hybrid (parents and progeny). Mol Biol Rep 2021; 48:623-635. [PMID: 33442830 DOI: 10.1007/s11033-020-06106-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/18/2020] [Indexed: 11/29/2022]
Abstract
Wild Solanum species are the important resources for potato improvement. With the availability of potato genome and sequencing progress, knowledge about genomic resources is essential for novel genes discovery. Hence, the aim of this study was to decipher draft genome sequences of unique potato genotypes i.e. somatic hybrid P8 (J1), wild species S. pinnatisectum (J2), progeny MSH/14-112 (P8 × cv. Kufri Jyoti) (J3), and S. tuberosum dihaploid C-13 (J4). Draft genome sequencing using Illumina platform and reference-based assemblies with the potato genome yielded genome assembly size of 725.01 Mb (J1), 724.95 Mb (J2), 725.01 Mb (J3), and 809.59 Mb (J4). Further, 39,260 (J1), 25,711 (J2), 39,730 (J3) and 30,241 (J4) genes were identified and 17,411 genes were found common in the genotypes particularly late blight resistance genes (R3a, RGA2, RGA3, R1B-16, Rpi-blb2, Rpi and Rpi-vnt1). Gene ontology (GO) analysis showed that molecular function was predominant and signal transduction was major KEGG pathways. Further, gene enrichment analysis revealed dominance of metabolic process (GO: 0008152) in all the samples. Phylogeny analysis showed relatedness with potato and other plant species. Heterozygous single nucleotide polymorphism (SNP) was more than homozygous, and SNP in genic region was more than inter-genic region. Copy number variation (CNV) analysis indicated greater number of deletions than duplications. Sequence diversity and conserved motifs analysis revealed variation for late blight resistance genes. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed differential expression of late blight resistance genes. Our study provides insights on genome sequence, structural variation and late blight resistance genes in potato somatic hybrid (parents and progeny) for future research.
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Affiliation(s)
- Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India.
| | - Shashi Rawat
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Satish K Luthra
- ICAR-Central Potato Research Institute, Regional Station, Modipuram, Meerut, 250110, Uttar Pradesh, India
| | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Sarika Sahu
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Shivangi Varshney
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Dalamu Dalamu
- ICAR-Central Potato Research Institute, Regional Station, Kufri, Shimla, 171012, Himachal Pradesh, India
| | - Nagesh Mandadi
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | | | - Atmakuri R Rao
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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Tiwari JK, Buckseth T, Singh RK, Kumar M, Kant S. Prospects of Improving Nitrogen Use Efficiency in Potato: Lessons From Transgenics to Genome Editing Strategies in Plants. Front Plant Sci 2020; 11:597481. [PMID: 33424892 PMCID: PMC7785987 DOI: 10.3389/fpls.2020.597481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/10/2020] [Indexed: 05/27/2023]
Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Tanuja Buckseth
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Manoj Kumar
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Faculty of Veterinary and Agricultural Sciences, Centre for Agricultural Innovation, School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
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11
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Tiwari JK, Buckseth T, Devi S, Varshney S, Sahu S, Patil VU, Zinta R, Ali N, Moudgil V, Singh RK, Rawat S, Dua VK, Kumar D, Kumar M, Chakrabarti SK, Rao AR, Rai A. Physiological and genome-wide RNA-sequencing analyses identify candidate genes in a nitrogen-use efficient potato cv. Kufri Gaurav. Plant Physiol Biochem 2020; 154:171-183. [PMID: 32563041 DOI: 10.1016/j.plaphy.2020.05.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/30/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
Nitrogen (N) is an important nutrient for plant growth. However, its excess application leads to environmental damage. Hence, improving nitrogen use efficiency (NUE) of plant is one of the plausible options to solve the problems. Aim of this study was to identify candidate genes involved in enhancing NUE in potato cv. Kufri Gaurav (N efficient). Plants were grown in aeroponic with two contrasting N regimes (low N: 0.75 mM, and high N: 7.5 mM). Higher NUE in Kufri Gaurav was observed in low N based on the parameters like NUE, NUpE (N uptake efficiency), NUtE (N utilization efficiency) and AgNUE (agronomic NUE). Further, global gene expression profiles in root, leaf and stolon tissues were analyzed by RNA-sequencing using Ion Proton™ System. Quality data (≥Q20) of 2.04-2.73 Gb per sample were mapped with the potato genome. Statistically significant (P ≤ 0.05) differentially expressed genes (DEGs) were identified such as 176 (up-regulated) and 30 (down-regulated) in leaves, 39 (up-regulated) and 105 (down-regulated) in roots, and 81 (up-regulated) and 694 (down-regulated) in stolons. The gene ontology (GO) terms like metabolic process, cellular process and catalytic activity were predominant. Our RT-qPCR analysis confirmed the gene expression profiles of RNA-seq. Overall, we identified candidate genes associated with improving NUE such as superoxide dismutase, GDSL esterase lipase, probable phosphatase 2C, high affinity nitrate transporters, sugar transporter, proline rich proteins, transcription factors (VQ motif, SPX domain, bHLH) etc. Our findings suggest that these candidate genes probably play crucial roles in enhancing NUE in potato.
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Affiliation(s)
- Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India.
| | - Tanuja Buckseth
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Sapna Devi
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Shivangi Varshney
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Sahu
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Virupaksh U Patil
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Nilofer Ali
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Vaishali Moudgil
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Rajesh K Singh
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Shashi Rawat
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Vijay K Dua
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Devendra Kumar
- CAR-Central Potato Research Institute, Regional Station, Modipuram, Meerut, 250110, Uttar Pradesh, India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India; CAR-Central Potato Research Institute, Regional Station, Modipuram, Meerut, 250110, Uttar Pradesh, India
| | | | - Atmakuri R Rao
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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12
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Tiwari JK, Buckseth T, Zinta R, Saraswati A, Singh RK, Rawat S, Chakrabarti SK. Genome-wide identification and characterization of microRNAs by small RNA sequencing for low nitrogen stress in potato. PLoS One 2020; 15:e0233076. [PMID: 32428011 PMCID: PMC7237020 DOI: 10.1371/journal.pone.0233076] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/28/2020] [Indexed: 11/18/2022] Open
Abstract
Nitrogen is an important nutrient for plant growth and tuber quality of potato. Since potato crop requires high dose of N, improving nitrogen use efficiency (NUE) of plant is an inevitable approach to minimize N fertilization. The aim of this study was to identify and characterize microRNAs (miRNAs) by small RNA sequencing in potato plants grown in aeroponic under two contrasting N (high and low) regimes. A total of 119 conserved miRNAs belonging to 41 miRNAs families, and 1002 putative novel miRNAs were identified. From total, 52 and 54 conserved miRNAs, and 404 and 628 putative novel miRNAs were differentially expressed in roots and shoots, respectively under low N stress. Of total 34,135 predicted targets, the gene ontology (GO) analysis indicated that maximum targets belong to biological process followed by molecular function and cellular component. Eexpression levels of the selected miRNAs and targets were validated by real time-quantitative polymerase chain reaction (RT-qPCR) analysis. Two predicted targets of potential miRNAs (miR397 and miR398) were validated by 5' RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). In general, predicted targets are associated with stress-related, kinase, transporters and transcription factors such as universal stress protein, heat shock protein, salt-tolerance protein, calmodulin binding protein, serine-threonine protein kinsae, Cdk10/11- cyclin dependent kinase, amino acid transporter, nitrate transporter, sugar transporter, transcription factor, F-box family protein, and zinc finger protein etc. Our study highlights that miR397 and miR398 play crucial role in potato during low N stress management. Moreover, study provides insights to modulate miRNAs and their predicted targets to develop N-use efficient potato using transgenic/genome-editing tools in future.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- * E-mail:
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Aastha Saraswati
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Shashi Rawat
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Swarup Kumar Chakrabarti
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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13
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Tiwari JK, Buckseth T, Zinta R, Saraswati A, Singh RK, Rawat S, Dua VK, Chakrabarti SK. Transcriptome analysis of potato shoots, roots and stolons under nitrogen stress. Sci Rep 2020; 10:1152. [PMID: 31980689 PMCID: PMC6981199 DOI: 10.1038/s41598-020-58167-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 07/16/2019] [Accepted: 01/13/2020] [Indexed: 12/19/2022] Open
Abstract
Potato crop requires high dose of nitrogen (N) to produce high tuber yield. Excessive application of N causes environmental pollution and increases cost of production. Hence, knowledge about genes and regulatory elements is essential to strengthen research on N metabolism in this crop. In this study, we analysed transcriptomes (RNA-seq) in potato tissues (shoot, root and stolon) collected from plants grown in aeroponic culture under controlled conditions with varied N supplies i.e. low N (0.2 milli molar N) and high N (4 milli molar N). High quality data ranging between 3.25 to 4.93 Gb per sample were generated using Illumina NextSeq500 that resulted in 83.60-86.50% mapping of the reads to the reference potato genome. Differentially expressed genes (DEGs) were observed in the tissues based on statistically significance (p ≤ 0.05) and up-regulation with ≥ 2 log2 fold change (FC) and down-regulation with ≤ -2 log2 FC values. In shoots, of total 19730 DEGs, 761 up-regulated and 280 down-regulated significant DEGs were identified. Of total 20736 DEGs in roots, 572 (up-regulated) and 292 (down-regulated) were significant DEGs. In stolons, of total 21494 DEG, 688 and 230 DEGs were significantly up-regulated and down-regulated, respectively. Venn diagram analysis showed tissue specific and common genes. The DEGs were functionally assigned with the GO terms, in which molecular function domain was predominant in all the tissues. Further, DEGs were classified into 24 KEGG pathways, in which 5385, 5572 and 5594 DEGs were annotated in shoots, roots and stolons, respectively. The RT-qPCR analysis validated gene expression of RNA-seq data for selected genes. We identified a few potential DEGs responsive to N deficiency in potato such as glutaredoxin, Myb-like DNA-binding protein, WRKY transcription factor 16 and FLOWERING LOCUS T in shoots; high-affinity nitrate transporter, protein phosphatase-2c, glutaredoxin family protein, malate synthase, CLE7, 2-oxoglutarate-dependent dioxygenase and transcription factor in roots; and glucose-6-phosphate/phosphate translocator 2, BTB/POZ domain-containing protein, F-box family protein and aquaporin TIP1;3 in stolons, and many genes of unknown function. Our study highlights that these potential genes play very crucial roles in N stress tolerance, which could be useful in augmenting research on N metabolism in potato.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Aastha Saraswati
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Shashi Rawat
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Vijay Kumar Dua
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Swarup Kumar Chakrabarti
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
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14
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Tiwari JK, Ali N, Devi S, Zinta R, Kumar V, Chakrabarti SK. Analysis of allelic variation in wild potato ( Solanum) species by simple sequence repeat (SSR) markers. 3 Biotech 2019; 9:262. [PMID: 31192087 DOI: 10.1007/s13205-019-1785-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/30/2019] [Indexed: 10/26/2022] Open
Abstract
Allelic variation in wild potato (Solanum) species was analysed using 14 simple sequence repeat (SSR) markers. SSR allelic profiles showed high polymorphism and distinctness among the wild species. A total of 109 alleles of 14 polymorphic SSR markers were scored in 82 accessions belonging to 22 wild potato species. Allele size ranged from a minimum of 104 bp (STI0030) to a maximum of 304 bp (STM5114). Number of SSR alleles per marker ranged from 4 (STM5127/STM1053) to 13 (STM0019), whereas PIC value varied between 0.66 (STM1053) and 0.91 (STM0019). Cluster analysis using SSR allelic profiles of 82 accessions grouped showed 5 major clusters (I-V) based on the Dice similarity coefficient using neighbour-joining clustering method. Distinct allelic variations were observed among the accessions irrespective of the origin country, series and species. Our study suggests that SSR-based molecular characterization of wild potato species is accession specific and development of an allelic dataset for all the accessions would strengthen their utilization in potato research in future.
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15
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Tiwari JK, Devi S, Sundaresha S, Chandel P, Ali N, Singh B, Bhardwaj V, Singh BP. Microarray analysis of gene expression patterns in the leaf during potato tuberization in the potato somatic hybrid Solanum tuberosum and Solanum etuberosum. Genome 2015; 58:305-13. [PMID: 26284309 DOI: 10.1139/gen-2014-0191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genes involved in photoassimilate partitioning and changes in hormonal balance are important for potato tuberization. In the present study, we investigated gene expression patterns in the tuber-bearing potato somatic hybrid (E1-3) and control non-tuberous wild species Solanum etuberosum (Etb) by microarray. Plants were grown under controlled conditions and leaves were collected at eight tuber developmental stages for microarray analysis. A t-test analysis identified a total of 468 genes (94 up-regulated and 374 down-regulated) that were statistically significant (p ≤ 0.05) and differentially expressed in E1-3 and Etb. Gene Ontology (GO) characterization of the 468 genes revealed that 145 were annotated and 323 were of unknown function. Further, these 145 genes were grouped based on GO biological processes followed by molecular function and (or) PGSC description into 15 gene sets, namely (1) transport, (2) metabolic process, (3) biological process, (4) photosynthesis, (5) oxidation-reduction, (6) transcription, (7) translation, (8) binding, (9) protein phosphorylation, (10) protein folding, (11) ubiquitin-dependent protein catabolic process, (12) RNA processing, (13) negative regulation of protein, (14) methylation, and (15) mitosis. RT-PCR analysis of 10 selected highly significant genes (p ≤ 0.01) confirmed the microarray results. Overall, we show that candidate genes induced in leaves of E1-3 were implicated in tuberization processes such as transport, carbohydrate metabolism, phytohormones, and transcription/translation/binding functions. Hence, our results provide an insight into the candidate genes induced in leaf tissues during tuberization in E1-3.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Sapna Devi
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - S Sundaresha
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Poonam Chandel
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Nilofer Ali
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Brajesh Singh
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Vinay Bhardwaj
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Bir Pal Singh
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
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16
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Tiwari JK, Saurabh S, Chandel P, Pal Singh B, Bhardwaj V. Analysis of genetic and epigenetic variation in in vitro propagated potato somatic hybrid by AFLP and MSAP marker. ELECTRON J BIOTECHN 2013. [DOI: 10.2225/vol16-issue6-fulltext-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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17
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Abstract
Neurons of the medullary raphe project widely to respiratory and autonomic nuclei and contain co-localized serotonin, thyrotropin-releasing hormone (TRH), and substance P, three neurotransmitters known to stimulate ventilation. Some medullary raphe neurons are highly sensitive to pH and CO2 and have been proposed to be central chemoreceptors. Here it was determined whether these chemosensitive neurons are serotonergic. Cells were microdissected from the rat medullary raphe and maintained in primary cell culture for 13–70 days. Immunoreactivity for serotonin, substance P, and TRH was present in these cultures. All acidosis-stimulated neurons ( n = 22) were immunoreactive for tryptophan hydroxylase (TpOH-IR), the rate-limiting enzyme for serotonin biosynthesis, whereas all acidosis-inhibited neurons ( n= 16) were TpOH-immunonegative. The majority of TpOH-IR medullary raphe neurons (73%) were stimulated by acidosis. The electrophysiological properties of TpOH-IR neurons in culture were similar to those previously reported for serotonergic neurons in vivo and in brain slices. These properties included wide action potentials (4.55 ± 0.5 ms) with a low variability of the interspike interval, a postspike afterhyperpolarization (AHP) that reversed 25 mV more positive than the Nernst potential for K+, prominent A current, spike frequency adaptation and a prolonged AHP after a depolarizing pulse. Thus the intrinsic cellular properties of serotonergic neurons were preserved in cell culture, indicating that the results obtained using this in vitro approach are relevant to serotonergic neurons in vivo. These results demonstrate that acidosis-stimulated neurons of the medullary raphe contain serotonin. We propose that serotonergic neurons initiate a homeostatic response to changes in blood CO2 that includes increased ventilation and modulation of autonomic function.
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Affiliation(s)
- W Wang
- Departments of Neurology and Cellular and Molecular Physiology, Yale University, New Haven Connecticut, 06510, USA
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18
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Tiwari JK, Sikdar SK. The kinetics of a non-inactivating K(+) current in alphaT3-1 pituitary gonadotropes is not affected by holding potential. Brain Res 2000; 873:218-24. [PMID: 10930547 DOI: 10.1016/s0006-8993(00)02470-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The non-inactivating K(+) currents in alphaT3-1, a gonadotroph cell line, were recorded in the presence of low intracellular free calcium concentration. The activation kinetics of the whole-cell currents and the gating charge measured from holding potential (V(HOLD)) of -10 mV, V(HOLD)=-80 mV in presence of 4-AP (4-aminopyridine), and V(HOLD)=-10 mV with a hyperpolarizing prepulse to -80 mV were similar. No difference was observed in the onset of currents elicited from the hyperpolarizing potentials, suggesting deviation from the Cole-Moore prediction of increase in the delay of current onset with increasing hyperpolarization. The data suggests that the channel opens with at least one rate-limiting voltage-dependent step, which may imply that the position of the voltage sensor is unaffected by hyperpolarization.
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Affiliation(s)
- J K Tiwari
- Molecular Biophysics Unit, Indian Institute of Science, 560012, Bangalore, India
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19
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Abstract
The chimeric channel, 4N/1, generated from two outwardly rectifying K+ channels by linking the N-terminal cytoplasmic domain of hKv1.4 with the transmembrane body of hKv1.1, functions as an inward rectifier. The operating range of the channel is shifted to hyperpolarizing potentials and it is inactivated at resting membrane potentials. Co-expression of a truncated form of hKv1.1 with the N-terminal domain of hKv1.4 results in the same physiology as the chimaera implying specific interactions between the two segments.
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Affiliation(s)
- B Chanda
- National Center for Biological Sciences, TIFR, Bangalore, India
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20
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Abstract
Temperature was used as a biophysical tool to investigate the energy changes associated with conformational change during the gating of a non-inactivating voltage-gated K+ channel present in the membrane of alpha T3-1 cells, a gonadotroph cell line. The time course of the current activation was described by a single exponential function at three temperatures: 15, 25 and 35 degrees C. The Q10 values were between 1.5 to 1.9 and in agreement with the activation energy determined from Arrhenius plots of the forward and backward rate constants associated with channel opening. The Gibb's free energy change associated with channel opening and closing at various membrane potentials estimated by two approaches yield similar values. The changes in Gibb's free energy (delta G degree) with depolarization potential is a quadratic and more prominent at 15 than at 25 or 35 degrees C. The results suggest that increase in temperature favours movement of voltage sensing segments, and reduces the restraint on them brought about by other parts of the channel molecule.
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Affiliation(s)
- J K Tiwari
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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21
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Abstract
A chimeric channel, 4N/1, was generated from two outwardly rectifying K+ channels by linking the N-terminal cytoplasmic domain of hKv1.4 (N terminus ball and chain of hKv1.4) with the transmembrane body of hKv1.1 (delta78N1 construct of hKv1.1). The recombinant channel has properties similar to the six transmembrane inward rectifiers and opens on hyperpolarization with a threshold of activation at -90 mV. Outward currents are seen on depolarization provided the channel is first exposed to a hyperpolarizing pulse of -100 mV or more. Hyperpolarization at and beyond -130 mV provides evidence of channel deactivation. Delta78N1 does not show inward currents on hyperpolarization but does open on depolarizing from -80 mV with characteristics similar to native hKv1.1. The outward currents seen in both delta78N1 and 4N/1 inactivate slowly at rates consistent with C-type inactivation. The inward rectification of the 4N/1 chimera is consistent with the inactivation gating mechanism. This implies that the addition of the N-terminus from hKv1.4 to hKv1.1 shifts channel activation to hyperpolarizing potentials. These results suggest a mechanism involving the N-terminal cytoplasmic domain for conversion of outward rectifiers to inward rectifiers.
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Affiliation(s)
- B Chanda
- National Centre for Biological Sciences, TIFR Centre, Indian Institute of Science Campus, Bangalore
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22
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Abstract
AlphaT3-1 cells showed a slope resistance of 1.8 Gomega. The cell membrane surface was not smooth and a scanning electron micrograph showed a complex structure with blebs and microvilli like projections. The cells showed spontaneous fluctuations at zero current resting membrane potential and hyperpolarization increased the amplitude of membrane potential fluctuations. The amplitude of membrane potential fluctuations at hyperpolarized membrane potential was attenuated on application of TTX to the bath solution. The potential at which half steady state inactivation of isolated sodium current occurred, was at a very hyperpolarized potential (-95.4 mV). The study presented in this paper shows that the voltage gated sodium channels contribute to the increase in the amplitude of electrical noise with hyperpolarization in alphaT3-1 cells.
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Affiliation(s)
- J K Tiwari
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
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