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Arutselvan R, Makeshkumar T. Single-tube colorimetric loop-mediated isothermal amplification (LAMP) assay for high-sensitivity detection of SLCMV in cassava from southern India. Microb Pathog 2024; 192:106718. [PMID: 38815777 DOI: 10.1016/j.micpath.2024.106718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/01/2024]
Abstract
Sri Lankan cassava mosaic virus (SLCMV) is a major cause for mosaic infections in cassava leaves, resulting in significant economic losses in southern India. SLCMV leads to growth retardation, leaf curl, and chlorosis in the host, with rapid transmission through whitefly insect vectors. Detecting SLCMV promptly is crucial, and the study introduces a novel and efficient colorimetric Loop-mediated isothermal amplification (LAMP) assay for successful detection in 60 min. Three primer sets were designed to target the conserved region of the SLCMV genome, specifically the coat protein gene, making the assay highly specific. The LAMP assay offers rapid and sensitive detection, completing within 60 min in a temperature-controlled water bath or thermal cycler. Compared to PCR techniques, it demonstrates 100 times superior sensitivity. The visual inspection of LAMP tube results using a nucleic acid dye and observing ladder-like pattern bands in a 2 % agarose gel confirms the presence of SLCMV. The assay is specific to SLCMV, showing no false positives or contaminations when tested against other virus. The standardized SLCMV LAMP assay proves technically efficient, providing a rapid, specific, simple, and low-cost solution, streamlining the detection and management of SLCMV.
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Affiliation(s)
- R Arutselvan
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - T Makeshkumar
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India.
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Jeevalatha A, Siddappa S, Kumar R, Tiwari RK, Lal MK, Sharma S, Chakrabarti SK, Singh BP. RNA-seq analysis reveals an early defense response to tomato leaf curl New Delhi virus in potato cultivar Kufri Bahar. Funct Integr Genomics 2023; 23:215. [PMID: 37389664 DOI: 10.1007/s10142-023-01138-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
Potatoes in India are very susceptible to apical leaf curl disease, which causes severe symptoms and greater yield losses. Because the majority of potato cultivars are susceptible to the virus, it is crucial to discover sources of resistance and investigate the mechanism of resistance/susceptibility in potato cultivars. In this study, the gene expression profile of two potato cultivars, Kufri Bahar (resistant) and Kufri Pukhraj (susceptible), varying in their level of resistance to ToLCNDV, was analyzed using RNA-Seq. The Ion ProtonTM system was used to sequence eight RiboMinus RNA libraries from inoculated and uninoculated potato plants at 15 and 20 days after inoculation (DAI). The findings indicated that the majority of differentially expressed genes (DEGs) were cultivar-or time-specific. These DEGs included genes for proteins that interact with viruses, genes linked with the cell cycle, genes for proteins involved in defense, transcription and translation initiation factors, and plant hormone signaling pathway genes. Interestingly, defense responses were generated early in Kufri Bahar, at 15 DAI, which may have impeded the replication and spread of ToLCNDV. This research provides a genome-wide transcriptional analysis of two potato cultivars with variable levels of ToLCNDV resistance. At an early stage, we observed suppression of genes that interact with viral proteins, induction of genes associated with restriction of cell division, genes encoding defense proteins, AP2/ERF transcription factors, and altered expression of zinc finger protein genes, HSPs, JA, and SA pathway-related genes. Our findings add to a greater comprehension of the molecular basis of potato resistance to ToLCNDV and may aid in the development of more effective disease management techniques.
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Affiliation(s)
- Arjunan Jeevalatha
- ICAR- Central Potato Research Institute, Shimla, 171 001, Himachal Pradesh, India
- ICAR- Indian Institute of Spices Research, Kozhikode, 673 012, Kerala, India
| | - Sundaresha Siddappa
- ICAR- Central Potato Research Institute, Shimla, 171 001, Himachal Pradesh, India
| | - Ravinder Kumar
- ICAR- Central Potato Research Institute, Shimla, 171 001, Himachal Pradesh, India.
| | - Rahul Kumar Tiwari
- ICAR- Central Potato Research Institute, Shimla, 171 001, Himachal Pradesh, India.
| | - Milan Kumar Lal
- ICAR- Central Potato Research Institute, Shimla, 171 001, Himachal Pradesh, India
| | - Sanjeev Sharma
- ICAR- Central Potato Research Institute, Shimla, 171 001, Himachal Pradesh, India
| | | | - Bir Pal Singh
- ICAR- Central Potato Research Institute, Shimla, 171 001, Himachal Pradesh, India
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Naga KC, Siddappa S, Kumar R, Tiwari RK, Subhash S, Verma G, Buckseth T, Bairwa A, Sharma S, Katare S, Srivastava RM, Bansode GM, Sarkar A, Patel JK. A new record of Asia II 5 genetic group of Bemisia tabaci (Gennadius) in the major potato growing areas of India and its relationship with tomato leaf curl New Delhi virus infecting potato. 3 Biotech 2021; 11:421. [PMID: 34603921 DOI: 10.1007/s13205-021-02966-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/19/2021] [Indexed: 01/09/2023] Open
Abstract
The whitefly, Bemisia tabaci (Gennadius), is responsible for significant yield losses in many crops, including potato, by sucking the phloem sap and transmitting a number of plant viruses. B. tabaci is a complex of cryptic species which is commonly designated as genetic groups. The B. tabaci genetic groups differ biologically with respect to host plant preference, insecticidal resistance, reproduction capacity, and ability to transmit begomoviruses. Therefore, understanding genetic variation among populations is important for establishing crop-specific distribution profile and management. We sequenced the mitochondrial cytochrome oxidase I (mtCOI) gene of B. tabaci collected from major potato growing areas of India. BLAST analysis of the 24 mtCOI sequences with reference Gene Bank sequences revealed four B. tabaci genetic groups prevailing in this region. mtCOI analysis exhibited the presence of Asia II 1, Asia II 5, Asia 1, and MEAM1 B. tabaci genetic groups. Our study highlighted that a new genetic group Asia II 5 has been detected in Indo-Gangetic Plains. Further virus-vector relationship study of ToLCNDV with Asia II 5 B. tabaci revealed that females are efficient vector of this virus as compared to males. This behavior of females might be due to their ability to acquire more virus titer than males. This study will help in better understanding of whitefly genetic group mediated virus diseases.
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Affiliation(s)
- Kailash C Naga
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Sundaresha Siddappa
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Rahul K Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - S Subhash
- ICAR-Central Potato Research Institute, Regional Station, Modipuram, Uttar Pradesh 250110 India
| | - Gaurav Verma
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Tanuja Buckseth
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Aarti Bairwa
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Subhash Katare
- Central Potato Research Station, Gwalior, Madhya Pradesh 474 020 India
| | - R M Srivastava
- GB Pant University of Agriculture & Technology, Pantnagar, Uttarakhand 263 145 India
| | - G M Bansode
- Regional Fruit Research Station, National Agricultural Research Project, Pune, Maharashtra 411 007 India
| | - Anirban Sarkar
- BC Krishi Vishwavidyalaya, Kalyani, West Bengal 741 235 India
| | - J K Patel
- Potato Research Station, Sardar Krushinagar Dantiwada Agricultural University, Deesa, Gujarat 385 535 India
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Lal MK, Tiwari RK, Kumar R, Naga KC, Kumar A, Singh B, Raigond P, Dutt S, Chourasia KN, Kumar D, Parmar V, Changan SS. Effect of potato apical leaf curl disease on glycemic index and resistant starch of potato (Solanum tuberosum L.) tubers. Food Chem 2021; 359:129939. [PMID: 33957333 DOI: 10.1016/j.foodchem.2021.129939] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 04/06/2021] [Accepted: 04/21/2021] [Indexed: 12/19/2022]
Abstract
Tomato leaf curl New Delhi virus-potato (ToLCNDV-potato) causes potato apical leaf curl disease which severely affects nutritional parameters such as carbohydrate, protein, and starch biosynthesis thereby altering glycemic index (GI) and resistant starch (RS) of potato. ToLCNDV-potato virus was inoculated on potato cultivars (Kufri Pukhraj [susceptible]; Kufri Bahar [resistant]) and various quality parameters of potato tuber were studied. There was a significant (P < 0.01) reduction in starch, amylose and resistant starch contents in the infected tubers. However, carbohydrate and amylopectin increased significantly (P < 0.01) which contributes to increased starch digestibility reflected with high GI and glycemic load values. Besides, ToLCNDV-potato infection leads to a significant increase in reducing sugar, sucrose, amino acid and protein in potato tubers. This is a first-ever study that highlights the impact of biotic stress on GI, RS and nutritional quality parameters of potato which is a matter of concern for consumers.
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Affiliation(s)
- Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India; ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India; ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
| | - Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India
| | | | - Awadhesh Kumar
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India
| | - Pinky Raigond
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India
| | - Som Dutt
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India
| | | | - Dharmendra Kumar
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India
| | - Vandana Parmar
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India
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Jeevalatha A, Vanishree G, Siddappa S, Kumar R, Kaundal P, Kumar A, Chakrabarti SK. Molecular characterization and infectivity analysis of tomato leaf curl New Delhi virus isolates infecting potato. 3 Biotech 2021; 11:203. [PMID: 33927993 DOI: 10.1007/s13205-021-02752-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/19/2021] [Indexed: 01/18/2023] Open
Abstract
Nucleotide sequence of complete genome of a new isolate (KAN-6) of tomato leaf curl New Delhi virus (ToLCNDV) from Kanpur, Uttar Pradesh, India was determined. Sequence analysis indicated that it shared maximum identity to ToLCNDV isolates from pumpkin and ashgourd. Infectious clones of isolate KAN-6 along with two other ToLCNDV isolates (MOD-21 & FAI-19) obtained from potato fields of Modipuram and Faizabad, India were produced and used in symptom expression studies in N. benthamiana and potato plants through agro-inoculation. These isolates produced different symptoms both in N. benthamiana and potato. Severe symptoms of yellow mottling, downward curling and stunted growth were observed in N. benthamiana plants inoculated with KAN-6. MOD-21-inoculated plants also showed downward curling, stunted growth, but yellow mottling was observed only in older leaves whereas FAI-19-inoculated plants produced only downward curling symptoms. In case of potato, typical symptoms of apical leaf curl disease were observed in cultivar Kufri Pukhraj inoculated with MOD-21 and KAN-6 that are similar to those produced by virus-infected plants in the field. However, MOD-21 produced more prominent yellow mosaic symptoms as compared to KAN-6. FAI-19 produced only restricted yellow spots in Kufri Pukhraj. Only mild symptoms appeared in KAN-6 and no symptoms were observed in MOD-21- and FAI-19-inoculated Kufri Bahar plants which is known to show lowest seed degeneration under field conditions. Analysis of genomic components indicated that these isolates had 94.8-94.9% and 87.9-97.3% identity among them in DNA A and DNA B, respectively. The results of the study indicate the association of ToLCNDV isolates of different symptomatology with apical leaf curl disease of potato. This is also a first experimental demonstration of Koch's postulate for a begomovirus associated with apical leaf curl disease of potato.Author names: Please confirm if the author names (Swarup Kumar Chakrabarti) are presented accurately and in the correct sequence (given name, middle name/initial, family name).Yes. It is correct. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02752-5.
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Jeevalatha A, Siddappa S, Kumar A, Kaundal P, Guleria A, Sharma S, Nagesh M, Singh BP. An insight into differentially regulated genes in resistant and susceptible genotypes of potato in response to tomato leaf curl New Delhi virus-[potato] infection. Virus Res 2017; 232:22-33. [PMID: 28115198 DOI: 10.1016/j.virusres.2017.01.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 01/04/2017] [Accepted: 01/08/2017] [Indexed: 12/13/2022]
Abstract
Apical leaf curl disease, caused by tomato leaf curl New Delhi virus-[potato] (ToLCNDV-[potato]) is one of the most important viral diseases of potato in India. Genetic resistance source for ToLCNDV in potato is not identified so far. However, the cultivar Kufri Bahar is known to show lowest seed degeneration even under high vector levels. Hence, microarray analysis was performed to identify differentially regulated genes during ToLCNDV-[potato] infection in a resistant (Kufri Bahar) and a susceptible cultivar (Kufri Pukhraj). Under artificial inoculation conditions, in Kufri Pukhraj, symptom expressions started at 15days after inoculation (DAI) and then progressed to severe symptoms, whereas no or only very mild symptoms were observed in Kufri Bahar up to 35 DAI. Correspondingly, qPCR assay indicated a high viral load in Kufri Pukhraj and a very low viral load in Kufri Bahar. Microarray analysis showed that a total of 1111 genes and 2588 genes were differentially regulated (|log2 (Fold Change)|>2) in Kufri Bahar and Kufri Pukhraj, respectively, following ToLCNDV-[potato] infection. Gene ontology and mapman analyses revealed that these altered transcripts were involved in various biological & metabolic processes. Several genes with unknown functions were 5 to 100 fold expressed after virus infection and further experiments are necessary to ascertain their role in disease resistance or susceptibility. This study gives an insight into differentially regulated genes in response to ToLCNDV-[potato] infection in resistant and susceptible cultivars and could serve as the basis for the development of new strategies for disease management.
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Affiliation(s)
- Arjunan Jeevalatha
- ICAR-Central Potato Research Institute, Shimla 171 001, Himachal Pradesh, India.
| | - Sundaresha Siddappa
- ICAR-Central Potato Research Institute, Shimla 171 001, Himachal Pradesh, India
| | - Ashwani Kumar
- ICAR-Central Potato Research Institute, Shimla 171 001, Himachal Pradesh, India
| | - Priyanka Kaundal
- ICAR-Central Potato Research Institute, Shimla 171 001, Himachal Pradesh, India
| | - Anupama Guleria
- ICAR-Central Potato Research Institute, Shimla 171 001, Himachal Pradesh, India
| | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla 171 001, Himachal Pradesh, India
| | - Mandadi Nagesh
- ICAR-Central Potato Research Institute, Shimla 171 001, Himachal Pradesh, India
| | - Bir Pal Singh
- ICAR-Central Potato Research Institute, Shimla 171 001, Himachal Pradesh, India
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