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Jinger D, Kaushal R, Kumar R, Paramesh V, Verma A, Shukla M, Chavan SB, Kakade V, Dobhal S, Uthappa AR, Roy T, Singhal V, Madegowda M, Kumar D, Khatri P, Dinesh D, Singh G, Singh AK, Nath AJ, Joshi N, Joshi E, Kumawat S. Degraded land rehabilitation through agroforestry in India: Achievements, current understanding, and future prospectives. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1088796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Land degradation is one of the most important factors responsible for the alarming situation of food security, human health, and socioeconomic development in the country. Currently, 120.7 M ha of land in the country is affected by land degradation, out of which 85.7 M ha of land is affected by soil erosion caused by water and wind. Moreover, physical, chemical, and biological degradation are the major forms of land degradation in the country. Deforestation or tree cover loss (2.07 M ha) from 2001 to 2021, intensive rainfall (>7.5 mm ha−1), uncontrolled grazing (5.65 M ha), indiscriminate use of fertilizers (32 MT year−1), and shifting cultivation (7.6 M ha) are other major factors that further aggravate the process of land degradation. In order to alleviate the problem of land degradation, numerous agroforestry technologies have been developed after years of research in different agroclimatic zones of the country. The major agroforestry systems observed in the country are agri-horticulture, silvipasture, and agri-silviculture. This review indicates the potential of agroforestry in enhancing carbon sequestration (1.80 Mg C ha−1 year−1 in the Western Himalayan region to 3.50 Mg C ha−1 year−1 in the island regions) and reduced soil loss and runoff by 94% and 78%, respectively, in Northeast India. This can be concluded that the adoption of the agroforestry system is imperative for the rehabilitation of degraded lands and also found to have enough potential to address the issues of food, environmental, and livelihood security. This review’s findings will benefit researchers, land managers, and decision-makers in understanding the role of agroforestry in combating land degradation to enhance ecosystem service in India and planning suitable policies for eradicating the problem effectively.
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Kumar R, Kumar A, Banyal R, Kumar M, Singh A, Yadav RK, Dobhal S, Sharma S. Seed and seedling diversity delimitation and differentiation of Indian populations of Melia dubia cav. Saudi J Biol Sci 2022; 29:489-498. [PMID: 35002445 PMCID: PMC8716888 DOI: 10.1016/j.sjbs.2021.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 09/03/2021] [Accepted: 09/05/2021] [Indexed: 11/21/2022] Open
Abstract
Melia dubia is one of the most important industrial tree species in the South East Asia. In last few decades, the populations of M. dubia has rapidly expanded in the Indian sub-continents, leading to an increase in the genetic diversity of species. However, very less information is available on intra-specific variation in Melia under the Indian subcontinent. Therefore, a present investigation was undertaken, to assess the level of diversity in seed and saplings of the Melia populations (ecotypes) collected from three agro-ecological regions of India. Results revealed that the seed and saplings of all the ecotypes are significantly different for all the traits, except for number of branches per plant, and the maximum variability was recorded in germination percentage, seed weight, internodal length, and sapling height of the species. The high heritability for seed weight (0.99), length (0.99), and width (0.97), and germination percentage (0.99) indicated that selection and genetic gain for these traits would be effective during the commencement of improvement program. Trait association analysis explained that higher seed weight significantly reduced sapling height, collar diameter, number of leaves per plant, internodal length, petiole length, and germination percentage (r = −0.86; p < 0.001) that ultimately reduced the seedling vigor in Melia dubia. Interestingly, the number of branches per plant were not associated with any of the morphological traits. The first principal component explained 50.09% of the entire variation and all the traits contributed greatly to the variation for this principal component, except for number of branches, leaf width and seed length. The clustering approach assorted geographic variation of M. dubia populations into three main sub-clusters i.e. South, North, and North East populations each consisting of five, seven and one populations (including cultivar), respectively. Among different ecotypes, Bahumukhi, Varsha and US Nagar seed sources outperformed all others in seedling vigour (sapling height) and rest of the growth parameters. Overall, findings explained that considerable scope exists for the development of superior planting material of M. dubia through exploration of seeds and selection at the early seedling stage.
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Affiliation(s)
- Raj Kumar
- ICAR-Central Soil Salinity Research Institute, Karnal 132001, Haryana, India
| | - Arvind Kumar
- ICAR-Central Soil Salinity Research Institute, Karnal 132001, Haryana, India
| | - Rakesh Banyal
- ICAR-Central Soil Salinity Research Institute, Karnal 132001, Haryana, India
| | - Manish Kumar
- ICAR-Central Soil Salinity Research Institute, Karnal 132001, Haryana, India
| | - Awtar Singh
- ICAR-Central Soil Salinity Research Institute, Karnal 132001, Haryana, India
| | - R K Yadav
- ICAR-Central Soil Salinity Research Institute, Karnal 132001, Haryana, India
| | - Sneha Dobhal
- Dr Yashwant Singh Parmar University of Horticulture and Forestry, Solan, India.,VCSG Uttarakhand University of Horticulture and Forestry, Ranichauri, Uttarakhand, India
| | - Samriti Sharma
- Dr Yashwant Singh Parmar University of Horticulture and Forestry, Solan, India
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Kumar R, Mehta H, Kumar A, Bhardwaj AK, Kaushal R, Dobhal S, Gupta AK, Banyal R, Kumar M, Kumar S, Verma K. Seed source variation affects the growth, biomass, carbon stock, and climate resilience potential: A case study of Celtis australis in Indian Himalayas. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Ramachandran S, Dobhal S, Alvarez AM, Arif M. Improved multiplex TaqMan qPCR assay with universal internal control offers reliable and accurate detection of Clavibacter michiganensis. J Appl Microbiol 2021; 131:1405-1416. [PMID: 33484618 DOI: 10.1111/jam.15017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/16/2020] [Accepted: 01/21/2021] [Indexed: 11/27/2022]
Abstract
AIM Clavibacter michiganensis (Cm) is a seed-borne plant pathogen that significantly reduces tomato production worldwide. Due to repeated outbreaks and rapid spread of the disease, seeds/transplants need to be certified free of the pathogen before planting. To this end, we developed a multiplex TaqMan qPCR assay that can accurately detect Cm in infected samples. METHODS AND RESULTS A specific region of Cm (clvG gene) was selected for primer design using comparative genomics approach. A fully synthetic universal internal control (UIC) was also designed to detect PCR inhibitors and false-negative results in qPCRs. The Cm primers can be used alone or in a triplex TaqMan qPCR assay with UIC and previously described Clavibacter primers. The assay was specific for Cm and detected up to 10 fg of Cm DNA in sensitivity and spiked assays. Addition of the UIC did not change the specificity or sensitivity of the multiplex TaqMan qPCR assay. CONCLUSION The triplex TaqMan qPCR provides a specific and sensitive diagnostic assay for Cm. SIGNIFICANCE AND IMPACT OF THE STUDY This assay can be used for biosecurity surveillance, routine diagnostics, estimating bacterial titres in infected material and for epidemiological studies. The UIC is fully synthetic, efficiently amplified and multiplex compatible with any other qPCR assay.
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Affiliation(s)
- S Ramachandran
- Foreign Disease and Weed Science Research Unit, USDA-ARS, Fort Detrick, MD, USA.,ARS Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - S Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - M Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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Dobhal S, Boluk G, Babler B, Stulberg MJ, Rascoe J, Nakhla MK, Chapman TA, Crockford AB, Melzer MJ, Alvarez AM, Arif M. Comparative genomics reveals signature regions used to develop a robust and sensitive multiplex TaqMan real-time qPCR assay to detect the genus Dickeya and Dickeya dianthicola. J Appl Microbiol 2020; 128:1703-1719. [PMID: 31950553 DOI: 10.1111/jam.14579] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/16/2019] [Accepted: 01/07/2020] [Indexed: 11/30/2022]
Abstract
AIMS Dickeya species are high consequence plant pathogenic bacteria; associated with potato disease outbreaks and subsequent economic losses worldwide. Early, accurate and reliable detection of Dickeya spp. is needed to prevent establishment and further dissemination of this pathogen. Therefore, a multiplex TaqMan qPCR was developed for sensitive detection of Dickeya spp. and specifically, Dickeya dianthicola. METHODS AND RESULTS A signature genomic region for the genus Dickeya (mglA/mglC) and unique genomic region for D. dianthicola (alcohol dehydrogenase) were identified using a whole genome-based comparative genomics approach. The developed multiplex TaqMan qPCR was validated using extensive inclusivity and exclusivity panels, and naturally/artificially infected samples to confirm broad range detection capability and specificity. Both sensitivity and spiked assays showed a detection limit of 10 fg DNA. CONCLUSION The developed multiplex assay is sensitive and reliable to detect Dickeya spp. and D. dianthicola with no false positives or false negatives. It was able to detect mixed infection from naturally and artificially infected plant materials. SIGNIFICANCE AND IMPACT OF THE STUDY The developed assay will serve as a practical tool for screening of propagative material, monitoring the presence and distribution, and quantification of target pathogens in a breeding programme. The assay also has applications in routine diagnostics, biosecurity and microbial forensics.
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Affiliation(s)
- S Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - G Boluk
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - B Babler
- Department of Plant Pathology, Wisconsin Seed Potato Lab, University of Wisconsin, Madison, WI, USA
| | - M J Stulberg
- Science and Technology, Plant Protection and Quarantine, Animal and Health Inspection Service, United States Department of Agriculture, Beltsville, MD, USA
| | - J Rascoe
- Science and Technology, Plant Protection and Quarantine, Animal and Health Inspection Service, United States Department of Agriculture, Beltsville, MD, USA
| | - M K Nakhla
- Science and Technology, Plant Protection and Quarantine, Animal and Health Inspection Service, United States Department of Agriculture, Beltsville, MD, USA
| | - T A Chapman
- Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - A B Crockford
- Department of Plant Pathology, Wisconsin Seed Potato Lab, University of Wisconsin, Madison, WI, USA
| | - M J Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - M Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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Dobhal S, Larrea-Sarmiento A, Alvarez AM, Arif M. Development of a loop-mediated isothermal amplification assay for specific detection of all known subspecies of Clavibacter michiganensis. J Appl Microbiol 2018; 126:388-401. [PMID: 30307676 DOI: 10.1111/jam.14128] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/02/2023]
Abstract
AIMS Clavibacter michiganensis is an important bacterial plant pathogen that causes vast destruction to agriculturally important crops worldwide. Early detection is critical to evaluate disease progression and to implement efficient control measures to avoid serious epidemics. In this study, we developed a sensitive, specific and robust loop-mediated isothermal amplification (LAMP) assay for detection of all known subspecies of C. michiganensis. METHODS AND RESULTS Whole genome comparative genomics approach was taken to identify a unique and conserved region within all known subspecies of C. michiganensis. Primer specificity was evaluated in silico and with 64 bacterial strains included in inclusivity and exclusivity panels; no false positives or false negatives were detected. Both the sensitivity and spiked assay of the developed LAMP assay was 1 fg of the pathogen DNA per reaction. A 100% accuracy was observed when tested with infected plant samples. CONCLUSIONS The developed LAMP assay is simple, sensitive, robust and easy to perform using different detection platforms and chemistries. SIGNIFICANCE AND IMPACT OF THE STUDY The developed LAMP assay can detect all known subspecies of C. michiganensis. The LAMP process can be performed isothermally at 65°C and results can be visually assessed, which makes this technology a promising tool for monitoring the disease progression and for accurate pathogen detection at point-of-care.
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Affiliation(s)
- S Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - M Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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Sharma S, Dobhal S, Thakur S. Analysis of genetic diversity in parents and hybrids of Populus deltoides bartr. using microsatellite markers. Appl Biol Res 2018. [DOI: 10.5958/0974-4517.2018.00036.8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Sanwal CS, Kumar R, Dobhal S, Kerkatta S, Bhardwaj SD. Production and Conservation of Medicinal Plants in Understorey of Degraded Chir Pine Forests Using Sustainable Techniques. CURR SCI INDIA 2017. [DOI: 10.18520/cs/v112/i12/2386-2391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Arif M, Dobhal S, Garrido PA, Orquera GK, Espíndola AS, Young CA, Ochoa-Corona FM, Marek SM, Garzón CD. Highly Sensitive End-Point PCR and SYBR Green qPCR Detection of Phymatotrichopsis omnivora, Causal Fungus of Cotton Root Rot. Plant Dis 2014; 98:1205-1212. [PMID: 30699612 DOI: 10.1094/pdis-05-13-0505-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phymatotrichopsis omnivora, the causal pathogen of cotton root rot, is a devastating ascomycete that affects numerous important dicotyledonous plants grown in the southwestern United States and northern Mexico. P. omnivora is notoriously difficult to isolate from infected plants; therefore methods for accurate and sensitive detection directly from symptomatic and asymptomatic plant samples are needed for disease diagnostics and pathogen identification. Primers were designed for P. omnivora based on consensus sequences of the nuclear ribosomal internal transcribed spacer (ITS) region of geographically representative isolates. Primers were compared against published P. omnivora sequences and validated against DNA from P. omnivora isolates and infected plant samples. The primer combinations amplified products from a range of P. omnivora isolates representative of known ITS haplotypes using standard end-point polymerase chain reaction (PCR) methodology. The assays detected P. omnivora from infected root samples of cotton (Gossypium hirsutum) and alfalfa (Medicago sativa). Healthy plants and other relevant root pathogens did not produce PCR products with the P. omnivora-specific primers. Primer pair PO2F/PO2R was the most sensitive in end-point PCR assays and is recommended for use for pathogen identification from mycelial tissue and infected plant materials when quantitative PCR (qPCR) is not available. Primer pair PO3F/PO2R was highly sensitive (1 fg) when used in SYBR Green qPCR assays and is recommended for screening of plant materials potentially infected by P. omnivora or samples with suboptimal DNA quality. The described PCR-based detection methods will be useful for rapid and sensitive screening of infected plants in diagnostic laboratories, plant health inspections, and plant breeding programs.
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Affiliation(s)
- M Arif
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, USA
| | - S Dobhal
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, USA
| | - P A Garrido
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, USA
| | - G K Orquera
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, USA
| | - A S Espíndola
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, USA
| | - C A Young
- Samuel Roberts Noble Foundation, Ardmore, OK, USA
| | - F M Ochoa-Corona
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, USA
| | - S M Marek
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, USA
| | - C D Garzón
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, USA
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Dobhal S, Zhang G, Rohla C, Smith M, Ma L. A simple, rapid, cost-effective and sensitive method for detection of Salmonella
in environmental and pecan samples. J Appl Microbiol 2014; 117:1181-90. [DOI: 10.1111/jam.12583] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/06/2014] [Accepted: 06/16/2014] [Indexed: 11/29/2022]
Affiliation(s)
- S. Dobhal
- National Institute for Microbial Forensics and Food and Agricultural Biosecurity; Department of Entomology and Plant Pathology; Oklahoma State University; Stillwater OK USA
| | - G. Zhang
- Center for Food Safety and Applied Nutrition; Food and Drug Administration; College Park MD USA
| | - C. Rohla
- Samuel Robert Noble Foundation; Ardmore OK USA
| | - M.W. Smith
- Department of Horticulture and Landscape Architecture; Oklahoma State University; Stillwater OK USA
| | - L.M. Ma
- National Institute for Microbial Forensics and Food and Agricultural Biosecurity; Department of Entomology and Plant Pathology; Oklahoma State University; Stillwater OK USA
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Dobhal S, Chaudhary VK, Singh A, Pandey D, Kumar A, Agrawal S. Expression of recombinant antibody (single chain antibody fragment) in transgenic plant Nicotiana tabacum cv. Xanthi. Mol Biol Rep 2013; 40:7027-37. [PMID: 24218164 DOI: 10.1007/s11033-013-2822-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 10/25/2013] [Indexed: 11/27/2022]
Abstract
Plants offer an alternative inexpensive and convenient technology for large scale production of recombinant proteins especially recombinant antibodies (plantibodies). In this paper, we describe the expression of a model single chain antibody fragment (B6scFv) in transgenic tobacco. Four different gene constructs of B6scFv with different target signals for expression in different compartments of a tobacco plant cell with and without endoplasmic reticulum (ER) retention signal were used. Agrobacterium mediated plant transformation of B6scFv gene was performed with tobacco leaf explants and the gene in regenerated plants was detected using histochemical GUS assay and PCR. The expression of B6scFv gene was detected by western blotting and the recombinant protein was purified from putative transgenic tobacco plants using metal affinity chromatography. The expression level of recombinant protein was determined by indirect enzyme-linked immunosorbent assay. The highest accumulation of protein was found up to 3.28 % of the total soluble protein (TSP) in plants expressing B6scFv 1003 targeted to the ER, and subsequently expression of 2.9 % of TSP in plants expressing B6scFv 1004 (with target to apoplast with ER retention signal). In contrast, lower expression of 0.78 and 0.58 % of TSP was found in plants expressing antibody fragment in cytosol and apoplast, without ER retention signal. The described method/system could be used in the future for diverse applications including expression of other recombinant molecules in plants for immunomodulation, obtaining pathogen resistance against plant pathogens, altering metabolic pathways and also for the expression of different antibodies of therapeutic and diagnostic uses.
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Affiliation(s)
- S Dobhal
- Department of Biochemistry, C.B.S.H., G. B. Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India,
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