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Negi A, Singh K, Jaiswal S, Kokkat JG, Angadi UB, Iquebal MA, Umadevi P, Rai A, Kumar D. Rapid Genome-Wide Location-Specific Polymorphic SSR Marker Discovery in Black Pepper by GBS Approach. Front Plant Sci 2022; 13:846937. [PMID: 35712605 PMCID: PMC9197322 DOI: 10.3389/fpls.2022.846937] [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: 12/31/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Black pepper (Piper nigrum), the "King of Spices," is an economically important spice in India and is known for its medicinal and cultural values. SSRs, the tandem repeats of small DNA sequences, are often polymorphic in nature with diverse applications. For population structure, QTL/gene discovery, MAS, and diversity analysis, it is imperative to have their location specificity. The existing PinigSSRdb catalogs ~70K putative SSR markers but these are anonymous (unknown chromosomal location), based on 916 scaffolds rather than 26 chromosomes. Under this study, we generated ddRAD sequence data of 29 black pepper genotypes from all over India, being low-cost and most efficient technique for the identification of polymorphic markers. The major limitation of ddRAD with compromised/non-uniform coverage has been successfully overcome by taking advantage of chromosome-wise data availability. The latest black pepper genome assembly was used to extract genome-wide SSRs. A total of 276,230 genomic SSRs were mined distributed over 26 chromosomes, with relative density of 362.88 SSRs/Mb and average distance of 2.76 Kb between two SSRs. This assembly was also used to find the polymorphic SSRs in the generated GBS data of 29 black pepper genotypes utilizing rapid and cost-effective method giving 3,176 polymorphic SSRs, out of which 2015 were found to be hypervariable. The developed web-genomic resource, BlackP2MSATdb (http://webtom.cabgrid.res.in/blackp2msatdb/), is the largest and first reported web resource for genomic and polymorphic SSRs of black pepper, which is useful to develop varietal signature, coreset, physical map, QTL/gene identification, and MAS in endeavor of black pepper production.
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Affiliation(s)
- Ankita Negi
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - Kalpana Singh
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - Johnson George Kokkat
- Indian Council of Agricultural Research-Indian Institute of Spices Research, Kozhikode, India
| | - Ulavappa B. Angadi
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - P. Umadevi
- Indian Council of Agricultural Research-Indian Institute of Spices Research, Kozhikode, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendragarh, India
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Gerashchenkov GA, Rozhnova NA, Kuluev BR, Kiryanova OY, Gumerova GR, Knyazev AV, Vershinina ZR, Mikhailova EV, Chemeris DA, Matniyazov RT, Baimiev AK, Gubaidullin IM, Baimiev AK, Chemeris AV. [Design of Guide RNA for CRISPR/Cas Plant Genome Editing]. Mol Biol (Mosk) 2020; 54:29-50. [PMID: 32163387 DOI: 10.31857/s0026898420010061] [Citation(s) in RCA: 2] [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: 05/31/2019] [Accepted: 07/08/2019] [Indexed: 11/24/2022]
Abstract
CRISPR/Cas technology of genome editing is a powerful tool for making targeted changes in the DNA of various organisms, including plants. The choice of the precise nucleotide sequence (protospacer) in the gene to be edited is important in the design of guide RNA, which can be carried out by specialized software. We review and compare all the known on-line and off-line resources for guide RNA design, with special attention paid to tools capable of searching for off-target edits sites in plant genomes. The use of Cas12a may be preferable to Cas9. Techniques allowing C→T and G→A base editing without DNA cleavage are discussed along with the basic requirements for the design of effective and highly specific guide RNAs. Ways for improving guide RNA design software are presented. We also discuss the lesser risks of off-target editing in plant genomes as opposed to animal genomes. Examples of edited plant genomes including those that do not lead to the creation of transgenic plants are reviewed.
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Affiliation(s)
- G A Gerashchenkov
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
| | - N A Rozhnova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
| | - B R Kuluev
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
| | - O Yu Kiryanova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
- Ufa State Petroleum Technological University, Ufa, 450062 Russia
| | - G R Gumerova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
| | - A V Knyazev
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
| | - Z R Vershinina
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
| | - E V Mikhailova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
| | - D A Chemeris
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
| | - R T Matniyazov
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
| | - An Kh Baimiev
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
| | - I M Gubaidullin
- Institute of Petrochemistry and Catalysis, Russian Academy of Sciences, Ufa, 450075 Russia
| | - Al Kh Baimiev
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
| | - A V Chemeris
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, 450054 Russia
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Kumar A, Pandeya A, Malik G, Sharma M, P. HK, S. AK, Gahlaut V, Gajula MP, Singh KP, Suravajhala P, Balyan HS, Gupta PK. ---A web resource for nutrient use efficiency-related genes, quantitative trait loci and microRNAs in important cereals and model plants. F1000Res 2018; 7:ISCB Comm J-673. [PMID: 30135718 PMCID: PMC6073097 DOI: 10.12688/f1000research.14561.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Cereals are key contributors to global food security. Genes involved in the uptake (transport), assimilation and utilization of macro- and micronutrients are responsible for the presence of these nutrients in grain and straw. Although many genomic databases for cereals are available, there is currently no cohesive web resource of manually curated nutrient use efficiency (NtUE)-related genes and quantitative trait loci (QTLs). In this study, we present a web-resource containing information on NtUE-related genes/QTLs and the corresponding available microRNAs for some of these genes in four major cereal crops (wheat ( Triticum aestivum), rice ( Oryza sativa), maize ( Zea mays), barley ( Hordeum vulgare)), two alien species related to wheat ( Triticum urartu and Aegilops tauschii), and two model species ( Brachypodium distachyon and Arabidopsis thaliana). Gene annotations integrated in the current web resource were manually curated from the existing databases and the available literature. The primary goal of developing this web resource is to provide descriptions of the NtUE-related genes and their functional annotation. MicroRNAs targeting some of the NtUE related genes and the QTLs for NtUE-related traits are also included. The genomic information embedded in the web resource should help users to search for the desired information.
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Affiliation(s)
- Anuj Kumar
- Advanced Centre for Computational and Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, Uttarakhand, 248007, India
| | - Ajay Pandeya
- Department of Biotechnology, Graphic Era University, Dehradun, Uttarakhand, 248002, India
| | - Girik Malik
- Bioclues.org, Hyderabad, 500072, India
- Labrynthe, New Delhi, India
| | - Mansi Sharma
- Bioinformatics Laboratory, Institute of Cytology and Preventative Oncology, Noida, 201301, India
| | - Hima Kumari P.
- Department of Genetics, Osmania University, Hyderabad, Telengana, 500007, India
| | - Anil Kumar S.
- Department of Genetics, Osmania University, Hyderabad, Telengana, 500007, India
| | - Vijay Gahlaut
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, 250004, India
| | - M.N.V. Prasad Gajula
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar , Telangana, 500030, India
| | - Krishna Pal Singh
- Advanced Centre for Computational and Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, Uttarakhand, 248007, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, 500072, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Technology & Science, Jaipur, Rajasthan, 302001, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, 250004, India
| | - Pushpendra K. Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, 250004, India
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