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Farinati S, Draga S, Betto A, Palumbo F, Vannozzi A, Lucchin M, Barcaccia G. Current insights and advances into plant male sterility: new precision breeding technology based on genome editing applications. FRONTIERS IN PLANT SCIENCE 2023; 14:1223861. [PMID: 37521915 PMCID: PMC10382145 DOI: 10.3389/fpls.2023.1223861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023]
Abstract
Plant male sterility (MS) represents the inability of the plant to generate functional anthers, pollen, or male gametes. Developing MS lines represents one of the most important challenges in plant breeding programs, since the establishment of MS lines is a major goal in F1 hybrid production. For these reasons, MS lines have been developed in several species of economic interest, particularly in horticultural crops and ornamental plants. Over the years, MS has been accomplished through many different techniques ranging from approaches based on cross-mediated conventional breeding methods, to advanced devices based on knowledge of genetics and genomics to the most advanced molecular technologies based on genome editing (GE). GE methods, in particular gene knockout mediated by CRISPR/Cas-related tools, have resulted in flexible and successful strategic ideas used to alter the function of key genes, regulating numerous biological processes including MS. These precision breeding technologies are less time-consuming and can accelerate the creation of new genetic variability with the accumulation of favorable alleles, able to dramatically change the biological process and resulting in a potential efficiency of cultivar development bypassing sexual crosses. The main goal of this manuscript is to provide a general overview of insights and advances into plant male sterility, focusing the attention on the recent new breeding GE-based applications capable of inducing MS by targeting specific nuclear genic loci. A summary of the mechanisms underlying the recent CRISPR technology and relative success applications are described for the main crop and ornamental species. The future challenges and new potential applications of CRISPR/Cas systems in MS mutant production and other potential opportunities will be discussed, as generating CRISPR-edited DNA-free by transient transformation system and transgenerational gene editing for introducing desirable alleles and for precision breeding strategies.
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Bhat MA, Mishra AK, Jan S, Bhat MA, Kamal MA, Rahman S, Shah AA, Jan AT. Plant Growth Promoting Rhizobacteria in Plant Health: A Perspective Study of the Underground Interaction. PLANTS (BASEL, SWITZERLAND) 2023; 12:629. [PMID: 36771713 PMCID: PMC9919780 DOI: 10.3390/plants12030629] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Plants are affected by various environmental stresses such as high or low temperatures, drought, and high salt levels, which can disrupt their normal cellular functioning and impact their growth and productivity. These stressors offer a major constraint to the morphological, physiological, and biochemical parameters; thereby attributing serious complications in the growth of crops such as rice, wheat, and corn. Considering the strategic and intricate association of soil microbiota, known as plant growth-promoting rhizobacteria (PGPR), with the plant roots, PGPR helps plants to adapt and survive under changing environmental conditions and become more resilient to stress. They aid in nutrient acquisition and regulation of water content in the soil and also play a role in regulating osmotic balance and ion homeostasis. Boosting key physiological processes, they contribute significantly to the alleviation of stress and promoting the growth and development of plants. This review examines the use of PGPR in increasing plant tolerance to different stresses, focusing on their impact on water uptake, nutrient acquisition, ion homeostasis, and osmotic balance, as well as their effects on crop yield and food security.
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Affiliation(s)
- Mudasir Ahmad Bhat
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, India
| | - Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Saima Jan
- Gene Expression Lab., School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, India
| | - Mujtaba Aamir Bhat
- Gene Expression Lab., School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, India
| | - Mohammad Azhar Kamal
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Safikur Rahman
- Department of Botany, Munshi Singh College, BR Ambedkar Bihar University, Muzaffarpur 845401, India
| | - Ali Asghar Shah
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, India
| | - Arif Tasleem Jan
- Gene Expression Lab., School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, India
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Sturme MHJ, van der Berg JP, Bouwman LMS, De Schrijver A, de Maagd RA, Kleter GA, Battaglia-de Wilde E. Occurrence and Nature of Off-Target Modifications by CRISPR-Cas Genome Editing in Plants. ACS AGRICULTURAL SCIENCE & TECHNOLOGY 2022; 2:192-201. [PMID: 35548699 PMCID: PMC9075866 DOI: 10.1021/acsagscitech.1c00270] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 12/26/2022]
Abstract
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CRISPR-Cas-based
genome editing allows for precise and targeted
genetic modification of plants. Nevertheless, unintended off-target
edits can arise that might confer risks when present in gene-edited
food crops. Through an extensive literature review we gathered information
on CRISPR-Cas off-target edits in plants. Most observed off-target
changes were small insertions or deletions (1–22 bp) or nucleotide
substitutions, and large deletions (>100 bp) were rare. One study
detected the insertion of vector-derived DNA sequences, which is important
considering the risk assessment of gene-edited plants. Off-target
sites had few mismatches (1–3 nt) with the target sequence
and were mainly located in protein-coding regions, often in target
gene homologues. Off-targets edits were predominantly detected via
biased analysis of predicted off-target sites instead of unbiased
genome-wide analysis. CRISPR-Cas-edited plants showed lower off-target
mutation frequencies than conventionally bred plants. This Review
can aid discussions on the relevance of evaluating off-target modifications
for risk assessment of CRISPR-Cas-edited plants.
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Affiliation(s)
- Mark H J Sturme
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Jan Pieter van der Berg
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Lianne M S Bouwman
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | | | - Ruud A de Maagd
- Wageningen Plant Research, Wageningen University and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Gijs A Kleter
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Evy Battaglia-de Wilde
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
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Ghosh N, Saha I, Sharma N. Palindromic target site identification in SARS-CoV-2, MERS-CoV and SARS-CoV-1 by adopting CRISPR-Cas technique. Gene 2022; 818:146136. [PMID: 34999179 PMCID: PMC8734054 DOI: 10.1016/j.gene.2021.146136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/26/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated Cas protein (CRISPR-Cas) has turned out to be a very important tool for the rapid detection of viruses. This can be used for the identification of the target site in a virus by identifying a 3–6 nt length Protospacer Adjacent Motif (PAM) adjacent to the potential target site, thus motivating us to adopt CRISPR-Cas technique to identify SARS-CoV-2 as well as other members of Coronaviridae family. In this regard, we have developed a fast and effective method using k-mer technique in order to identify the PAM by scanning the whole genome of the respective virus. Subsequently, palindromic sequences adjacent to the PAM locations are identified as the potential target sites. Palindromes are considered in this work as they are known to identify viruses. Once all the palindrome-PAM combinations are identified, PAMs specific for the RNA-guided DNA Cas9/Cas12 endonuclease are identified to bind and cut the target sites. In this regard, PAMs such as 5’-TGG-3’ and 5’-TTTA-3’ in NSP3 and Exon for SARS-CoV-2, 5’-GGG-3’ and 5’-TGG-3’ in Exon and NSP2 for MERS-CoV and 5’-AGG-3’ and 5’-TTTG-3’ in Helicase and NSP3 respectively for SARS-CoV-1 are identified corresponding to SpCas9 and FnCas12a endonucleases. Finally, to recognise the target sites of Coronaviridae family as cleaved by SpCas9 and FnCas12a, complements of the palindromic target regions are designed as primers or guide RNA (gRNA). Therefore, such complementary gRNAs along with respective Cas proteins can be considered in assays for the identification of SARS-CoV-2, MERS-CoV and SARS-CoV-1.
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Affiliation(s)
- Nimisha Ghosh
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Poland; Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India.
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
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Tripathi DK, Punj V, Singh NK, Guerriero G, Deshmukh R, Sharma S. Recent biotechnological avenues in crop improvement and stress management. J Biotechnol 2022; 349:21-24. [DOI: 10.1016/j.jbiotec.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abdellatif IMY, Yuan S, Na R, Yoshihara S, Hamada H, Suzaki T, Ezura H, Miura K. Functional Characterization of Tomato Phytochrome A and B1B2 Mutants in Response to Heat Stress. Int J Mol Sci 2022; 23:ijms23031681. [PMID: 35163602 PMCID: PMC8835780 DOI: 10.3390/ijms23031681] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/09/2022] [Accepted: 01/29/2022] [Indexed: 02/04/2023] Open
Abstract
Heat stress (HS) is a prevalent negative factor affecting plant growth and development, as it is predominant worldwide and threatens agriculture on a large scale. PHYTOCHROMES (PHYs) are photoreceptors that control plant growth and development, and the stress signaling response partially interferes with their activity. PHYA, B1, and B2 are the most well-known PHY types in tomatoes. Our study aimed to identify the role of tomato 'Money Maker' phyA and phyB1B2 mutants in stable and fluctuating high temperatures at different growth stages. In the seed germination and vegetative growth stages, the phy mutants were HS tolerant, while during the flowering stage the phy mutants revealed two opposing roles depending on the HS exposure period. The response of the phy mutants to HS during the fruiting stage showed similarity to WT. The most obvious stage that demonstrated phy mutants' tolerance was the vegetative growth stage, in which a high degree of membrane stability and enhanced water preservation were achieved by the regulation of stomatal closure. In addition, both mutants upregulated the expression of heat-responsive genes related to heat tolerance. In addition to lower malondialdehyde accumulation, the phyA mutant enhanced proline levels. These results clarified the response of tomato phyA and phyB1B2 mutants to HS.
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Affiliation(s)
- Islam M. Y. Abdellatif
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (I.M.Y.A.); (S.Y.); (R.N.); (T.S.); (H.E.)
- Department of Horticulture, Faculty of Agriculture, Minia University, El-Minia 61517, Egypt
| | - Shaoze Yuan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (I.M.Y.A.); (S.Y.); (R.N.); (T.S.); (H.E.)
| | - Renhu Na
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (I.M.Y.A.); (S.Y.); (R.N.); (T.S.); (H.E.)
| | - Shizue Yoshihara
- Department of Biological Science, Osaka Prefecture University, Sakai 599-8531, Japan;
| | - Haruyasu Hamada
- Pharma and Supplemental Nutrition Solutions Vehicle, Kaneka Corporation, Iwata 438-0802, Japan;
| | - Takuya Suzaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (I.M.Y.A.); (S.Y.); (R.N.); (T.S.); (H.E.)
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (I.M.Y.A.); (S.Y.); (R.N.); (T.S.); (H.E.)
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; (I.M.Y.A.); (S.Y.); (R.N.); (T.S.); (H.E.)
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Japan
- Correspondence:
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Singh A, Tiwari S, Pandey J, Lata C, Singh IK. Role of nanoparticles in crop improvement and abiotic stress management. J Biotechnol 2021; 337:57-70. [PMID: 34175328 DOI: 10.1016/j.jbiotec.2021.06.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022]
Abstract
Nanoparticles (NPs) possess specific physical and chemical features and they are capable enough to cross cellular barriers and show their effect on living organisms. Their capability to cross cellular barriers have been noticed for their application not only in medicine, electronics, chemical and physical sciences, but also in agriculture. In agriculture, nanotechnology can help to improve the growth and crop productivity by the use of various nanoscale products such as nanofertilizers, nanoherbicides, nanofungicides, nanopesticides etc. An optimized concentration of NPs can be administered by incubation of seeds, roots, pollen, isolated cells and protoplast, foliar spraying, irrigation with NPs, direct injection, hydroponic treatment and delivery by biolistics. Once NPs come in contact with plant cells, they are uptaken by plasmodesmatal or endocytosed pathways and translocated via apoplastic and / symplastic routes. Once beneficial NPs reach different parts of plants, they boost photosynthetic rate, biomass measure, chlorophyll content, sugar level, buildup of osmolytes and antioxidants. NPs also improve nitrogen metabolism, enhance chlorophyll as well as protein content and upregulate the expression of abiotic- and biotic stress-related genes. Herein, we review the state of art of different modes of application, uptake, transport and prospective beneficial role of NPs in stress management and crop improvement.
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Affiliation(s)
- Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Shalini Tiwari
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Jyotsna Pandey
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Charu Lata
- CSIR-National Institute of Science Communication and Information Resources, 14 Satsang Vihar Marg, New Delhi, 110067, India.
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India; i4 Centre, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India.
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Bhat MA, Mir RA, Kumar V, Shah AA, Zargar SM, Rahman S, Jan AT. Mechanistic insights of CRISPR/Cas-mediated genome editing towards enhancing abiotic stress tolerance in plants. PHYSIOLOGIA PLANTARUM 2021; 172:1255-1268. [PMID: 33576013 DOI: 10.1111/ppl.13359] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/21/2021] [Accepted: 02/01/2021] [Indexed: 05/28/2023]
Abstract
Abiotic stresses such as temperature (high/low), drought, salinity, and others make the environment hostile to plants. Abiotic stressors adversely affect plant growth and development; and thereby makes a direct impact on overall plant productivity. Plants confront stress by developing an internal defense system orchestrated by compatible solutes, reactive oxygen species scavengers and phytohormones. However, routine exposure to unpredictable environmental stressors makes it essential to equip plants with a system that contributes to sustainable agricultural productivity, besides imparting multi-stress tolerance. The sustainable approach against abiotic stress is accomplished through breeding of tolerant cultivars. Though eco-friendly, tedious screening and crossing protocol limits its usage to overcome stress and in attaining the goal of global food security. Advancement on the technological front has enabled adoption of genomic engineering approaches to perform site-specific modification in the plant genome for improving adaptability, increasing the yield and in attributing resilience against different stressors. Of the different genome editing approaches, CRISPR/Cas has revolutionized biological research with wider applicability to crop plants. CRISPR/Cas emerged as a versatile tool in editing genomes for desired traits in highly accurate and precise manner. The present study summarizes advancement of the CRISPR/Cas genome editing tool in its adoption to manipulate plant genomes for novel traits towards developing high-yielding and climate-resilient crop varieties.
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Affiliation(s)
- Mujtaba Aamir Bhat
- Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Vijay Kumar
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Ali Asghar Shah
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Sajad Majeed Zargar
- Proteomics Lab., Division of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Kashmir, India
| | - Safikur Rahman
- Department of Botany, MS College, BR Ambedkar Bihar University, Muzaffarpur, India
| | - Arif Tasleem Jan
- Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
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