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Bhat JA, Feng X, Mir ZA, Raina A, Siddique KHM. Recent advances in artificial intelligence, mechanistic models, and speed breeding offer exciting opportunities for precise and accelerated genomics-assisted breeding. Physiol Plant 2023; 175:e13969. [PMID: 37401892 DOI: 10.1111/ppl.13969] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/11/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023]
Abstract
Given the challenges of population growth and climate change, there is an urgent need to expedite the development of high-yielding stress-tolerant crop cultivars. While traditional breeding methods have been instrumental in ensuring global food security, their efficiency, precision, and labour intensiveness have become increasingly inadequate to address present and future challenges. Fortunately, recent advances in high-throughput phenomics and genomics-assisted breeding (GAB) provide a promising platform for enhancing crop cultivars with greater efficiency. However, several obstacles must be overcome to optimize the use of these techniques in crop improvement, such as the complexity of phenotypic analysis of big image data. In addition, the prevalent use of linear models in genome-wide association studies (GWAS) and genomic selection (GS) fails to capture the nonlinear interactions of complex traits, limiting their applicability for GAB and impeding crop improvement. Recent advances in artificial intelligence (AI) techniques have opened doors to nonlinear modelling approaches in crop breeding, enabling the capture of nonlinear and epistatic interactions in GWAS and GS and thus making this variation available for GAB. While statistical and software challenges persist in AI-based models, they are expected to be resolved soon. Furthermore, recent advances in speed breeding have significantly reduced the time (3-5-fold) required for conventional breeding. Thus, integrating speed breeding with AI and GAB could improve crop cultivar development within a considerably shorter timeframe while ensuring greater accuracy and efficiency. In conclusion, this integrated approach could revolutionize crop breeding paradigms and safeguard food production in the face of population growth and climate change.
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Affiliation(s)
| | - Xianzhong Feng
- Zhejiang Lab, Hangzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Zahoor A Mir
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Aamir Raina
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, Perth, Western Australia, Australia
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Ali S, Mir RA, Tyagi A, Manzar N, Kashyap AS, Mushtaq M, Raina A, Park S, Sharma S, Mir ZA, Lone SA, Bhat AA, Baba U, Mahmoudi H, Bae H. Chromium Toxicity in Plants: Signaling, Mitigation, and Future Perspectives. Plants (Basel) 2023; 12:plants12071502. [PMID: 37050128 PMCID: PMC10097182 DOI: 10.3390/plants12071502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 05/31/2023]
Abstract
Plants are very often confronted by different heavy metal (HM) stressors that adversely impair their growth and productivity. Among HMs, chromium (Cr) is one of the most prevalent toxic trace metals found in agricultural soils because of anthropogenic activities, lack of efficient treatment, and unregulated disposal. It has a huge detrimental impact on the physiological, biochemical, and molecular traits of crops, in addition to being carcinogenic to humans. In soil, Cr exists in different forms, including Cr (III) "trivalent" and Cr (VI) "hexavalent", but the most pervasive and severely hazardous form to the biota is Cr (VI). Despite extensive research on the effects of Cr stress, the exact molecular mechanisms of Cr sensing, uptake, translocation, phytotoxicity, transcript processing, translation, post-translational protein modifications, as well as plant defensive responses are still largely unknown. Even though plants lack a Cr transporter system, it is efficiently accumulated and transported by other essential ion transporters, hence posing a serious challenge to the development of Cr-tolerant cultivars. In this review, we discuss Cr toxicity in plants, signaling perception, and transduction. Further, we highlight various mitigation processes for Cr toxicity in plants, such as microbial, chemical, and nano-based priming. We also discuss the biotechnological advancements in mitigating Cr toxicity in plants using plant and microbiome engineering approaches. Additionally, we also highlight the role of molecular breeding in mitigating Cr toxicity in sustainable agriculture. Finally, some conclusions are drawn along with potential directions for future research in order to better comprehend Cr signaling pathways and its mitigation in sustainable agriculture.
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Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Rakeeb A. Mir
- Department of Biotechnology, Central University of Kashmir, Ganderbal 191201, India
| | - Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Nazia Manzar
- Plant Pathology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Abhijeet Shankar Kashyap
- Plant Pathology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Muntazir Mushtaq
- MS Swaminathan School of Agriculture, Shoolini University, Bajhol 173229, India
| | - Aamir Raina
- Mutation Breeding Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Suvin Park
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Zahoor A. Mir
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Showkat A. Lone
- Centre of Research for Development, University of Kashmir, Srinagar 190006, India
| | - Ajaz A. Bhat
- Govt. Degree College for Women, University of Kashmir, Baramulla 193101, India
| | - Uqab Baba
- Centre of Research for Development, University of Kashmir, Srinagar 190006, India
| | - Henda Mahmoudi
- Directorate of Programs, International Center for Biosaline Agriculture, Dubai P.O. Box 14660, United Arab Emirates
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
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Mushtaq M, Bhat JA, Mir ZA, Sakina A, Ali S, Singh AK, Tyagi A, Salgotra RK, Dar AA, Bhat R. CRISPR/Cas approach: A new way of looking at plant-abiotic interactions. J Plant Physiol 2018; 224-225:156-162. [PMID: 29655033 DOI: 10.1016/j.jplph.2018.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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: 12/01/2017] [Revised: 03/26/2018] [Accepted: 04/02/2018] [Indexed: 05/20/2023]
Abstract
It is not the most grounded of the species that survive, nor the most shrewd, however one most receptive to change. Crop plants being sessile are subjected to various abiotic stresses resulting significant yield losses about an average of more than 50 percent, thus greatly threatening the global crop production. In this regard, plant breeding innovations and genetic engineering approaches have been used in the past for generating stress tolerant crop genotypes, but due to complex inheritance of abiotic stress tolerance these approaches are not enough to bring significant trait improvement and to guarantee world's future sustenance security. Although, RNA interference (RNAi) technology has been utilized amid the most recent decades to produce plants tolerant to environmental stress. But this technique ordinarily prompts to down-regulate as opposed to complete inhibition of target genes. Therefore, scientist/researchers were looking for techniques that should be efficient, precise and reliable as well as have potential to solve the issues experienced by previous approaches, and hence the CRISPR/Cas system came into spotlight. Although, only few studies using CRISPR/Cas approach for targeting abiotic stress tolerance related genes have been reported, but suggested its effective role for future applications in molecular breeding to improve abiotic stress tolerance. Hence, genome engineering via CRISPR-Cas system for targeted mutagenesis promise its immense potential in generating elite cultivars of crop plants with enhanced and durable climate resilience. Lastly, CRISPR-Cas will be future of crop breeding as well as to target minor gene variation of complex quantitative traits, and thus will be the key approach to release global hunger and maintain food security.
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Affiliation(s)
- Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India.
| | - Javaid Akhter Bhat
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India
| | - Zahoor A Mir
- National Research Centre for Plant Biotechnology, New Delhi, India
| | - Afreen Sakina
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Sajad Ali
- Centre of Research for Develoment, University of Kashmir, Srinagar, India
| | - Anil Kumar Singh
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India
| | - Anshika Tyagi
- National Research Centre for Plant Biotechnology, New Delhi, India
| | - Romesh Kumar Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India
| | - Ajaz Ahmad Dar
- Division of Mirobiology, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India
| | - Rohini Bhat
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India
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Mir ZA, Ali S, Tyagi A, Ali A, Bhat JA, Jaiswal P, Qari HA, Oves M. Degradation and conversion of endosulfan by newly isolated Pseudomonas mendocina ZAM1 strain. 3 Biotech 2017; 7:211. [PMID: 28667651 DOI: 10.1007/s13205-017-0823-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 01/18/2017] [Accepted: 04/19/2017] [Indexed: 11/28/2022] Open
Abstract
Endosulfan contamination is one of the major concerns of soil ecosystem, which causes detrimental effects not only to humans but also to animals and plants. Therefore, the aim of this study was to isolate and identify a novel bacterial strain capable of degrading endosulfan in agriculture contaminated soils. A novel bacterial strain was isolated from the sugarcane field contaminated with endosulfan, and was named as ZAM1 strain. The ZAM1 bacterial strain was further identified as Pseudomonas mendocina based on the biochemical and molecular analysis. 16sRNA sequence analysis of ZAM1 strain shows maximum similarity with known endosulfan-degrading bacteria (Pseudomonas putida), respectively. Enrichment was carried out using the endosulfan as sole sulfur source. The ZAM1 strain was able to use α and β endosulfan as a sole sulfur source. Our results showed that ZAM1 strain degrades endosulfan >64.5% (50 mg/l) after 12 days of incubation. The residues were analyzed by GC-MS analysis and confirmed the formation of metabolites of dieldrin, 2 heptanone, methyl propionate, and endosulfan lactone compounds. Hence, these results indicate that the ZAM1 strain is a promising bacterial source for detoxification of endosulfan residues in the environment.
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Affiliation(s)
- Zahoor A Mir
- MSCAS College of Arts and Science, Chennai, Tamil Nadu, India
| | - Sajad Ali
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Anshika Tyagi
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ajaz Ali
- St Xavier's College, Tirunelveli, Tamil Nadu, India
| | - Javaid A Bhat
- Department of Genetics, IARI, PUSA Campus, New Delhi, India
| | - Praful Jaiswal
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Huda A Qari
- Center of Excellence in Environmental Studies, King Abdul-Aziz University, Jeddah, 21589, Kingdom of Saudi Arabia
| | - Mohammad Oves
- Center of Excellence in Environmental Studies, King Abdul-Aziz University, Jeddah, 21589, Kingdom of Saudi Arabia.
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Ali S, Mir ZA, Tyagi A, Mehari H, Meena RP, Bhat JA, Yadav P, Papalou P, Rawat S, Grover A. Overexpression of NPR1 in Brassica juncea Confers Broad Spectrum Resistance to Fungal Pathogens. Front Plant Sci 2017; 8:1693. [PMID: 29046679 PMCID: PMC5632730 DOI: 10.3389/fpls.2017.01693] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 09/14/2017] [Indexed: 05/18/2023]
Abstract
Brassica juncea (Indian mustard) is a commercially important oil seed crop, which is highly affected by many biotic stresses. Among them, Alternaria leaf blight and powdery mildew are the most devastating diseases leading to huge yield losses in B. juncea around the world. In this regard, genetic engineering is a promising tool that may possibly allow us to enhance the B. juncea disease resistance against these pathogens. NPR1 (non-expressor of pathogen-related gene 1) is a bonafide receptor of salicylic acid (SA) which modulates multiple immune responses in plants especially activation of induced and systemic acquired resistance (SAR). Here, we report the isolation and characterization of new NPR1 homolog (BjNPR1) from B. juncea. The phylogenetic tree constructed based on the deduced sequence of BjNPR1 with homologs from other species revealed that BjNPR1 grouped together with other known NPR1 proteins of Cruciferae family, and was nearest to B. napus. Furthermore, expression analysis showed that BjNPR1 was upregulated after SA treatment and fungal infection but not by jasmonic acid or abscisic acid. To understand the defensive role of this gene, we generated B. juncea transgenic lines overexpressing BjNPR1, and further confirmed by PCR and Southern blotting. The transgenic lines showed no phenotypic abnormalities, and constitutive expression of BjNPR1 activates defense signaling pathways by priming the expression of antifungal PR genes. Moreover, BjNPR1 transgenic lines showed enhanced resistance to Alternaria brassicae and Erysiphe cruciferarum as there was delay in symptoms and reduced disease severity than non-transgenic plants. In addition, the rate of disease spreading to uninfected or distal parts was also delayed in transgenic plants thus suggesting the activation of SAR. Altogether, the present study suggests that BjNPR1 is involved in broad spectrum of disease resistance against fungal pathogens.
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Affiliation(s)
- Sajad Ali
- National Research Centre on Plant Biotechnology, New Delhi, India
- Centre of Research for Development, University of Kashmir, Srinagar, India
| | - Zahoor A. Mir
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Anshika Tyagi
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Hailay Mehari
- National Research Centre on Plant Biotechnology, New Delhi, India
| | | | - Javaid A. Bhat
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Prashant Yadav
- National Research Centre on Plant Biotechnology, New Delhi, India
| | | | - Sandhya Rawat
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Anita Grover
- National Research Centre on Plant Biotechnology, New Delhi, India
- *Correspondence: Anita Grover,
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Bhat JA, Ali S, Salgotra RK, Mir ZA, Dutta S, Jadon V, Tyagi A, Mushtaq M, Jain N, Singh PK, Singh GP, Prabhu KV. Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding. Front Genet 2016; 7:221. [PMID: 28083016 PMCID: PMC5186759 DOI: 10.3389/fgene.2016.00221] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [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: 08/10/2016] [Accepted: 12/12/2016] [Indexed: 12/31/2022] Open
Abstract
Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.
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Affiliation(s)
- Javaid A Bhat
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Sajad Ali
- National Research Centre for Plant Biotechnology New Delhi, India
| | - Romesh K Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu Chatha, India
| | - Zahoor A Mir
- National Research Centre for Plant Biotechnology New Delhi, India
| | - Sutapa Dutta
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Vasudha Jadon
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Anshika Tyagi
- National Research Centre for Plant Biotechnology New Delhi, India
| | - Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu Chatha, India
| | - Neelu Jain
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Pradeep K Singh
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Gyanendra P Singh
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - K V Prabhu
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
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