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Madhawan A, Bhunia RK, Kumar P, Sharma V, Sinha K, Fandade V, Rahim MS, Parveen A, Mishra A, Roy J. Interaction between long noncoding RNA (lnc663) and microRNA (miR1128) regulates PDAT-like gene activity in bread wheat (Triticum aestivum L.). Plant Physiol Biochem 2023; 203:108040. [PMID: 37738867 DOI: 10.1016/j.plaphy.2023.108040] [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] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023]
Abstract
Amylose, a starch subcomponent, can bind lipids within its helical groove and form an amylose-lipid complex, known as resistant starch type 5 (RS-5). RS contributes to lower glycaemic index of grain with health benefits. Unfortunately, genes involved in lipid biosynthesis in wheat grain remain elusive. Our study aims to characterize the lipid biosynthesis gene and its post-transcriptional regulation using the parent bread wheat variety 'C 306' and its EMS-induced mutant line 'TAC 75' varying in amylose content. Quantitative analyses of starch-bound lipids showed that 'TAC 75' has significantly higher lipid content in grains than 'C 306' variety. Furthermore, expression analyses revealed the higher expression of wheat phospholipid: diacylglycerol acyltransferase-like (PDAT-like) in the 'TAC 75' compared to the 'C 306'. Overexpression and ectopic expression of TaPDAT in yeast and tobacco leaf confirmed its ability to accumulate lipids in vivo. Enzyme activity assay showed that TaPDAT catalyzes the triacylglycerol synthesis by acylating 1,2-diacylglycerol. Interestingly, the long non-coding RNA, lnc663, was upregulated with the TaPDAT gene, while the miRNA, miR1128, downregulated in the 'TAC 75', indicating a regulatory relationship. The GFP reporter assay confirmed that the lnc663 acts as a positive regulator, and the miR1128 as a negative regulator of the TaPDAT gene, which controls lipid accumulation in wheat grain. Our findings outline TaPDAT-mediated biosynthesis of lipid accumulation and reveal the molecular mechanism of the lnc663 and miR1128 mediated regulation of the TaPDAT gene in wheat grain.
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Affiliation(s)
- Akansha Madhawan
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India; Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
| | - Rupam Kumar Bhunia
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India; Plant Biotechnology Department, Gujarat Biotechnology University, Near Gujarat International Finance Tec (GIFT)-City, Gandhinagar, Gujarat, India.
| | - Prashant Kumar
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India; Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
| | - Vinita Sharma
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
| | - Kshitija Sinha
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
| | - Vikas Fandade
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India; Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
| | - Mohammed Saba Rahim
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
| | - Afsana Parveen
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
| | - Ankita Mishra
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
| | - Joy Roy
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
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Kumar A, Thomas J, Gill N, Dwiningsih Y, Ruiz C, Famoso A, Pereira A. Molecular mapping and characterization of QTLs for grain quality traits in a RIL population of US rice under high nighttime temperature stress. Sci Rep 2023; 13:4880. [PMID: 36966148 PMCID: PMC10039871 DOI: 10.1038/s41598-023-31399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/10/2023] [Indexed: 03/27/2023] Open
Abstract
Elevated nighttime temperatures resulting from climate change significantly impact the rice crop worldwide. The rice (Oryza sativa L.) plant is highly sensitive to high nighttime temperature (HNT) during grain-filling (reproductive stage). HNT stress negatively affects grain quality traits and has a major impact on the value of the harvested rice crop. In addition, along with grain dimensions determining rice grain market classes, the grain appearance and quality traits determine the rice grain market value. During the last few years, there has been a major concern for rice growers and the rice industry over the prevalence of rice grains opacity and the reduction of grain dimensions affected by HNT stress. Hence, the improvement of heat-stress tolerance to maintain grain quality of the rice crop under HNT stress will bolster future rice value in the market. In this study, 185 F12-recombinant inbred lines (RILs) derived from two US rice cultivars, Cypress (HNT-tolerant) and LaGrue (HNT-sensitive) were screened for the grain quality traits grain length (GL), grain width (GW), and percent chalkiness (%chalk) under control and HNT stress conditions and evaluated to identify the genomic regions associated with the grain quality traits. In total, there were 15 QTLs identified; 6 QTLs represented under control condition explaining 3.33% to 8.27% of the phenotypic variation, with additive effects ranging from - 0.99 to 0.0267 on six chromosomes and 9 QTLs represented under HNT stress elucidating 6.39 to 51.53% of the phenotypic variation, with additive effects ranging from - 8.8 to 0.028 on nine chromosomes for GL, GW, and % chalk. These 15 QTLs were further characterized and scanned for natural genetic variation in a japonica diversity panel (JDP) to identify candidate genes for GL, GW, and %chalk. We found 6160 high impact single nucleotide polymorphisms (SNPs) characterized as such depending on their type, region, functional class, position, and proximity to the gene and/or gene features, and 149 differentially expressed genes (DEGs) in the 51 Mbp genomic region comprising of the 15 QTLs. Out of which, 11 potential candidate genes showed high impact SNP associations. Therefore, the analysis of the mapped QTLs and their genetic dissection in the US grown Japonica rice genotypes at genomic and transcriptomic levels provide deep insights into genetic variation beneficial to rice breeders and geneticists for understanding the mechanisms related to grain quality under heat stress in rice.
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Affiliation(s)
- Anuj Kumar
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Julie Thomas
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Navdeep Gill
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Yheni Dwiningsih
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Charles Ruiz
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Adam Famoso
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, Rayne, LA, 70578, USA
| | - Andy Pereira
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
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Aher RR, Reddy PS, Bhunia RK, Flyckt KS, Shankhapal AR, Ojha R, Everard JD, Wayne LL, Ruddy BM, Deonovic B, Gupta SK, Sharma KK, Bhatnagar-Mathur P. Loss-of-function of triacylglycerol lipases are associated with low flour rancidity in pearl millet [ Pennisetum glaucum (L.) R. Br.]. Front Plant Sci 2022; 13:962667. [PMID: 36267938 PMCID: PMC9577237 DOI: 10.3389/fpls.2022.962667] [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: 06/16/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
Pearl millet is an important cereal crop of semi-arid regions since it is highly nutritious and climate resilient. However, pearl millet is underutilized commercially due to the rapid onset of hydrolytic rancidity of seed lipids post-milling. We investigated the underlying biochemical and molecular mechanisms of rancidity development in the flour from contrasting inbred lines under accelerated aging conditions. The breakdown of storage lipids (triacylglycerols; TAG) was accompanied by free fatty acid accumulation over the time course for all lines. The high rancidity lines had the highest amount of FFA by day 21, suggesting that TAG lipases may be the cause of rancidity. Additionally, the high rancidity lines manifested substantial amounts of volatile aldehyde compounds, which are characteristic products of lipid oxidation. Lipases with expression in seed post-milling were sequenced from low and high rancidity lines. Polymorphisms were identified in two TAG lipase genes (PgTAGLip1 and PgTAGLip2) from the low rancidity line. Expression in a yeast model system confirmed these mutants were non-functional. We provide a direct mechanism to alleviate rancidity in pearl millet flour by identifying mutations in key TAG lipase genes that are associated with low rancidity. These genetic variations can be exploited through molecular breeding or precision genome technologies to develop elite pearl millet cultivars with improved flour shelf life.
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Affiliation(s)
- Rasika Rajendra Aher
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
- Department of Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Rupam Kumar Bhunia
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | | | - Aishwarya R Shankhapal
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Rabishankar Ojha
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | | | | | | | | | - Shashi K Gupta
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Kiran K Sharma
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
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Winichayakul S, Curran A, Moraga R, Cookson R, Xue H, Crowther T, Roldan M, Bryan G, Roberts N. An alternative angiosperm DGAT1 topology and potential motifs in the N-terminus. Front Plant Sci 2022; 13:951389. [PMID: 36186081 PMCID: PMC9523541 DOI: 10.3389/fpls.2022.951389] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
The highly variable cytoplasmic N-terminus of the plant diacylglycerol acyltransferase 1 (DGAT1) has been shown to have roles in oligomerization as well as allostery; however, the biological significance of the variation within this region is not understood. Comparing the coding sequences over the variable N-termini revealed the Poaceae DGAT1s contain relatively high GC compositional gradients as well as numerous direct and inverted repeats in this region. Using a variety of reciprocal chimeric DGAT1s from angiosperms we show that related N-termini had similar effects (positive or negative) on the accumulation of the recombinant protein in Saccharomyces cerevisiae. When expressed in Camelina sativa seeds the recombinant proteins of specific chimeras elevated total lipid content of the seeds as well as increased seed size. In addition, we combine N- and C-terminal as well as internal tags with high pH membrane reformation, protease protection and differential permeabilization. This led us to conclude the C-terminus is in the ER lumen; this contradicts earlier reports of the cytoplasmic location of plant DGAT1 C-termini.
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Affiliation(s)
- Somrutai Winichayakul
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Amy Curran
- ZeaKal Inc., San Diego, CA, United States
| | - Roger Moraga
- Bioinformatics and Statistics, AgResearch Ltd., Palmerston North, New Zealand
| | - Ruth Cookson
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Hong Xue
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Tracey Crowther
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Marissa Roldan
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Greg Bryan
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
- ZeaKal Inc., San Diego, CA, United States
| | - Nick Roberts
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
- ZeaKal Inc., San Diego, CA, United States
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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Jiang W, Li C, Li Y, Peng H. Metabolic Engineering Strategies for Improved Lipid Production and Cellular Physiological Responses in Yeast Saccharomyces cerevisiae. J Fungi (Basel) 2022; 8:427. [PMID: 35628683 PMCID: PMC9144191 DOI: 10.3390/jof8050427] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 02/01/2023] Open
Abstract
Microbial lipids have been a hot topic in the field of metabolic engineering and synthetic biology due to their increased market and important applications in biofuels, oleochemicals, cosmetics, etc. This review first compares the popular hosts for lipid production and explains the four modules for lipid synthesis in yeast, including the fatty acid biosynthesis module, lipid accumulation module, lipid sequestration module, and fatty acid modification module. This is followed by a summary of metabolic engineering strategies that could be used for enhancing each module for lipid production. In addition, the efforts being invested in improving the production of value-added fatty acids in engineered yeast, such as cyclopropane fatty acid, ricinoleic acid, gamma linoleic acid, EPA, and DHA, are included. A discussion is further made on the potential relationships between lipid pathway engineering and consequential changes in cellular physiological properties, such as cell membrane integrity, intracellular reactive oxygen species level, and mitochondrial membrane potential. Finally, with the rapid development of synthetic biology tools, such as CRISPR genome editing tools and machine learning models, this review proposes some future trends that could be employed to engineer yeast with enhanced intracellular lipid production while not compromising much of its cellular health.
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Ojha R, Kaur S, Sinha K, Chawla K, Kaur S, Jadhav H, Kaur M, Bhunia RK. Characterization of oleosin genes from forage sorghum in Arabidopsis and yeast reveals their role in storage lipid stability. Planta 2021; 254:97. [PMID: 34655341 DOI: 10.1007/s00425-021-03744-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/03/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Overexpression of forage sorghum oleosin genes in Arabidopsis oleosin-deficient mutant and yeast showed increased germination rate, triacylglycerol content, and protection against lipase-mediated TAG degradation. Plant lipids are an important source of ration for cattle or other livestock animals to fulfil their energy needs. Poor energy containing green forages are still one of the major sources of food for livestock animals, leaving the animals undernourished. This lowers the milk and meat production efficiency, thereby affecting human consumption. Oleosin, an essential oil body surface protein, is capable of enhancing and stabilizing the lipid content in plants. We identified and functionally characterized three forage sorghum oleosin genes (SbOle1, SbOle2, and SbOle3) in Arabidopsis and yeast. Phylogenetic analysis of SbOle proteins showed a close relationship with rice and maize oleosins. Expression analysis of SbOle genes determined a higher expression pattern in embryo followed by endosperm, while its expression in the non-seed tissues remained negligible. Overexpression of SbOle genes in Arabidopsis ole1-deficient mutants showed restoration of normal germination whereas control mutant seeds showed lower germination rates. Heterologous overexpression of SbOle in yeast cells resulted in increased TAG accumulation. Additionally, the TAG turnover assay showed the effectiveness of SbOle genes in reducing the yeast endogenous and rumen bacterial lipase-mediated TAG degradation. Taken together, our findings not only provide insights into forage sorghum oleosin for increasing the energy content in non-seed organs but also opened up the direction towards implication of oleosin in rumen protection of fodders.
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Affiliation(s)
- Rabishankar Ojha
- Plant Tissue Culture and Genetic Engineering, National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), Mohali, Punjab, 140306, India
| | - Simranjit Kaur
- Plant Tissue Culture and Genetic Engineering, National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), Mohali, Punjab, 140306, India
| | - Kshitija Sinha
- Plant Tissue Culture and Genetic Engineering, National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), Mohali, Punjab, 140306, India
- Department of Biotechnology, Panjab University, Sector-25, Chandigarh, 160014, India
| | - Kirti Chawla
- Plant Tissue Culture and Genetic Engineering, National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), Mohali, Punjab, 140306, India
| | - Sumandeep Kaur
- Plant Tissue Culture and Genetic Engineering, National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), Mohali, Punjab, 140306, India
- Department of Biotechnology, Panjab University, Sector-25, Chandigarh, 160014, India
| | - Harish Jadhav
- Plant Tissue Culture and Genetic Engineering, National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), Mohali, Punjab, 140306, India
| | - Manmehar Kaur
- Plant Tissue Culture and Genetic Engineering, National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), Mohali, Punjab, 140306, India
- Department of Biotechnology, Panjab University, Sector-25, Chandigarh, 160014, India
| | - Rupam Kumar Bhunia
- Plant Tissue Culture and Genetic Engineering, National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), Mohali, Punjab, 140306, India.
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Affiliation(s)
- Kirti Chawla
- Plant Tissue Culture and Genetic Engineering National Agri‐Food Biotechnology Institute (NABI) Mohali Punjab India
| | - Sumandeep Kaur
- Department of Biotechnology, Sector‐25 Panjab University Chandigarh India
| | - Ranjeet Kaur
- Department of Genetics University of Delhi South Campus New Delhi India
| | - Rupam Kumar Bhunia
- Plant Tissue Culture and Genetic Engineering National Agri‐Food Biotechnology Institute (NABI) Mohali Punjab India
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