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Kaul T, Thangaraj A, Jain R, Bharti J, Kaul R, Verma R, Sony SK, Abdel Motelb KF, Yadav P, Agrawal PK. CRISPR/Cas9-mediated homology donor repair base editing system to confer herbicide resistance in maize (Zea mays L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108374. [PMID: 38310724 DOI: 10.1016/j.plaphy.2024.108374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/20/2023] [Accepted: 01/12/2024] [Indexed: 02/06/2024]
Abstract
Weed infestation is a significant concern to crop yield loss, globally. The potent broad-spectrum glyphosate (N-phosphomethyl-glycine) has a widely utilized herbicide, acting on the shikimic acid pathway within chloroplast by inhibiting 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). This crucial enzyme plays a vital role in aromatic amino acid synthesis. Repurposing of CRISPR/Cas9-mediated gene-editing was the inflection point for generating novel crop germplasm with diverse genetic variations in essential agronomic traits, achieved through the introduction of nucleotide substitutions at target sites within the native genes, and subsequent induction of indels through error-prone non-homologous end-joining DNA repair mechanisms. Here, we describe the development of efficient herbicide-resistant maize lines by using CRISPR/Cas9 mediated site-specific native ZmEPSPS gene fragment replacement via knock-out of conserved region followed by knock-in of desired homologous donor repair (HDR-GATIPS-mZmEPSPS) with triple amino acid substitution. The novel triple substitution conferred high herbicide tolerance in edited maize plants. Transgene-free progeny harbouring the triple amino acid substitutions revealed agronomic performances similar to that of wild-type plants, suggesting that the GATIPS-mZmEPSPS allele substitutions are crucial for developing elite maize varieties with significantly enhanced glyphosate resistance. Furthermore, the aromatic amino acid contents in edited maize lines were significantly higher than in wild-type plants. The present study describing the introduction of site-specific CRISPR/Cas9- GATIPS mutations in the ZmEPSPS gene via genome editing has immense potential for higher tolerance to glyphosate with no yield penalty in maize.
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Affiliation(s)
- Tanushri Kaul
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India.
| | - Arulprakash Thangaraj
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Rashmi Jain
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Jyotsna Bharti
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Rashmi Kaul
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Rachana Verma
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Sonia Khan Sony
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Khaled Fathy Abdel Motelb
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Pranjal Yadav
- Indian Council of Agricultural Research- Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Pawan Kumar Agrawal
- Indian Council of Agricultural Research, New Delhi, 110012, India; ICAR-National Institute of Biotic Stress Management, Raipur, 493225, Chhattisgarh, India
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Meng Y, Zhang W, Wang Z, Yuan F, Guo S, Lin H, Niu L. Co-expression of GR79 EPSPS and GAT generates high glyphosate-resistant alfalfa with low glyphosate residues. ABIOTECH 2023; 4:352-358. [PMID: 38106433 PMCID: PMC10721576 DOI: 10.1007/s42994-023-00119-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/07/2023] [Indexed: 12/19/2023]
Abstract
Weed competition seriously threatens the yield of alfalfa, the most important forage legume worldwide, thus generating herbicide-resistant alfalfa varieties is becoming a necessary cost-effective strategy to assist farmers for weed control. Here, we report the co-expression of plant codon-optimized forms of GR79 EPSPS (pGR79 EPSPS) and N-acetyltransferase (pGAT) genes, in alfalfa, via Agrobacterium-mediated transformation. We established that the pGR79 EPSPS-pGAT co-expression alfalfa lines were able to tolerate up to tenfold higher commercial usage of glyphosate and produced approximately ten times lower glyphosate residues than the conventional cultivar. Our findings generate an elite herbicide-resistant germplasm for alfalfa breeding and provide a promising strategy for developing high-glyphosate-resistant and low-glyphosate-residue forages. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00119-3.
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Affiliation(s)
- Yingying Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Wenwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhaoming Wang
- Inner Mongolia Pratacultural Technology Innovation Center Co., Ltd, Hohhot, 010010 China
- National Center of Pratacultural Technology Innovation (Under Preparation), Hohhot, 010010 China
| | - Feng Yuan
- Inner Mongolia Pratacultural Technology Innovation Center Co., Ltd, Hohhot, 010010 China
- National Center of Pratacultural Technology Innovation (Under Preparation), Hohhot, 010010 China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hao Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lifang Niu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Li S, Li P, Li X, Wen N, Wang Y, Lu W, Lin M, Lang Z. In maize, co-expression of GAT and GR79-EPSPS provides high glyphosate resistance, along with low glyphosate residues. ABIOTECH 2023; 4:277-290. [PMID: 38106436 PMCID: PMC10721750 DOI: 10.1007/s42994-023-00114-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/01/2023] [Indexed: 12/19/2023]
Abstract
Herbicide tolerance has been the dominant trait introduced during the global commercialization of genetically modified (GM) crops. Herbicide-tolerant crops, especially glyphosate-resistant crops, offer great advantages for weed management; however, despite these benefits, glyphosate-resistant maize (Zea mays L.) has not yet been commercially deployed in China. To develop a new bio-breeding resource for glyphosate-resistant maize, we introduced a codon-optimized glyphosate N-acetyltransferase gene, gat, and the enolpyruvyl-shikimate-3-phosphate synthase gene, gr79-epsps, into the maize variety B104. We selected a genetically stable high glyphosate resistance (GR) transgenic event, designated GG2, from the transgenic maize population through screening with high doses of glyphosate. A molecular analysis demonstrated that single copy of gat and gr79-epsps were integrated into the maize genome, and these two genes were stably transcribed and translated. Field trials showed that the transgenic event GG2 could tolerate 9000 g acid equivalent (a.e.) glyphosate per ha with no effect on phenotype or yield. A gas chromatography-mass spectrometry (GC-MS) analysis revealed that, shortly after glyphosate application, the glyphosate (PMG) and aminomethylphosphonic acid (AMPA) residues in GG2 leaves decreased by more than 90% compared to their levels in HGK60 transgenic plants, which only harbored the epsps gene. Additionally, PMG and its metabolic residues (AMPA and N-acetyl-PMG) were not detected in the silage or seeds of GG2, even when far more than the recommended agricultural dose of glyphosate was applied. The co-expression of gat and gr79-epsps, therefore, confers GG2 with high GR and a low risk of herbicide residue accumulation, making this germplasm a valuable GR event in herbicide-tolerant maize breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00114-8.
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Affiliation(s)
- Shengyan Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pengcheng Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangyin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ning Wen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yinxiao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhihong Lang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan China
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Zhou Q, Li S, Zhao M, Liu Y, He N, Zhou X, Zhou D, Qian Z. Subchronic feeding study of glyphosate-tolerant maize GG2 with the gr79-epsps and gat genes in Wistar Han RCC rats. Regul Toxicol Pharmacol 2023; 145:105520. [PMID: 37884076 DOI: 10.1016/j.yrtph.2023.105520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/07/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023]
Abstract
The genetically modified (GM) maize GG2 contains gr79-epsps and gat genes, conferring glyphosate tolerance. The present study aimed to investigate potential effects of maize GG2 in a 90-day subchronic feeding study on Wistar Han RCC rats. Maize grains from GG2 or non-GM maize were incorporated into diets at concentrations of 25% and 50% and administered to Wistar Han RCC rats (n = 10/sex/group) for 90 days. The basal-diet group of rats (n = 10/sex/group) were fed with common commercialized rodent diet. Compared with rats fed with the corresponding non-GM maize and the basal-diet, no biologically relevant differences were observed in rats fed with the maize GG2, according to the results of body weight/gain, feed consumption/utilization, clinical signs, mortality, ophthalmology, clinical pathology (hematology, prothrombin time, urinalysis, serum chemistry), organ weights, and gross and microscopic pathology. Under the conditions of this study, these results indicated that maize GG2 is as safe as the non-GM maize in this 90-day feeding study.
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Affiliation(s)
- Qinghong Zhou
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Shufei Li
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Miao Zhao
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Yinghua Liu
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Ning He
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Xiaoli Zhou
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Dianming Zhou
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Zhiyong Qian
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China.
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Li Z, Zhang Z, Liu Y, Ma Y, Lv X, Zhang D, Gu Q, Ke H, Wu L, Zhang G, Ma Z, Wang X, Sun Z. Identification and Expression Analysis of EPSPS and BAR Families in Cotton. PLANTS (BASEL, SWITZERLAND) 2023; 12:3366. [PMID: 37836107 PMCID: PMC10574212 DOI: 10.3390/plants12193366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Weeds seriously affect the yield and quality of crops. Because manual weeding is time-consuming and laborious, the use of herbicides becomes an effective way to solve the harm caused by weeds in fields. Both 5-enolpyruvyl shikimate-3-phosphate synthetase (EPSPS) and acetyltransferase genes (bialaphos resistance, BAR) are widely used to improve crop resistance to herbicides. However, cotton, as the most important natural fiber crop, is not tolerant to herbicides in China, and the EPSPS and BAR family genes have not yet been characterized in cotton. Therefore, we explore the genes of these two families to provide candidate genes for the study of herbicide resistance mechanisms. In this study, 8, 8, 4, and 5 EPSPS genes and 6, 6, 5, and 5 BAR genes were identified in allotetraploid Gossypium hirsutum and Gossypium barbadense, diploid Gossypium arboreum and Gossypium raimondii, respectively. Members of the EPSPS and BAR families were classified into three subgroups based on the distribution of phylogenetic trees, conserved motifs, and gene structures. In addition, the promoter sequences of EPSPS and BAR family members included growth and development, stress, and hormone-related cis-elements. Based on the expression analysis, the family members showed tissue-specific expression and differed significantly in response to abiotic stresses. Finally, qRT-PCR analysis revealed that the expression levels of GhEPSPS3, GhEPSPS4, and GhBAR1 were significantly upregulated after exogenous spraying of herbicides. Overall, we characterized the EPSPS and BAR gene families of cotton at the genome-wide level, which will provide a basis for further studying the functions of EPSPS and BAR genes during growth and development and herbicide stress.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, College of Agronomy, Hebei Agricultural University, Baoding 071000, China; (Z.L.); (Z.Z.); (Y.L.); (Y.M.); (X.L.); (D.Z.); (Q.G.); (H.K.); (L.W.); (G.Z.); (Z.M.)
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, College of Agronomy, Hebei Agricultural University, Baoding 071000, China; (Z.L.); (Z.Z.); (Y.L.); (Y.M.); (X.L.); (D.Z.); (Q.G.); (H.K.); (L.W.); (G.Z.); (Z.M.)
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Jie Chen Z, Yan Zhai X, Liu J, Zhang N, Yang H. Detoxification and catabolism of mesotrione and fomesafen facilitated by a Phase II reaction acetyltransferase in rice. J Adv Res 2023; 51:1-11. [PMID: 36494064 PMCID: PMC10491983 DOI: 10.1016/j.jare.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 10/16/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION The excessive dosage of pesticides required for agronomic reality results in growing contamination of pesticide residues in environment, thus bringing high risks to crop production and human health. OBJECTIVES This study aims to unveil a novel mechanism for catabolism of two pesticides MTR and FSA facilitated by an uncharacterized Phase II reaction enzyme termed acetyltransferase-1 (ACE1) in rice and to make assessment of its potential for bioremediation to minimize the risks to crop production and food safety. METHODS We developed genetically improved cultivars overexpressing OsACE1 (OE) and knockout mutant lines by CRISPR-Cas9 technology to identify the MTR and FSA detoxic and metabolic functions and characterized their metabolites and conjugates by HPLC-LTQ-MS/MS. RESULTS OsACE1 overexpression conferred rice resistance to toxicity of MTR/FSA compared to wild-type, manifested by improved plant elongation and biomass, attenuated cellular injury, and increased chlorophyll accumulation. The OE plants accumulated significantly less parent MTR/FSA and more degradative metabolites, and removed MTR/FSA from their growth medium by 1.38 and 1.61 folds over the wild-type. In contrast, knocking out OsACE1 led to compromised growth fitness and intensified toxic symptoms under MTR/FSA stress and accumulation of more toxic MTR and FSA in rice. The reduced metabolites of MTR and FSA detected in the Cas9 plants suggest the impaired capability of OsACE1 function. CONCLUSIONS These results signified that OsACE1 expression is required for detoxifying the two poisoning chemicals in rice and plays a critical role in accelerating breakdown of the pesticides mainly through Phase II reaction mechanism pathways.
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Affiliation(s)
- Zhao Jie Chen
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Yan Zhai
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jintong Liu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Nan Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Yang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China.
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Chen ZJ, Qiao Y, Zhang N, Yang H, Liu J. Acetyltransferase OsACE2 acts as a regulator to reduce the environmental risk of oxyfluorfen to rice production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161599. [PMID: 36640869 DOI: 10.1016/j.scitotenv.2023.161599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
The constant use of the pesticide oxyfluorfen (OFF) in farmland contaminates the soil, posing threats to crop growth and human health. To avoid the contamination of food crops with OFF, it is critically important to understand its absorption and degradation mechanisms. In this study, we characterized a new functional locus encoding an acetyltransferase (OsACE2) that can facilitate OFF degradation in rice. OsACE2 was drastically induced by OFF at 0.04-0.2 mg L-1 for 6 days and the rice growth was significantly inhibited. To demonstrate the regulatory role of OsACE2 in resistance to OFF toxicity, we generated OsACE2 overexpression (OE) and knockout mutant using genetic transformation and gene-editing technologies (CRISPR/Cas9). The OE plants grown in the hydroponic medium showed improved growth (plant elongation and biomass), increased chlorophyll content, and reduced OFF-induced oxidative stress. The OsACE2-improved growth phenotypes of rice were attributed to the significantly lower OFF accumulation in OE plants. Conversely, knocking out OsACE2 resulted in compromised growth phenotypes compared to the wild-type (WT). Using LC-LTQ-HRMS/MS, five mono-metabolites and eleven conjugates of OFF were characterized through various canonical pathways, such as hydrolysis, oxidation, reduction, glycosylation, acetylation, malonylation, and interaction with amino acids. These metabolites increased in the OE plants, and five acetylated conjugates were reported for the first time. Collectively, OsACE2 plays a primary role in catabolizing OFF residues in rice through multiple degradation pathways and reducing OFF in its growth environment.
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Affiliation(s)
- Zhao Jie Chen
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China; Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, Guangxi University, Nanning, Guangxi 530004, China
| | - Yuxin Qiao
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Nan Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Yang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jintong Liu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
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Sony SK, Kaul T, Motelb KFA, Thangaraj A, Bharti J, Kaul R, Verma R, Nehra M. CRISPR/Cas9-mediated homology donor repair base editing confers glyphosate resistance to rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1122926. [PMID: 36959937 PMCID: PMC10027715 DOI: 10.3389/fpls.2023.1122926] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Globally, CRISPR-Cas9-based genome editing has ushered in a novel era of crop advancements. Weeds pose serious a threat to rice crop productivity. Among the numerous herbicides, glyphosate [N-(phosphonomethyl)-glycine] has been employed as a post-emergent, broad-spectrum herbicide that represses the shikimate pathway via inhibition of EPSPS (5'-enolpyruvylshikimate-3-phosphate synthase) enzyme in chloroplasts. Here, we describe the development of glyphosate-resistant rice lines by site-specific amino acid substitutions (G172A, T173I, and P177S: GATIPS-mOsEPSPS) and modification of phosphoenolpyruvate-binding site in the native OsEPSPS gene employing fragment knockout and knock-in of homology donor repair (HDR) template harboring desired mutations through CRISPR-Cas9-based genome editing. The indigenously designed two-sgRNA OsEPSPS-NICTK-1_pCRISPR-Cas9 construct harboring rice codon-optimized SpCas9 along with OsEPSPS-HDR template was transformed into rice. Stable homozygous T2 edited rice lines revealed significantly high degree of glyphosate-resistance both in vitro (4 mM/L) and field conditions (6 ml/L; Roundup Ready) in contrast to wild type (WT). Edited T2 rice lines (ER1-6) with enhanced glyphosate resistance revealed lower levels of endogenous shikimate (14.5-fold) in contrast to treated WT but quite similar to WT. ER1-6 lines exhibited increased aromatic amino acid contents (Phe, two-fold; Trp, 2.5-fold; and Tyr, two-fold) than WT. Interestingly, glyphosate-resistant Cas9-free EL1-6 rice lines displayed a significant increment in grain yield (20%-22%) in comparison to WT. Together, results highlighted that the efficacy of GATIPS mutations in OsEPSPS has tremendously contributed in glyphosate resistance (foliar spray of 6 ml/L), enhanced aromatic amino acids, and improved grain yields in rice. These results ensure a novel strategy for weed management without yield penalties, with a higher probability of commercial release.
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Chen R, Wang S, Sun Y, Li H, Wan S, Lin F, Xu H. Comparison of Glyphosate-Degradation Ability of Aldo-Keto Reductase (AKR4) Proteins in Maize, Soybean and Rice. Int J Mol Sci 2023; 24:ijms24043421. [PMID: 36834831 PMCID: PMC9966811 DOI: 10.3390/ijms24043421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Genes that participate in the degradation or isolation of glyphosate in plants are promising, for they endow crops with herbicide tolerance with a low glyphosate residue. Recently, the aldo-keto reductase (AKR4) gene in Echinochloa colona (EcAKR4) was identified as a naturally evolved glyphosate-metabolism enzyme. Here, we compared the glyphosate-degradation ability of theAKR4 proteins from maize, soybean and rice, which belong to a clade containing EcAKR4 in the phylogenetic tree, by incubation of glyphosate with AKR proteins both in vivo and in vitro. The results indicated that, except for OsALR1, the other proteins were characterized as glyphosate-metabolism enzymes, with ZmAKR4 ranked the highest activity, and OsAKR4-1 and OsAKR4-2 exhibiting the highest activity among the AKR4 family in rice. Moreover, OsAKR4-1 was confirmed to endow glyphosate-tolerance at the plant level. Our study provides information on the mechanism underlying the glyphosate-degradation ability of AKR proteins in crops, which enables the development of glyphosate-resistant crops with a low glyphosate residue, mediated by AKRs.
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Affiliation(s)
| | | | | | | | | | - Fei Lin
- Correspondence: (F.L.); (H.X.); Tel.: +86-20-85285127 (H.X.)
| | - Hanhong Xu
- Correspondence: (F.L.); (H.X.); Tel.: +86-20-85285127 (H.X.)
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Vennapusa AR, Agarwal S, Rao Hm H, Aarthy T, Babitha KC, Thulasiram HV, Kulkarni MJ, Melmaiee K, Sudhakar C, Udayakumar M, S Vemanna R. Stacking herbicide detoxification and resistant genes improves glyphosate tolerance and reduces phytotoxicity in tobacco (Nicotiana tabacum L.) and rice (Oryza sativa L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 189:126-138. [PMID: 36084528 DOI: 10.1016/j.plaphy.2022.08.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/15/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Glyphosate residues retained in the growing meristematic tissues or in grains of glyphosate-resistant crops affect the plants physiological functions and crop yield. Removing glyphosate residues in the plants is desirable with no penalty on crop yield and quality. We report a new combination of scientific strategy to detoxify glyphosate that reduces the residual levels and improve crop resistance. The glyphosate detoxifying enzymes Aldo-keto reductase (AKR1) and mutated glycine oxidase (mGO) with different modes of action were co-expressed with modified EPSPS, which is insensitive to glyphosate in tobacco (Nicotiana tabacum L.) and rice (Oryza sativa L.). The transgenic tobacco plants expressing individual PsAKR1, mGO, CP4-EPSPS, combinations of PsAKR1:CP4EPSPS, PsAKR1:mGO, and multigene with PsAKR1: mGO: CP4EPSPS genes were developed. The bio-efficacy studies of in-vitro leaf regeneration on different concentrations of glyphosate, seedling bioassay, and spray on transgenic tobacco plants demonstrate that glyphosate detoxification with enhanced resistance. Comparative analysis of the transgenic tobacco plants reveals that double and multigene expressing transgenics had reduced accumulation of shikimic acid, glyphosate, and its primary residue AMPA, and increased levels of sarcosine were observed in all PsAKR1 expressing transgenics. The multigene expressing rice transgenics showed improved glyphosate resistance with yield maintenance. In summary, results suggest that stacking genes with two different detoxification mechanisms and insensitive EPSPS is a potential approach for developing glyphosate-resistant plants with less residual content.
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Affiliation(s)
- Amaranatha Reddy Vennapusa
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, 560065, India; Department of Botany, Sri Krishnadevaraya University, Anantapur, 515001, India; Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, 19901, USA.
| | - Subham Agarwal
- Laboratory of Plant Functional Genomics, Regional Center for Biotechnology, Faridabad, 121001, India
| | - Hanumanth Rao Hm
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, 560065, India
| | | | - K C Babitha
- Laboratory of Plant Functional Genomics, Regional Center for Biotechnology, Faridabad, 121001, India
| | | | | | - Kalpalatha Melmaiee
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, 19901, USA
| | - Chinta Sudhakar
- Department of Botany, Sri Krishnadevaraya University, Anantapur, 515001, India
| | - M Udayakumar
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, 560065, India
| | - Ramu S Vemanna
- Laboratory of Plant Functional Genomics, Regional Center for Biotechnology, Faridabad, 121001, India.
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11
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Yu H, Yang Q, Fu F, Li W. Three strategies of transgenic manipulation for crop improvement. FRONTIERS IN PLANT SCIENCE 2022; 13:948518. [PMID: 35937379 PMCID: PMC9354092 DOI: 10.3389/fpls.2022.948518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Heterologous expression of exogenous genes, overexpression of endogenous genes, and suppressed expression of undesirable genes are the three strategies of transgenic manipulation for crop improvement. Up to 2020, most (227) of the singular transgenic events (265) of crops approved for commercial release worldwide have been developed by the first strategy. Thirty-eight of them have been transformed by synthetic sequences transcribing antisense or double-stranded RNAs and three by mutated copies for suppressed expression of undesirable genes (the third strategy). By the first and the third strategies, hundreds of transgenic events and thousands of varieties with significant improvement of resistance to herbicides and pesticides, as well as nutritional quality, have been developed and approved for commercial release. Their application has significantly decreased the use of synthetic pesticides and the cost of crop production and increased the yield of crops and the benefits to farmers. However, almost all the events overexpressing endogenous genes remain at the testing stage, except one for fertility restoration and another for pyramiding herbicide tolerance. The novel functions conferred by the heterologously expressing exogenous genes under the control of constitutive promoters are usually absent in the recipient crops themselves or perform in different pathways. However, the endogenous proteins encoded by the overexpressing endogenous genes are regulated in complex networks with functionally redundant and replaceable pathways and are difficult to confer the desirable phenotypes significantly. It is concluded that heterologous expression of exogenous genes and suppressed expression by RNA interference and clustered regularly interspaced short palindromic repeats-cas (CRISPR/Cas) of undesirable genes are superior to the overexpression of endogenous genes for transgenic improvement of crops.
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Affiliation(s)
| | | | - Fengling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wanchen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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12
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Zhang Q, Liang M, Zeng J, Yang C, Qin J, Qiang W, Lan X, Chen M, Lin M, Liao Z. Engineering tropane alkaloid production and glyphosate resistance by overexpressing AbCaM1 and G2-EPSPS in Atropa belladonna. Metab Eng 2022; 72:237-246. [PMID: 35390492 DOI: 10.1016/j.ymben.2022.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 03/16/2022] [Accepted: 03/26/2022] [Indexed: 11/27/2022]
Abstract
Atropa belladonna is an important industrial crop for producing anticholinergic tropane alkaloids (TAs). Using glyphosate as selection pressure, transgenic homozygous plants of A. belladonna are generated, in which a novel calmodulin gene (AbCaM1) and a reported EPSPS gene (G2-EPSPS) are co-overexpressed. AbCaM1 is highly expressed in secondary roots of A. belladonna and has calcium-binding activity. Three transgenic homozygous lines were generated and their glyphosate tolerance and TAs' production were evaluated in the field. Transgenic homozygous lines produced TAs at much higher levels than wild-type plants. In the leaves of T2GC02, T2GC05, and T2GC06, the hyoscyamine content was 8.95-, 10.61-, and 9.96 mg/g DW, the scopolamine content was 1.34-, 1.50- and 0.86 mg/g DW, respectively. Wild-type plants of A. belladonna produced hyoscyamine and scopolamine respectively at the levels of 2.45 mg/g DW and 0.30 mg/g DW in leaves. Gene expression analysis indicated that AbCaM1 significantly up-regulated seven key TA biosynthesis genes. Transgenic homozygous lines could tolerate a commercial recommended dose of glyphosate in the field. In summary, new varieties of A. belladonna not only produce pharmaceutical TAs at high levels but tolerate glyphosate, facilitating industrial production of TAs and weed management at a much lower cost.
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Affiliation(s)
- Qiaozhuo Zhang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Mengjiao Liang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Junlan Zeng
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Chunxian Yang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jianbo Qin
- Chongqing Academy of Science and Technology, Chongqing, 401123, China
| | - Wei Qiang
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Centre, Xizang Agricultural and Husbandry College, Nyingchi of Tibet, 860000, China
| | - Min Chen
- College of Pharmaceutical Sciences, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Ministry of Education), Southwest University, Chongqing, 400715, China
| | - Min Lin
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Zhihua Liao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China; Chongqing Academy of Science and Technology, Chongqing, 401123, China.
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13
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Chen ZJ, Liu J, Zhang N, Yang H. Identification, characterization and expression of rice (Oryza sativa) acetyltransferase genes exposed to realistic environmental contamination of mesotrione and fomesafen. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 233:113349. [PMID: 35219957 DOI: 10.1016/j.ecoenv.2022.113349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
The plant acetyltransferases (ACEs) belong to a super family of proteins that contribute to secondary metabolisms and involve various abiotic and biotic stress responses. However, how rice ACEs respond to toxic agrochemicals is largely unknown. This study demonstrates that 86 and 83 genes coding ACEs in the transcriptome profiling were expressed under mesotrione (MTR) and fomesafen (FSA) exposure, respectively. Of these, 18 and 8 ACE differentially expressed genes (DEGs) were identified in MTR- and FSA-exposed rice transcriptome datasets. Some of the ACE genes were validated by quantitative RT-PCR analysis. Analysis of biochemical properties of ACEs revealed that many genes have various cis-elements and structural domain which may cope with a variety of biotic and abiotic stress responses and detoxification of xenobiotics. Moreover, the ACE activities in rice were induced under MTR and FSA exposure and reached out to the highest value at the 0.1 mg L-1. The ACE activities in the MTR and FSA treated roots were 2.6 and 3.5 fold over the control and those in shoots with MTR and FSA were 4.0 and 26.1 fold over the control, respectively. These results indicate that the ACE-coding genes can respond to the MTR and FSA stress by increasing their transcriptional level, along with the enhanced specific ACE protein activities in rice tissues.
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Affiliation(s)
- Zhao Jie Chen
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Jintong Liu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Nan Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Yang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China.
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14
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Guo BF, Hong HL, Sun LP, Guo Y, Qiu LJ. Transcriptome analysis reveals differing response and tolerance mechanism of EPSPS and GAT genes among transgenic soybeans. Mol Biol Rep 2021; 48:7351-7360. [PMID: 34676504 DOI: 10.1007/s11033-021-06742-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 10/01/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Glyphosate is a broad-spectrum, non-selective systemic herbicide. Introduction of glyphosate tolerance genes such as EPSPS or detoxification genes such as GAT can confer glyphosate tolerance on plants. Our previous study revealed that co-expression of EPSPS and GAT genes conferred higher glyphosate tolerance without "yellow flashing". However, the plant response to glyphosate at the transcriptional level was not investigated. METHODS AND RESULTS To investigate the glyphosate tolerance mechanism, RNA-seq was conducted using four soybean genotypes, including two non-transgenic (NT) soybeans, ZH10 and MD12, and two GM soybeans, HJ698 and ZH10-6. Differentially expressed genes (DEGs) were identified in these soybeans before and after glyphosate treatment. Similar response to glyphosate in the two NT soybeans and the different effects of glyphosate on the two GM soybeans were identified. As treatment time was prolonged, the expression level of some DEGs involved in shikimate biosynthetic pathway and herbicide targeted cross-pathways was increased or declined continuously in NT soybeans, and altered slightly in HJ698. However, the expression level of some DEGs was altered in ZH10-6 at 12 hpt, while similar expression level of some DEGs involved in shikimate biosynthetic pathway and herbicide targeted cross-pathways was observed in ZH10-6 at 0 hpt and 72 hpt. These observations likely explain the higher glyphosate tolerance in ZH10-6 than in HJ698 and NT soybeans. CONCLUSIONS These results suggested that GAT and EPSPS genes together play a crucial role in response to glyphosate, the GAT gene may work at the early stage of glyphosate exposure, whereas the EPSPS gene may be activated after the uptake of glyphosate by plants. These findings will provide valuable insight for the molecular basis underlying glyphosate tolerance or glyphosate detoxication.
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Affiliation(s)
- Bing-Fu Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
- Jiangxi Province Key Laboratory of Oilcrops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Hui-Long Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
- College of Agriculture, Northeast Agricultural University, Harbin, People's Republic of China
| | - Li-Ping Sun
- Jiangxi Province Key Laboratory of Oilcrops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China.
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China.
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15
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Ouyang C, Liu W, Chen S, Zhao H, Chen X, Jin X, Li X, Wu Y, Zeng X, Huang P, He X, An B. The Naturally Evolved EPSPS From Goosegrass Confers High Glyphosate Resistance to Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:756116. [PMID: 34777434 PMCID: PMC8586540 DOI: 10.3389/fpls.2021.756116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Glyphosate-resistant crops developed by the CP4-EPSPS gene from Agrobacterium have been planted on a massive scale globally, which benefits from the high efficiency and broad spectrum of glyphosate in weed control. Some glyphosate-resistant (GR) genes from microbes have been reported, which might raise biosafety concerns. Most of them were obtained through a hygromycin-HPT transformation system. Here we reported the plant source with 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene from goosegrass endowed rice with high resistance to glyphosate. The integrations and inheritability of the transgenes in the rice genome were investigated within two generations. The EiEPSPS transgenic plants displayed similar growth and development to wild type under no glyphosate selection pressure but better reproductive performance under lower glyphosate selection pressure. Furthermore, we reconstructed a binary vector pCEiEPSPS and established the whole stage glyphosate selection using the vector. The Glyphosate-pCEiEPSPS selection system showed a significantly higher transformation efficiency compared with the hygromycin-HPT transformation system. Our results provided a promising alternative gene resource to the development of GR plants and also extended the plant transformation toolbox.
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Affiliation(s)
- Chao Ouyang
- Hainan Bolian Rice Gene Technology Co., Ltd., Haikou, China
| | - Wei Liu
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Silan Chen
- Hainan Bolian Rice Gene Technology Co., Ltd., Haikou, China
| | - Huimin Zhao
- Hainan Bolian Rice Gene Technology Co., Ltd., Haikou, China
| | - Xinyan Chen
- Hainan Bolian Rice Gene Technology Co., Ltd., Haikou, China
| | - Xiongxia Jin
- Hainan Bolian Rice Gene Technology Co., Ltd., Haikou, China
| | - Xinpeng Li
- Hainan Bolian Rice Gene Technology Co., Ltd., Haikou, China
| | - Yongzhong Wu
- Hainan Bolian Rice Gene Technology Co., Ltd., Haikou, China
| | - Xiang Zeng
- Hainan Bolian Rice Gene Technology Co., Ltd., Haikou, China
| | - Peijin Huang
- Hainan Bolian Rice Gene Technology Co., Ltd., Haikou, China
| | - Xiuying He
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Baoguang An
- Hainan Bolian Rice Gene Technology Co., Ltd., Haikou, China
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16
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Mehta S, Kumar A, Achary VMM, Ganesan P, Rathi N, Singh A, Sahu KP, Lal SK, Das TK, Reddy MK. Antifungal activity of glyphosate against fungal blast disease on glyphosate-tolerant OsmEPSPS transgenic rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 311:111009. [PMID: 34482912 DOI: 10.1016/j.plantsci.2021.111009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/20/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
Weeds, pests, and pathogens are among the pre-harvest constraints in rice farming across rice-growing countries. For weed management, manual weeding and herbicides are widely practiced. Among the herbicides, glyphosate [N-(phosphonomethyl) glycine] is a broad-spectrum systemic chemical extensively used in agriculture. Being a competitive structural analog to phosphoenolpyruvate, it selectively inhibits the conserved 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme required for the biosynthesis of aromatic amino acids and essential metabolites in eukaryotes and prokaryotes. In the present study, we investigated the antifungal and defense elicitor activity of glyphosate against Magnaporthe oryzae on transgenic-rice overexpressing a glyphosate-resistance OsEPSPS gene (T173I + P177S; TIPS OsmEPSPS) for blast disease management. The glyphosate foliar spray on OsmEPSPS transgenic rice lines showed both prophylactic and curative suppression of blast disease comparable to a blasticide, tricyclazole. The glyphosate displayed direct antifungal activity on Magnaporthe oryzae as well as enhanced the levels of antioxidant enzymes and photosynthetic pigments in rice. However, the genes associated with phytohormones-mediated defense (OsPAD4, OsNPR1.3, and OsFMO) and innate immunity pathway (OsCEBiP and OsCERK1) were found repressed upon glyphosate spray. Altogether, the current study is the first report highlighting the overexpression of a crop-specific TIPS mutation in conjugation with glyphosate application showing potential for blast disease management in rice cultivation.
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Affiliation(s)
- Sahil Mehta
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Aundy Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - V Mohan Murali Achary
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Prakash Ganesan
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Neelmani Rathi
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Asmita Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Shambhu Krishan Lal
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - T K Das
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Malireddy K Reddy
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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17
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Chen K, Peng Y, Zhang L, Wang L, Mao D, Zhao Z, Bai L, Wang L. Whole transcriptome analysis resulted in the identification of Chinese sprangletop (Leptochloa chinensis) genes involved in cyhalofop-butyl tolerance. BMC Genomics 2021; 22:521. [PMID: 34238252 PMCID: PMC8268407 DOI: 10.1186/s12864-021-07856-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/25/2021] [Indexed: 12/05/2022] Open
Abstract
Background Chinese sprangletop [Leptochloa chinensis (L.) Nees] is an annual malignant weed, which can often be found in paddy fields. Cyhalofop-butyl is a specialized herbicide which is utilized to control L. chinensis. However, in many areas, L. chinensis has become tolerant to this key herbicide due to its continuous long-term use. Results In this study, we utilized a tolerant (LC18002) and a sensitive (LC17041) L. chinensis populations previously identified in our laboratory, which were divided into four different groups. We then employed whole transcriptome analysis to identify candidate genes which may be involved in cyhalofop-butyl tolerance. This analysis resulted in the identification of six possible candidate genes, including three cytochrome P450 genes and three ATP-binding cassette transporter genes. We then carried out a phylogenetic analysis to identify homologs of the differentially expressed cytochrome P450 genes. This phylogenetic analysis indicated that all genes have close homologs in other species, some of which have been implicated in non-target site resistance (NTSR). Conclusions This study is the first to use whole transcriptome analysis to identify herbicide non-target resistance genes in L. chinensis. The differentially expressed genes represent promising targets for better understanding herbicide tolerance in L. chinensis. The six genes belonging to classes already associated in herbicide tolerance may play important roles in the metabolic resistance of L. chinensis to cyhalofop-butyl, although the exact mechanisms require further study. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07856-z.
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Affiliation(s)
- Ke Chen
- Longping Branch, Graduate School of Hunan University, Changsha, People's Republic of China.,Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China.,Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Yajun Peng
- Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Liang Zhang
- Longping Branch, Graduate School of Hunan University, Changsha, People's Republic of China.,Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China.,Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Long Wang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, 410082, Changsha, People's Republic of China
| | - Donghai Mao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, 410125, Changsha, People's Republic of China
| | - Zhenghong Zhao
- Longping Branch, Graduate School of Hunan University, Changsha, People's Republic of China
| | - Lianyang Bai
- Longping Branch, Graduate School of Hunan University, Changsha, People's Republic of China. .,Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China. .,Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China.
| | - Lifeng Wang
- Longping Branch, Graduate School of Hunan University, Changsha, People's Republic of China. .,Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China. .,Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China.
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18
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Wen L, Zhong J, Cui Y, Duan Z, Zhou F, Li C, Ma W, Yin C, Chen H, Lin Y. Coexpression of I. variabilis-EPSPS* and WBceGO-B3S1 Genes Contributes to High Glyphosate Tolerance and Low Glyphosate Residues in Transgenic Rice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:7388-7398. [PMID: 33909432 DOI: 10.1021/acs.jafc.1c00880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Weeds are one of the main factors that affect the yield and quality of rice. The combination of glyphosate-resistant transgenic crops and glyphosate is regarded as an important strategy for weed management in modern agriculture. In this study, a codon-optimized glyphosate oxidase gene WBceGO-B3S1 from a variant BceGO-B3S1 and a glyphosate-tolerant gene I. variabilis-EPSPS* from the bacterium Isoptericola variabilis were transformed into an Oryza sativa subsp. geng rice variety Zhonghua11 by Agrobacterium-mediated genetic transformation. Molecular detection and field agronomic trait analysis contributed to the selection of three homozygous lines with stable expression of a single copy of the transferred genes integrated into the intergenic region. Under the treatment of glyphosate at a test amount in the field, transgenic lines exhibited no differences in agronomic traits. Under the treatment by 3600 g ha-1 glyphosate, the glyphosate residues in the aboveground tissues of the three candidate transgenic homozygous lines were significantly lower than those in the transgenic homozygous line with I. variabilis-EPSPS* alone at 1, 5, and 10 days. The transgenic line coexpressing I. variabilis-EPSPS* and WBceGO-B3S1 has great application value in breeding of transgenic rice varieties with high glyphosate resistance and low glyphosate residues. This study is a step forward in solving the problem of herbicide residues in food crops by taking advantage of genes that degrade glyphosate.
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Affiliation(s)
- Lixian Wen
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jue Zhong
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Ying Cui
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zhenchun Duan
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - ChangYan Li
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Weihua Ma
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Changxi Yin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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19
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Hertel R, Gibhardt J, Martienssen M, Kuhn R, Commichau FM. Molecular mechanisms underlying glyphosate resistance in bacteria. Environ Microbiol 2021; 23:2891-2905. [PMID: 33876549 DOI: 10.1111/1462-2920.15534] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 11/29/2022]
Abstract
Glyphosate is a nonselective herbicide that kills weeds and other plants competing with crops. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, thereby depleting the cell of EPSP serving as a precursor for biosynthesis of aromatic amino acids. Glyphosate is considered to be toxicologically safe for animals and humans. Therefore, it became the most-important herbicide in agriculture. However, its intensive application in agriculture is a serious environmental issue because it may negatively affect the biodiversity. A few years after the discovery of the mode of action of glyphosate, it has been observed that bacteria evolve glyphosate resistance by acquiring mutations in the EPSP synthase gene, rendering the encoded enzyme less sensitive to the herbicide. The identification of glyphosate-resistant EPSP synthase variants paved the way for engineering crops tolerating increased amounts of the herbicide. This review intends to summarize the molecular mechanisms underlying glyphosate resistance in bacteria. Bacteria can evolve glyphosate resistance by (i) reducing glyphosate sensitivity or elevating production of the EPSP synthase, by (ii) degrading or (iii) detoxifying glyphosate and by (iv) decreasing the uptake or increasing the export of the herbicide. The variety of glyphosate resistance mechanisms illustrates the adaptability of bacteria to anthropogenic substances due to genomic alterations.
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Affiliation(s)
- Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Johannes Gibhardt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Marion Martienssen
- Institute of Environmental Technology, Chair of Biotechnology of Water Treatment, BTU Cottbus-Senftenberg, Cottbus, 03046, Germany
| | - Ramona Kuhn
- Institute of Environmental Technology, Chair of Biotechnology of Water Treatment, BTU Cottbus-Senftenberg, Cottbus, 03046, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
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iTRAQ-based quantitative proteomic analysis of transgenic and non-transgenic maize seeds. J Food Compost Anal 2020. [DOI: 10.1016/j.jfca.2020.103564] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Karthik K, Nandiganti M, Thangaraj A, Singh S, Mishra P, Rathinam M, Sharma M, Singh NK, Dash PK, Sreevathsa R. Transgenic Cotton ( Gossypium hirsutum L.) to Combat Weed Vagaries: Utility of an Apical Meristem-Targeted in planta Transformation Strategy to Introgress a Modified CP4-EPSPS Gene for Glyphosate Tolerance. FRONTIERS IN PLANT SCIENCE 2020; 11:768. [PMID: 32733492 PMCID: PMC7358616 DOI: 10.3389/fpls.2020.00768] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/14/2020] [Indexed: 05/23/2023]
Abstract
Weeds burden plant growth as they compete for space, sunlight, and soil nutrients leading to 25-80% yield losses. Glyphosate [N-(phosphonomethyl)glycine] is a widely used broad spectrum non-selective herbicide that controls weeds by inhibiting 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme and interfering with the shikimate biosynthesis pathway. Cotton (Gossypium hirsutum L.) is one of the most important commercial crops grown worldwide for its fiber. We have developed herbicide tolerant transgenic cotton (cv. P8-6) by introgression of a codon-optimized and modified EPSPS gene (CP4-EPSPS) possessing an N-terminal chloroplast targeting peptide from Petunia hybrida. Because of the recalcitrant nature of cotton, a genotype-independent non-tissue culture-based apical meristem-targeted in planta transformation approach was used to develop transformants. Although in planta transformation methodologies are advantageous in developing a large number of transgenic plants, effective screening strategies are essential for initial identification of transformants. In the present study, the use of a two-level rigorous screening strategy identified 2.27% of T1 generation plants as tolerant to 800 and 1,500 mg/L of commercially available glyphosate (Roundup). Precise molecular characterization revealed stable integration, expression, and inheritance of CP4-EPSPS in advanced generations of the promising transgenic events. Further, superiority of selected transgenic plants in tolerating increasing levels of glyphosate (500-4,000 mg/L) was ascertained through reduced accumulation of shikimate. This report is the first of its kind where cotton transformants tolerating high levels of glyphosate (up to 4,000 mg/L) and accumulating low levels of shikimate have been identified. This study not only reiterated the genotype-independent nature of the transformation strategy but also reiterated the translational utility of the CP4-EPSPS gene in management of weeds.
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Affiliation(s)
- Kesiraju Karthik
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, India
| | | | | | - Shweta Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Pragya Mishra
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Maniraj Rathinam
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Manju Sharma
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, India
| | | | - Prasanta K. Dash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
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22
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Yi D, Ma L, Lin M, Li C. Development of glyphosate-resistant alfalfa (Medicago sativa L.) upon transformation with the GR79Ms gene encoding 5-enolpyruvylshikimate-3-phosphate synthase. PLANTA 2018; 248:211-219. [PMID: 29687223 DOI: 10.1007/s00425-018-2898-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/16/2018] [Indexed: 05/15/2023]
Abstract
MAIN CONCLUSION The glyphosate-resistant gene, GR79Ms, was successfully introduced into the genome of alfalfa. The transgenic events may serve as novel germplasm resources in alfalfa breeding. Weed competition can reduce the alfalfa yield, generating new alfalfa germplasm with herbicide resistance is essential. To obtain transgenic alfalfa lines with glyphosate resistance, a new synthetic glyphosate-resistant gene GR79Ms encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) was introduced into alfalfa germplasm by Agrobacterium tumefaciens-mediated transformation. In total, 67 transformants were obtained. PCR and Southern blot analyses confirmed that GR79Ms was successfully inserted into the genome of alfalfa. Reverse transcription-PCR and western blot analyses further demonstrated the expression of GR79Ms and its product, GR79Ms EPSPS. Moreover, two homozygous transgenic lines were developed in the T2 generation by means of molecular-assisted selection. Herbicide tolerance spray tests showed that the transgenic plants T0-GR1, T0-GR2, T0-GR3 and two homozygous lines were able to tolerate fourfold higher commercial usage of glyphosate than non-transgenic plants.
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Affiliation(s)
- Dengxia Yi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lin Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cong Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Ashraf J, Zuo D, Wang Q, Malik W, Zhang Y, Abid MA, Cheng H, Yang Q, Song G. Recent insights into cotton functional genomics: progress and future perspectives. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:699-713. [PMID: 29087016 PMCID: PMC5814580 DOI: 10.1111/pbi.12856] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/03/2017] [Accepted: 10/18/2017] [Indexed: 05/11/2023]
Abstract
Functional genomics has transformed from futuristic concept to well-established scientific discipline during the last decade. Cotton functional genomics promise to enhance the understanding of fundamental plant biology to systematically exploit genetic resources for the improvement of cotton fibre quality and yield, as well as utilization of genetic information for germplasm improvement. However, determining the cotton gene functions is a much more challenging task, which has not progressed at a rapid pace. This article presents a comprehensive overview of the recent tools and resources available with the major advances in cotton functional genomics to develop elite cotton genotypes. This effort ultimately helps to filter a subset of genes that can be used to assemble a final list of candidate genes that could be employed in future novel cotton breeding programme. We argue that next stage of cotton functional genomics requires the draft genomes refinement, re-sequencing broad diversity panels with the development of high-throughput functional genomics tools and integrating multidisciplinary approaches in upcoming cotton improvement programmes.
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Affiliation(s)
- Javaria Ashraf
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Dongyun Zuo
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Qiaolian Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Waqas Malik
- Genomics LabDepartment of Plant Breeding and GeneticsFaculty of Agricultural Sciences and TechnologyBahauddin Zakariya UniversityMultanPunjabPakistan
| | - Youping Zhang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Muhammad Ali Abid
- Genomics LabDepartment of Plant Breeding and GeneticsFaculty of Agricultural Sciences and TechnologyBahauddin Zakariya UniversityMultanPunjabPakistan
| | - Hailiang Cheng
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Qiuhong Yang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Guoli Song
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
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Fartyal D, Agarwal A, James D, Borphukan B, Ram B, Sheri V, Yadav R, Manna M, Varakumar P, Achary VMM, Reddy MK. Co-expression of P173S Mutant Rice EPSPS and igrA Genes Results in Higher Glyphosate Tolerance in Transgenic Rice. FRONTIERS IN PLANT SCIENCE 2018; 9:144. [PMID: 29487608 PMCID: PMC5816812 DOI: 10.3389/fpls.2018.00144] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/25/2018] [Indexed: 05/11/2023]
Abstract
Weeds and their devastating effects have been a great threat since the start of agriculture. They compete with crop plants in the field and negatively influence the crop yield quality and quantity along with survival of the plants. Glyphosate is an important broad-spectrum systemic herbicide which has been widely used to combat various weed problems since last two decades. It is very effective even at low concentrations, and possesses low environmental toxicity and soil residual activity. However, the residual concentration of glyphosate inside the plant has been of major concern as it severely affects the important metabolic pathways, and results in poor plant growth and grain yield. In this study, we compared the glyphosate tolerance efficiency of two different transgenic groups over expressing proline/173/serine (P173S) rice EPSPS glyphosate tolerant mutant gene (OsmEPSPS) alone and in combination with the glyphosate detoxifying encoding igrA gene, recently characterized from Pseudomonas. The molecular analysis of all transgenic plant lines showed a stable integration of transgenes and their active expression in foliar tissues. The physiological analysis of glyphosate treated transgenic lines at seed germination and vegetative stages showed a significant difference in glyphosate tolerance between the two transgenic groups. The transgenic plants with OsmEPSPS and igrA genes, representing dual glyphosate tolerance mechanisms, showed an improved root-shoot growth, physiology, overall phenotype and higher level of glyphosate tolerance compared to the OsmEPSPS transgenic plants. This study highlights the advantage of igrA led detoxification mechanism as a crucial component of glyphosate tolerance strategy in combination with glyphosate tolerant OsmEPSPS gene, which offered a better option to tackle in vivo glyphosate accumulation and imparted more robust glyphosate tolerance in rice transgenic plants.
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Affiliation(s)
- Dhirendra Fartyal
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Biotechnology, Uttarakhand Technical University, Dehradun, India
| | - Aakrati Agarwal
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Plant Molecular Biology Lab, Department of Botany, University of Delhi, New Delhi, India
| | - Donald James
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Bhabesh Borphukan
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Babu Ram
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Biotechnology, Uttarakhand Technical University, Dehradun, India
| | - Vijay Sheri
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Renu Yadav
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mrinalini Manna
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Panditi Varakumar
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - V. Mohan M. Achary
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Malireddy K. Reddy
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Iquebal MA, Soren KR, Gangwar P, Shanmugavadivel PS, Aravind K, Singla D, Jaiswal S, Jasrotia RS, Chaturvedi SK, Singh NP, Varshney RK, Rai A, Kumar D. Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome Sequencing. FRONTIERS IN PLANT SCIENCE 2017; 8:958. [PMID: 28638398 PMCID: PMC5461349 DOI: 10.3389/fpls.2017.00958] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/22/2017] [Indexed: 05/06/2023]
Abstract
Background: Chickpea (Cicer arietinum L.) contributes 75% of total pulse production. Being cheaper than animal protein, makes it important in dietary requirement of developing countries. Weed not only competes with chickpea resulting into drastic yield reduction but also creates problem of harboring fungi, bacterial diseases and insect pests. Chemical approach having new herbicide discovery has constraint of limited lead molecule options, statutory regulations and environmental clearance. Through genetic approach, transgenic herbicide tolerant crop has given successful result but led to serious concern over ecological safety thus non-transgenic approach like marker assisted selection is desirable. Since large variability in tolerance limit of herbicide already exists in chickpea varieties, thus the genes offering herbicide tolerance can be introgressed in variety improvement programme. Transcriptome studies can discover such associated key genes with herbicide tolerance in chickpea. Results: This is first transcriptomic studies of chickpea or even any legume crop using two herbicide susceptible and tolerant genotypes exposed to imidazoline (Imazethapyr). Approximately 90 million paired-end reads generated from four samples were processed and assembled into 30,803 contigs using reference based assembly. We report 6,310 differentially expressed genes (DEGs), of which 3,037 were regulated by 980 miRNAs, 1,528 transcription factors associated with 897 DEGs, 47 Hub proteins, 3,540 putative Simple Sequence Repeat-Functional Domain Marker (SSR-FDM), 13,778 genic Single Nucleotide Polymorphism (SNP) putative markers and 1,174 Indels. Randomly selected 20 DEGs were validated using qPCR. Pathway analysis suggested that xenobiotic degradation related gene, glutathione S-transferase (GST) were only up-regulated in presence of herbicide. Down-regulation of DNA replication genes and up-regulation of abscisic acid pathway genes were observed. Study further reveals the role of cytochrome P450, xyloglucan endotransglucosylase/hydrolase, glutamate dehydrogenase, methyl crotonoyl carboxylase and of thaumatin-like genes in herbicide resistance. Conclusion: Reported DEGs can be used as genomic resource for future discovery of candidate genes associated with herbicide tolerance. Reported markers can be used for future association studies in order to develop marker assisted selection (MAS) for refinement. In endeavor of chickpea variety development programme, these findings can be of immense use in improving productivity of chickpea germplasm.
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Affiliation(s)
- Mir A. Iquebal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
| | - Khela R. Soren
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - Priyanka Gangwar
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - P. S. Shanmugavadivel
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - K. Aravind
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - Deepak Singla
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
| | - Rahul S. Jasrotia
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
| | - Sushil K. Chaturvedi
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - Narendra P. Singh
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - Rajeev K. Varshney
- Genetic Gains, International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
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