1
|
Zhang L, Meng S, Liu Y, Han F, Xu T, Zhao Z, Li Z. Advances in and Perspectives on Transgenic Technology and CRISPR-Cas9 Gene Editing in Broccoli. Genes (Basel) 2024; 15:668. [PMID: 38927604 PMCID: PMC11203320 DOI: 10.3390/genes15060668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 06/28/2024] Open
Abstract
Broccoli, a popular international Brassica oleracea crop, is an important export vegetable in China. Broccoli is not only rich in protein, vitamins, and minerals but also has anticancer and antiviral activities. Recently, an Agrobacterium-mediated transformation system has been established and optimized in broccoli, and transgenic transformation and CRISPR-Cas9 gene editing techniques have been applied to improve broccoli quality, postharvest shelf life, glucoraphanin accumulation, and disease and stress resistance, among other factors. The construction and application of genetic transformation technology systems have led to rapid development in broccoli worldwide, which is also good for functional gene identification of some potential traits in broccoli. This review comprehensively summarizes the progress in transgenic technology and CRISPR-Cas9 gene editing for broccoli over the past four decades. Moreover, it explores the potential for future integration of digital and smart technologies into genetic transformation processes, thus demonstrating the promise of even more sophisticated and targeted crop improvements. As the field continues to evolve, these innovations are expected to play a pivotal role in the sustainable production of broccoli and the enhancement of its nutritional and health benefits.
Collapse
Affiliation(s)
- Li Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (S.M.); (Y.L.); (F.H.); (T.X.)
- College of Horticulture, Shanxi Agricultural University, Taigu 030801, China
| | - Sufang Meng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (S.M.); (Y.L.); (F.H.); (T.X.)
| | - Yumei Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (S.M.); (Y.L.); (F.H.); (T.X.)
| | - Fengqing Han
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (S.M.); (Y.L.); (F.H.); (T.X.)
| | - Tiemin Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (S.M.); (Y.L.); (F.H.); (T.X.)
- Shouguang R&D Center of Vegetables, CAAS, Shouguang 262700, China;
| | - Zhiwei Zhao
- Shouguang R&D Center of Vegetables, CAAS, Shouguang 262700, China;
| | - Zhansheng Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (S.M.); (Y.L.); (F.H.); (T.X.)
- Shouguang R&D Center of Vegetables, CAAS, Shouguang 262700, China;
| |
Collapse
|
2
|
Jadhav Y, Thakur NR, Ingle KP, Ceasar SA. The role of phenomics and genomics in delineating the genetic basis of complex traits in millets. PHYSIOLOGIA PLANTARUM 2024; 176:e14349. [PMID: 38783512 DOI: 10.1111/ppl.14349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Millets, comprising a diverse group of small-seeded grains, have emerged as vital crops with immense nutritional, environmental, and economic significance. The comprehension of complex traits in millets, influenced by multifaceted genetic determinants, presents a compelling challenge and opportunity in agricultural research. This review delves into the transformative roles of phenomics and genomics in deciphering these intricate genetic architectures. On the phenomics front, high-throughput platforms generate rich datasets on plant morphology, physiology, and performance in diverse environments. This data, coupled with field trials and controlled conditions, helps to interpret how the environment interacts with genetics. Genomics provides the underlying blueprint for these complex traits. Genome sequencing and genotyping technologies have illuminated the millet genome landscape, revealing diverse gene pools and evolutionary relationships. Additionally, different omics approaches unveil the intricate information of gene expression, protein function, and metabolite accumulation driving phenotypic expression. This multi-omics approach is crucial for identifying candidate genes and unfolding the intricate pathways governing complex traits. The review highlights the synergy between phenomics and genomics. Genomically informed phenotyping targets specific traits, reducing the breeding size and cost. Conversely, phenomics identifies promising germplasm for genomic analysis, prioritizing variants with superior performance. This dynamic interplay accelerates breeding programs and facilitates the development of climate-smart, nutrient-rich millet varieties and hybrids. In conclusion, this review emphasizes the crucial roles of phenomics and genomics in unlocking the genetic enigma of millets.
Collapse
Affiliation(s)
- Yashoda Jadhav
- International Crops Research Institutes for the Semi-Arid Tropics, Patancheru, TS, India
| | - Niranjan Ravindra Thakur
- International Crops Research Institutes for the Semi-Arid Tropics, Patancheru, TS, India
- Vasantrao Naik Marathwada Agricultural University, Parbhani, MS, India
| | | | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kochi, KL, India
| |
Collapse
|
3
|
Barrera M, Olmedo B, Zúñiga C, Cepeda M, Olivares F, Vergara R, Cordero-Lara K, Prieto H. Somatic Embryogenesis and Agrobacterium-Mediated Gene Transfer Procedures in Chilean Temperate Japonica Rice Varieties for Precision Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:416. [PMID: 38337949 PMCID: PMC10857379 DOI: 10.3390/plants13030416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/08/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
Rice (Oryza sativa) varieties are generated through breeding programs focused on local requirements. In Chile, the southernmost rice producer, rice productivity relies on the use and generation of temperate japonica germplasms, which need to be adapted to the intensifying effects of climate change. Advanced biotechnological tools can contribute to these breeding programs; new technologies associated with precision breeding, including gene editing, rely on procedures such as regeneration and gene transfer. In this study, the local rice varieties Platino, Cuarzo, Esmeralda, and Zafiro were evaluated for somatic embryogenesis potential using a process that involved the combined use of auxins and cytokinins. An auxin-based (2,4-D) general medium (2N6) allowed for the induction of embryogenic masses in all the genotypes. After induction, masses required culturing either in N6R (kinetin; Platino) or N6RN (BAP, kinetin, IBA, and 2,4-D; Cuarzo, Esmeralda, and Zafiro) to yield whole plants using regeneration medium (N6F, no hormone). The sprouting rates indicated Platino as the most responsive genotype; for this reason, this variety was evaluated for gene transfer. Fifteen-day-old embryo masses were assayed for Agrobacterium-mediated transformation using the bacterial strain EHA105 harboring pFLC-Myb/HPT/GFP, a modified T-DNA vector harboring a geminivirus-derived replicon. The vector included the green fluorescent protein reporter gene, allowing for continuous traceability. Reporter mRNA was produced as early as 3 d after agroinfiltration, and stable expression of the protein was observed along the complete process. These achievements enable further biotechnological steps in these and other genotypes from our breeding program.
Collapse
Affiliation(s)
- Marion Barrera
- Natural Sciences, Mathematics, and Environment Faculty, Metropolitan Technological University, Santiago 8330526, Chile;
- Biotechnology Laboratory, La Platina Research Station, INIA-Chile, Santiago 8831314, Chile; (B.O.); (C.Z.); (M.C.); (F.O.); (R.V.)
| | - Blanca Olmedo
- Biotechnology Laboratory, La Platina Research Station, INIA-Chile, Santiago 8831314, Chile; (B.O.); (C.Z.); (M.C.); (F.O.); (R.V.)
| | - Carolina Zúñiga
- Biotechnology Laboratory, La Platina Research Station, INIA-Chile, Santiago 8831314, Chile; (B.O.); (C.Z.); (M.C.); (F.O.); (R.V.)
| | - Mario Cepeda
- Biotechnology Laboratory, La Platina Research Station, INIA-Chile, Santiago 8831314, Chile; (B.O.); (C.Z.); (M.C.); (F.O.); (R.V.)
| | - Felipe Olivares
- Biotechnology Laboratory, La Platina Research Station, INIA-Chile, Santiago 8831314, Chile; (B.O.); (C.Z.); (M.C.); (F.O.); (R.V.)
| | - Ricardo Vergara
- Biotechnology Laboratory, La Platina Research Station, INIA-Chile, Santiago 8831314, Chile; (B.O.); (C.Z.); (M.C.); (F.O.); (R.V.)
| | - Karla Cordero-Lara
- Rice Breeding Program, Quilamapu Research Station, INIA-Chile, Chillán 3780000, Chile;
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Research Station, INIA-Chile, Santiago 8831314, Chile; (B.O.); (C.Z.); (M.C.); (F.O.); (R.V.)
| |
Collapse
|
4
|
Maiti S, Banik A. Strategies to fortify the nutritional values of polished rice by implanting selective traits from brown rice: A nutrigenomics-based approach. Food Res Int 2023; 173:113271. [PMID: 37803581 DOI: 10.1016/j.foodres.2023.113271] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 10/08/2023]
Abstract
Whole-grain cereals are important components of a healthy diet. It reduces the risk of many deadly diseases like cardiovascular diseases, diabetes, cancer, etc. Brown rice is an example of whole grain food, which is highly nutritious due to the presence of various bioactive compounds (flavonoids, phenolics, vitamins, phytosterols, oils, etc.) associated with the rice bran layer of brown rice. White rice is devoid of the nutritious rice bran layer and thus lacks the bioactive compounds which are the major attractants of brown rice. Therefore, to confer health benefits to the public at large, the nutrigenomic potential of white rice may be improved by integrating the phytochemicals associated with the rice bran layer of brown rice into it via biofortification processes like conventional breeding, agronomic practices, metabolic engineering, CRISPR/Cas9 technology, and RNAi techniques. Thus, this review article focuses on improving the nutritional qualities of white/polished rice through biofortification processes, utilizing new breeding technologies (NBTs).
Collapse
Affiliation(s)
- Somdatta Maiti
- Laboratory of Microbial Interaction, Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India
| | - Avishek Banik
- Laboratory of Microbial Interaction, Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India.
| |
Collapse
|
5
|
Ye X, Shrawat A, Moeller L, Rode R, Rivlin A, Kelm D, Martinell BJ, Williams EJ, Paisley A, Duncan DR, Armstrong CL. Agrobacterium-mediated direct transformation of wheat mature embryos through organogenesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1202235. [PMID: 37324676 PMCID: PMC10264787 DOI: 10.3389/fpls.2023.1202235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/11/2023] [Indexed: 06/17/2023]
Abstract
Transgenic plant production in monocotyledonous species has primarily relied on embryogenic callus induction from both immature and mature embryos as the pathway for plant regeneration. We have efficiently regenerated fertile transgenic wheat plants through organogenesis after Agrobacterium-mediated direct transformation of mechanically isolated mature embryos from field-grown seed. Centrifugation of the mature embryos in the presence of Agrobacterium was found to be essential for efficient T-DNA delivery to the relevant regenerable cells. The inoculated mature embryos formed multiple buds/shoots on high-cytokinin medium, which directly regenerated into transgenic shoots on hormone-free medium containing glyphosate for selection. Rooted transgenic plantlets were obtained within 10-12 weeks after inoculation. Further optimization of this transformation protocol resulted in significant reduction of chimeric plants to below 5%, as indicated by leaf GUS staining and T1 transgene segregation analysis. Direct transformation of wheat mature embryos has substantial advantages over traditional immature embryo-based transformation systems, including long-term storability of the mature dry explants, scalability, and greatly improved flexibility and consistency in transformation experiments.
Collapse
|
6
|
Wang W, Guo J, Ma J, Wang Z, Zhang L, Wang Z, Meng M, Zhang C, Sun F, Xi Y. Comprehensive Transcriptomic and Metabolic Profiling of Agrobacterium- tumefaciens-Infected Immature Wheat Embryos. Int J Mol Sci 2023; 24:ijms24098449. [PMID: 37176157 PMCID: PMC10179373 DOI: 10.3390/ijms24098449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/30/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
The transformation efficiency (TE) was improved by a series of special chemical and physical methods using immature embryos from the cultivar Fielder, with the PureWheat technique. To analyze the reaction of immature embryos infected, which seemed to provide the necessary by Agrobacterium tumefaciens in PureWheat, a combination of scanning electron microscopy (SEM), complete transcriptome analysis, and metabolome analysis was conducted to understand the progress. The results of the SEM analysis revealed that Agrobacterium tumefaciens were deposited under the damaged cortex of immature embryos as a result of pretreatment and contacted the receptor cells to improve the TE. Transcriptome analysis indicated that the differentially expressed genes were mainly enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, plant-pathogen interaction, plant hormone signal transduction, and the MAPK (Mitogen-activated protein kinase) signaling pathway. By analyzing the correlation between differentially expressed genes and metabolites, the expression of many genes and the accumulation of metabolites were changed in glucose metabolism and the TCA cycle (Citrate cycle), as well as the amino acid metabolism; this suggests that the infection of wheat embryos with Agrobacterium is an energy-demanding process. The shikimate pathway may act as a hub between glucose metabolism and phenylpropanoid metabolism during Agrobacterium infection. The downregulation of the F5H gene and upregulation of the CCR gene led to the accumulation of lignin precursors through phenylpropanoid metabolism. In addition, several metabolic pathways and oxidases were found to be involved in the infection treatment, including melatonin biosynthesis, benzoxazinoid biosynthesis, betaine biosynthesis, superoxide dismutase, and peroxidase, suggesting that wheat embryos may be under the stress of Agrobacterium and, thus, undergo an oxidative stress response. These findings explore the physiological and molecular changes of immature embryos during the co-culture stage of the PureWheat technique and provide insights for Agrobacterium-mediated transgenic wheat experiments.
Collapse
Affiliation(s)
- Weiwei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jinliang Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jiayang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhulin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Lining Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zixu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Min Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Fengli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yajun Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| |
Collapse
|
7
|
Langyan S, Bhardwaj R, Kumari J, Jacob SR, Bisht IS, Pandravada SR, Singh A, Singh PB, Dar ZA, Kumar A, Rana JC. Nutritional Diversity in Native Germplasm of Maize Collected From Three Different Fragile Ecosystems of India. Front Nutr 2022; 9:812599. [PMID: 35479746 PMCID: PMC9037594 DOI: 10.3389/fnut.2022.812599] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/26/2022] [Indexed: 12/05/2022] Open
Abstract
Native germplasm resources are adapted to specific ecological niches. They have sustained over generations owing to the preference of local communities for their unique taste, the utility to particular dishes, and the low cost of cultivation. They may help eradicate malnutrition and act as a source for trait-linked genes. The present dataset comprises thirty-three native germplasm of maize collected from Rajasthan, Himachal Pradesh, and Andhra Pradesh states of India with an altitudinal variation of 386–2,028 m. They were evaluated for proximate composition, minerals, nutritional attributes, and antioxidant activity and compared with the standard values reported in the Indian Food Composition Table 2017 (IFCT2017). The nutritional profile showed moisture content in the range of 7.16–10.9%, ash 0.73–1.93%, crude protein 8.68–12.0%, crude fat 3.72–8.03%, dietary fiber 5.21–11.2%, and available carbohydrates 60.6–69.8%. Three accessions, namely, Malan 11 (7.06%), Malan 24 (7.20%), and Yellow Chamba Local 02 (8.03%) exhibited almost double the crude fat content as compared with the values notified in IFCT2017 (3.77). Total sugar content obtained was in the range of 5.00–11.3%, whereas the starch content was found between 50.9 and 64.9%. All the germplasm except Yellow Chamba Local reflected a higher protein content than reported values in IFCT2017 (8.80). Sathi, Safed Chamba Local, and Ragal Makka had nearly 12% protein content. Mineral malnutrition, mainly due to iron (Fe) deficiency, is a worldwide issue to science, humanity, and society. The mineral profile revealed that most germplasm had a higher iron content. Accessions with the iron content of nearly three times of IFCT2017 reported value were identified in germplasm belonging to three states. A negative relationship was observed between the altitude of the sample collection site and available carbohydrate content. In contrast, available carbohydrate showed inverse correlations with dietary fiber, protein, and fat content. The information generated in this study can be utilized to promote these germplasm as nutrifood, nutritional surveillance, labeling, and crop improvement programs.
Collapse
Affiliation(s)
- Sapna Langyan
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Rakesh Bhardwaj
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Jyoti Kumari
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | | | | | | | - Archna Singh
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Pratap Bhan Singh
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | | | - Ashok Kumar
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Jai Chand Rana
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| |
Collapse
|
8
|
Barbosa da Costa N, Hébert MP, Fugère V, Terrat Y, Fussmann GF, Gonzalez A, Shapiro BJ. A Glyphosate-Based Herbicide Cross-Selects for Antibiotic Resistance Genes in Bacterioplankton Communities. mSystems 2022; 7:e0148221. [PMID: 35266795 PMCID: PMC9040730 DOI: 10.1128/msystems.01482-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/17/2022] [Indexed: 01/22/2023] Open
Abstract
Agrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, the herbicide glyphosate has the potential to indirectly select for antibiotic-resistant bacteria. Such cross-selection could occur if the same genes (encoding efflux pumps, for example) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added a glyphosate-based herbicide (GBH) to 1,000-liter mesocosms filled with water from a pristine lake. Over 57 days, we tracked changes in bacterial communities with shotgun metagenomic sequencing and annotated metagenome-assembled genomes (MAGs) for the presence of known antibiotic resistance genes (ARGs), plasmids, and resistance mutations in the enzyme targeted by glyphosate (enolpyruvyl-shikimate-3-phosphate synthase; EPSPS). We found that high doses of GBH significantly increased ARG frequency and selected for multidrug efflux pumps in particular. The relative abundance of MAGs after a high dose of GBH was predictable based on the number of ARGs in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS. Together, these results indicate that GBHs can cross-select for antibiotic resistance in natural freshwater bacteria. IMPORTANCE Glyphosate-based herbicides (GBHs) such as Roundup formulations may have the unintended consequence of selecting for antibiotic resistance genes (ARGs), as demonstrated in previous experiments. However, the effects of GBHs on ARGs remain unknown in natural aquatic communities, which are often contaminated with pesticides from agricultural runoff. Moreover, the resistance provided by ARGs compared to canonical mutations in the glyphosate target enzyme, EPSPS, remains unclear. Here, we performed a freshwater mesocosm experiment showing that a GBH strongly selects for ARGs, particularly multidrug efflux pumps. These selective effects were evident after just a few days, and the ability of bacteria to survive and thrive after GBH stress was predictable by the number of ARGs in their genomes and, to a lesser extent, by mutations in EPSPS. Intensive GBH application may therefore have the unintended consequence of selecting for ARGs in natural freshwater communities.
Collapse
Affiliation(s)
- Naíla Barbosa da Costa
- Département des Sciences Biologiques, Université de Montréal, Montreal, Canada
- Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montreal, Canada
| | - Marie-Pier Hébert
- Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montreal, Canada
- Department of Biology, McGill University, Montreal, Canada
| | - Vincent Fugère
- Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montreal, Canada
- Québec Centre for Biodiversity Science (QCBS), Montreal, Canada
- Département des Sciences de l’Environnement, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - Yves Terrat
- Département des Sciences Biologiques, Université de Montréal, Montreal, Canada
| | - Gregor F. Fussmann
- Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montreal, Canada
- Department of Biology, McGill University, Montreal, Canada
- Québec Centre for Biodiversity Science (QCBS), Montreal, Canada
| | - Andrew Gonzalez
- Department of Biology, McGill University, Montreal, Canada
- Québec Centre for Biodiversity Science (QCBS), Montreal, Canada
| | - B. Jesse Shapiro
- Département des Sciences Biologiques, Université de Montréal, Montreal, Canada
- Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montreal, Canada
- Québec Centre for Biodiversity Science (QCBS), Montreal, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
- McGill Genome Centre, McGill University, Montreal, Canada
| |
Collapse
|
9
|
So many rhizobial partners, so little nitrogen fixed: The intriguing symbiotic promiscuity of common bean (Phaseolus vulgaris L.). Symbiosis 2022. [DOI: 10.1007/s13199-022-00831-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
10
|
Development of a new recombineering system for Agrobacterium species. Appl Environ Microbiol 2022; 88:e0249921. [PMID: 35044833 DOI: 10.1128/aem.02499-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Discovery of new and efficient genetic engineering technologies for Agrobacterium will broaden the capacity for fundamental research on this genus and for its utilization as a transgenic vehicle. In this study, we aim to develop an efficient recombineering system for Agrobacterium species. We examined isolates of Agrobacterium and the closely related genus Rhizobium to identify pairs of ET-like recombinases that would aid in the recombineering of Agrobacterium species. Four pairs of ET-like recombinases, named RecETh1h2h3h4AGROB6, RecETh1h2P3RHI597, RecETRHI145, and RecEThRHI483, were identified in Agrobacterium tumefaciens str. B6, Rhizobium leguminosarum bv. trifolii WSM597, Rhizobium sp. LC145, and Rhizobium sp. Root483D2, respectively. Eight more candidate recombineering systems were generated by combining the new ET-like recombinases with Redγ or Pluγ. The PluγETRHI145 system, RecETh1h2h3h4AGROB6 system, and PluγEThRHI483 system were determined to be the most efficient recombineering system for the type strains A. tumefaciens C58, A. tumefaciens EHA105, and R. rhizogenes NBCR13257, respectively. The utility of these systems was demonstrated by knocking out the istB and istA fusion gene in C58, the celI gene in EHA105, and the 3'-5' exonuclease gene and endoglucanase gene in NBCR13257. Our work provides an effective genetic manipulation strategy for Agrobacterium species. IMPORTANCE Agrobacterium is a powerful transgenic vehicle for the genetic manipulation of numerous plant and fungal species and even animal cells. In addition to improving the utility of Agrobacterium as a transgenic vehicle, genetic engineering tools are important for revealing crucial components that are functionally involved in T-DNA translocation events. This work developed an efficient and versatile recombineering system for Agrobacterium. Successful genome modification of Agrobacterium strains revealed that this new recombineering system could be used for the genetic engineering of Agrobacterium.
Collapse
|
11
|
Recent advances in molecular farming using monocot plants. Biotechnol Adv 2022; 58:107913. [DOI: 10.1016/j.biotechadv.2022.107913] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/22/2022]
|
12
|
Bellido AM, Souza Canadá ED, Permingeat HR, Echenique V. Genetic Transformation of Apomictic Grasses: Progress and Constraints. FRONTIERS IN PLANT SCIENCE 2021; 12:768393. [PMID: 34804102 PMCID: PMC8602796 DOI: 10.3389/fpls.2021.768393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/05/2021] [Indexed: 05/17/2023]
Abstract
The available methods for plant transformation and expansion beyond its limits remain especially critical for crop improvement. For grass species, this is even more critical, mainly due to drawbacks in in vitro regeneration. Despite the existence of many protocols in grasses to achieve genetic transformation through Agrobacterium or biolistic gene delivery, their efficiencies are genotype-dependent and still very low due to the recalcitrance of these species to in vitro regeneration. Many plant transformation facilities for cereals and other important crops may be found around the world in universities and enterprises, but this is not the case for apomictic species, many of which are C4 grasses. Moreover, apomixis (asexual reproduction by seeds) represents an additional constraint for breeding. However, the transformation of an apomictic clone is an attractive strategy, as the transgene is immediately fixed in a highly adapted genetic background, capable of large-scale clonal propagation. With the exception of some species like Brachiaria brizantha which is planted in approximately 100 M ha in Brazil, apomixis is almost non-present in economically important crops. However, as it is sometimes present in their wild relatives, the main goal is to transfer this trait to crops to fix heterosis. Until now this has been a difficult task, mainly because many aspects of apomixis are unknown. Over the last few years, many candidate genes have been identified and attempts have been made to characterize them functionally in Arabidopsis and rice. However, functional analysis in true apomictic species lags far behind, mainly due to the complexity of its genomes, of the trait itself, and the lack of efficient genetic transformation protocols. In this study, we review the current status of the in vitro culture and genetic transformation methods focusing on apomictic grasses, and the prospects for the application of new tools assayed in other related species, with two aims: to pave the way for discovering the molecular pathways involved in apomixis and to develop new capacities for breeding purposes because many of these grasses are important forage or biofuel resources.
Collapse
Affiliation(s)
- Andrés M. Bellido
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS – CCT – CONICET Bahía Blanca), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | | | | | - Viviana Echenique
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS – CCT – CONICET Bahía Blanca), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| |
Collapse
|
13
|
Dhaka A, Singh RK, Muthamilarasan M, Prasad M. Genetics and Genomics Interventions for Promoting Millets as Functional Foods. Curr Genomics 2021; 22:154-163. [PMID: 34975288 PMCID: PMC8640850 DOI: 10.2174/1389202922666210225084212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/05/2021] [Accepted: 01/21/2021] [Indexed: 11/22/2022] Open
Abstract
Several crops, including millets with immense nutritional and therapeutic values, were once a part of our regular diet. However, due to domestication and selection pressures, many of them have become marginally cultivated crops confined to a particular region, race, or locality. Millets are a perfect example of neglected species that have the potential to address both food and nutritional insecurities prevalent among the ever-growing global population. Starvation and malnutrition contribute to a large number of health-related issues, being the main reason behind the occurrence of most of the severe diseases worldwide. These constraints are repeatedly disturbing both the social and economic health of global society. Naturally, millets are rich in minerals, nutrients, and bioactive compounds, and these crops are less dependent on synthetic fertilizers, systemic irrigation, and pest/weed control. Given this, the review emphasizes the nutritional values, health benefits, processing techniques, and genomic advancements of millets. In addition, it proposes a roadmap for enhancing the utility and commercialization of millets.
Collapse
Affiliation(s)
- Annvi Dhaka
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
14
|
Choudhury A, Rajam MV. Genetic transformation of legumes: an update. PLANT CELL REPORTS 2021; 40:1813-1830. [PMID: 34230986 DOI: 10.1007/s00299-021-02749-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
This review summarizes the recent advances in legume genetic transformation and provides an insight into the critical factors that play a major role in the process. It also sheds light on some of the potential areas which may ameliorate the transformation of legumes. Legumes are an important group of dicotyledonous plants, highly enriched in proteins and minerals. Majority of the legume plants are cultivated in the arid and semi-arid parts of the world, and hence said to be climate resilient. They have the capability of atmospheric nitrogen fixation and thus play a vital role in the ecological sphere. However, the worldwide production of legumes is somehow not up to the mark and the yields are greatly affected by various biotic and abiotic stress factors. Genetic engineering strategies have emerged as a core of plant biology and remarkably facilitate the crop improvement programmes. A significant progress has been made towards the optimization of efficient transformation system for legume plants over the years but this group is still underutilized in comparison to other crops. Among the variety of available DNA delivery systems, Agrobacterium-mediated and particle bombardment have been primarily deployed for optimization and trait improvement. However, recalcitrance and genotype-dependence are some of the major bottlenecks for successful transformation. In this context, the present review summarizes the advances taken place in the area of legume transformation and provides an insight into the present scenario. The challenges and future possibilities for yield improvement have also been discussed.
Collapse
Affiliation(s)
- Aparajita Choudhury
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Manchikatla V Rajam
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
| |
Collapse
|
15
|
Shi L, Wang K, Du L, Song Y, Li H, Ye X. Genome-Wide Identification and Expression Profiling Analysis of WOX Family Protein-Encoded Genes in Triticeae Species. Int J Mol Sci 2021; 22:ijms22179325. [PMID: 34502234 PMCID: PMC8431079 DOI: 10.3390/ijms22179325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/05/2021] [Accepted: 08/25/2021] [Indexed: 11/16/2022] Open
Abstract
The WOX family is a group of plant-specific transcription factors which regulate plant growth and development, cell division and differentiation. From the available genome sequence databases of nine Triticeae species, 199 putative WOX genes were identified. Most of the identified WOX genes were distributed on the chromosomes of homeologous groups 1 to 5 and originated via the orthologous evolution approach. Parts of WOX genes in Triticum aestivum were confirmed by the specific PCR markers using a set of Triticum. durum-T. aestivum genome D substitution lines. All of these identified WOX proteins could be grouped into three clades, similar to those in rice and Arabidopsis. WOX family members were conserved among these Triticeae plants; all of them contained the HOX DNA-binding homeodomain, and WUS clade members contained the characteristic WUS-box motif, while only WUS and WOX9 contained the EAR motif. The RNA-seq and qPCR analysis revealed that the TaWOX genes had tissue-specific expression feature. From the expression patterns of TaWOX genes during immature embryo callus production, TaWOX9 is likely closely related with the regulation of regeneration process in T. aestivum. The findings in this study could provide a basis for evolution and functional investigation and practical application of the WOX family genes in Triticeae species.
Collapse
Affiliation(s)
- Lei Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (K.W.); (L.D.)
- Key Laboratory of Agricultural Biotechnology of Ningxia, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China;
| | - Ke Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (K.W.); (L.D.)
| | - Lipu Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (K.W.); (L.D.)
| | - Yuxia Song
- Key Laboratory of Agricultural Biotechnology of Ningxia, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China;
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (K.W.); (L.D.)
- Correspondence: (H.L.); (X.Y.)
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (K.W.); (L.D.)
- National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (H.L.); (X.Y.)
| |
Collapse
|
16
|
Tamzil MS, Alfiko Y, Mubarok AF, Purwantomo S, Suwanto A, Budiarti S. Development of Auxotrophic Agrobacterium tumefaciens AGL1 by Tn5 Transposon for Rice (Oryza sativa L.) Transformation. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0244-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
17
|
Ahmar S, Mahmood T, Fiaz S, Mora-Poblete F, Shafique MS, Chattha MS, Jung KH. Advantage of Nanotechnology-Based Genome Editing System and Its Application in Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:663849. [PMID: 34122485 PMCID: PMC8194497 DOI: 10.3389/fpls.2021.663849] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/26/2021] [Indexed: 05/05/2023]
Abstract
Agriculture is an important source of human food. However, current agricultural practices need modernizing and strengthening to fulfill the increasing food requirements of the growing worldwide population. Genome editing (GE) technology has been used to produce plants with improved yields and nutritional value as well as with higher resilience to herbicides, insects, and diseases. Several GE tools have been developed recently, including clustered regularly interspaced short palindromic repeats (CRISPR) with nucleases, a customizable and successful method. The main steps of the GE process involve introducing transgenes or CRISPR into plants via specific gene delivery systems. However, GE tools have certain limitations, including time-consuming and complicated protocols, potential tissue damage, DNA incorporation in the host genome, and low transformation efficiency. To overcome these issues, nanotechnology has emerged as a groundbreaking and modern technique. Nanoparticle-mediated gene delivery is superior to conventional biomolecular approaches because it enhances the transformation efficiency for both temporal (transient) and permanent (stable) genetic modifications in various plant species. However, with the discoveries of various advanced technologies, certain challenges in developing a short-term breeding strategy in plants remain. Thus, in this review, nanobased delivery systems and plant genetic engineering challenges are discussed in detail. Moreover, we have suggested an effective method to hasten crop improvement programs by combining current technologies, such as speed breeding and CRISPR/Cas, with nanotechnology. The overall aim of this review is to provide a detailed overview of nanotechnology-based CRISPR techniques for plant transformation and suggest applications for possible crop enhancement.
Collapse
Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, Universidad de Talca, Talca, Chile
| | - Tahir Mahmood
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | | | | | - Ki-Hung Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| |
Collapse
|
18
|
Debler JW, Henares BM, Lee RC. Agroinfiltration for transient gene expression and characterisation of fungal pathogen effectors in cool-season grain legume hosts. PLANT CELL REPORTS 2021; 40:805-818. [PMID: 33811500 PMCID: PMC8058004 DOI: 10.1007/s00299-021-02671-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 01/30/2021] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE Modified pEAQ-HT-DEST1 vectors were used for agroinfiltration in legumes. We demonstrate protein expression and export in pea, lentil, and faba bean; however, the method for chickpea was not successful. Agroinfiltration is a valuable research method for investigating virulence and avirulence effector proteins from pathogens and pests, where heterologous effector proteins are transiently expressed in plant leaves and hypersensitive necrosis responses and other effector functions can be assessed. Nicotiana benthamiana is widely used for agroinfiltration and the characterisation of broad-spectrum effectors. The method has also been used in other plant species including field pea, but not yet developed for chickpea, lentil, or faba bean. Here, we have modified the pEAQ-HT-DEST1 vector for expression of 6 × histidine-tagged green-fluorescent protein (GFP) and the known necrosis-inducing broad-spectrum effector necrosis and ethylene-inducing peptide (Nep1)-like protein (NLP). Modified pEAQ-based vectors were adapted to encode signal peptide sequences for apoplast targeting of expressed proteins. We used confocal microscopy to assess the level of GFP expression in agroinfiltrated leaves. While at 3 days after infiltration in N. benthamiana, GFP was expressed at a relatively high level, expression in field pea and faba bean at the same time point was relatively low. In lentil, an expression level of GFP similar to field pea and faba bean at 3 days was only observed after 5 days. Chickpea leaf cells were transformed at low frequency and agroinfiltration was concluded to not be successful for chickpea. We concluded that the pEAQ vector is suitable for testing host-specific effectors in field pea, lentil, and faba bean, but low transformation efficiency limits the utility of the method for chickpea.
Collapse
Affiliation(s)
- Johannes W Debler
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, 1 Kent St, Bentley, WA, 6102, Australia
| | - Bernadette M Henares
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, 1 Kent St, Bentley, WA, 6102, Australia
| | - Robert C Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, 1 Kent St, Bentley, WA, 6102, Australia.
| |
Collapse
|
19
|
Singh RK, Muthamilarasan M, Prasad M. Biotechnological approaches to dissect climate-resilient traits in millets and their application in crop improvement. J Biotechnol 2021; 327:64-73. [PMID: 33422569 DOI: 10.1016/j.jbiotec.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 10/22/2022]
Abstract
'Small millets' is a generic term that includes all the millets except pearl millet and sorghum. These small or minor millets constitute eleven species that are marginally cultivated and consumed worldwide. These small millets possess excellent agronomic-, climate-resilient, and nutritional traits, although they lack popularity. Small millets withstand a broad spectrum of environmental stresses and possess better water-use and nitrogen-use efficiencies. Of note, small millets are five- to seven-fold nutritionally rich in terms of protein, bioactive compounds, micro- and macro-nutrients as compared to major cereals. Irrespective of these merits, small millets have received little research attention compared to major millets and cereals. However, the knowledge generated from such studies is significant for the improvement of millets per se and for translating the information to improve major cereals through breeding and transgene-based approaches. Given this, the review enumerates the efforts invested in dissecting the climate-resilient traits in small millets and provides a roadmap for deploying the information in crop improvement of millets as well as cereals in the scenario of climate change.
Collapse
Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi 110067, India.
| |
Collapse
|
20
|
Particle bombardment technology and its applications in plants. Mol Biol Rep 2020; 47:9831-9847. [PMID: 33222118 DOI: 10.1007/s11033-020-06001-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022]
Abstract
Particle bombardment, or biolistics, has emerged as an excellent alternative approach for plant genetic transformation which circumvents the limitations of Agrobacterium-mediated genetic transformation. The method has no biological constraints and can transform a wide range of plant species. Besides, it has been the most efficient way to achieve organelle transformation (for both chloroplasts and mitochondria) so far. Along with the recent advances in genome editing technologies, conventional gene delivery tools are now being repurposed to deliver targeted gene editing reagents into the plants. One of the key advantages is that the particle bombardment allows DNA-free gene editing of the genome. It enables the direct delivery of proteins, RNAs, and RNPs into plants. Owing to the versatility and wide-range applicability of the particle bombardment, it will likely remain one of the major genetic transformation methods in the future. This article provides an overview of the current status of particle bombardment technology and its applications in the field of plant research and biotechnology.
Collapse
|
21
|
Singh RK, Prasad A, Muthamilarasan M, Parida SK, Prasad M. Breeding and biotechnological interventions for trait improvement: status and prospects. PLANTA 2020; 252:54. [PMID: 32948920 PMCID: PMC7500504 DOI: 10.1007/s00425-020-03465-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/12/2020] [Indexed: 05/06/2023]
Abstract
Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.
Collapse
Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
22
|
Motta EVS, Mak M, De Jong TK, Powell JE, O'Donnell A, Suhr KJ, Riddington IM, Moran NA. Oral or Topical Exposure to Glyphosate in Herbicide Formulation Impacts the Gut Microbiota and Survival Rates of Honey Bees. Appl Environ Microbiol 2020; 86:e01150-20. [PMID: 32651208 PMCID: PMC7480383 DOI: 10.1128/aem.01150-20] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/06/2020] [Indexed: 01/04/2023] Open
Abstract
Honey bees are important agricultural pollinators that rely on a specific gut microbiota for the regulation of their immune system and defense against pathogens. Environmental stressors that affect the bee gut microbial community, such as antibiotics and glyphosate, can indirectly compromise bee health. Most of the experiments demonstrating these effects have been done under laboratory conditions with pure chemicals. Here, we investigated the oral and topical effects of various concentrations of glyphosate in a herbicide formulation on the honey bee gut microbiota and health under laboratory and field conditions. Under all of these conditions, the formulation, dissolved in sucrose syrup or water, affected the abundance of beneficial bacteria in the bee gut in a dose-dependent way. Mark-recapture experiments also demonstrated that bees exposed to the formulation were more likely to disappear from the colony, once reintroduced after exposure. Although no visible effects were observed for hives exposed to the formulation in field experiments, challenge trials with the pathogen Serratia marcescens, performed under laboratory conditions, revealed that bees from hives exposed to the formulation exhibited increased mortality compared with bees from control hives. In the field experiments, glyphosate was detected in honey collected from exposed hives, showing that worker bees transfer xenobiotics to the hive, thereby extending exposure and increasing the chances of exposure to recently emerged bees. These findings show that different routes of exposure to glyphosate-based herbicide can affect honey bees and their gut microbiota.IMPORTANCE The honey bee gut microbial community plays a vital role in immune response and defense against opportunistic pathogens. Environmental stressors, such as the herbicide glyphosate, may affect the gut microbiota, with negative consequences for bee health. Glyphosate is usually sprayed in the field mixed with adjuvants, which enhance herbicidal activity. These adjuvants may also enhance undesired effects in nontargeted organisms. This seems to be the case for glyphosate-based herbicide on honey bees. As we show in this study, oral exposure to either pure glyphosate or glyphosate in a commercial herbicide formulation perturbs the gut microbiota of honey bees, and topical exposure to the formulation also has a direct effect on honey bee health, increasing mortality in a dose-dependent way and leaving surviving bees with a perturbed microbiota. Understanding the effects of herbicide formulations on honey bees may help to protect these important agricultural pollinators.
Collapse
Affiliation(s)
- Erick V S Motta
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Myra Mak
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Tyler K De Jong
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - J Elijah Powell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Angela O'Donnell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Kristin J Suhr
- Mass Spectrometry Facility, Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
| | - Ian M Riddington
- Mass Spectrometry Facility, Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
23
|
Yang J, Pan X, Xu Y, Li Y, Xu N, Huang Z, Ye J, Gao D, Guo M. Agrobacterium tumefaciens ferritins play an important role in full virulence through regulating iron homeostasis and oxidative stress survival. MOLECULAR PLANT PATHOLOGY 2020; 21:1167-1178. [PMID: 32678502 PMCID: PMC7411545 DOI: 10.1111/mpp.12969] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 05/23/2023]
Abstract
Ferritins are a large family of iron storage proteins, which are used by bacteria and other organisms to avoid iron toxicity and as a safe iron source in the cytosol. Agrobacterium tumefaciens, a phytopathogen, has two ferritin-encoding genes: atu2771 and atu2477. Atu2771 is annotated as a Bfr-encoding gene (Bacterioferritin, Bfr) and atu2477 as a Dps-encoding gene (DNA binding protein from starved cells, Dps). Three deletion mutants (Δbfr, Δdps, and bfr-dps double-deletion mutant ΔbdF) of these two ferritin-encoding genes were constructed to investigate the effects of ferritin deficiency on the iron homeostasis, oxidative stress resistance, and pathogenicity of A. tumefaciens. Deficiency of two ferritins affects the growth of A. tumefaciens under iron starvation and excess. When supplied with moderate iron, the growth of A. tumefaciens is not affected by the deficiency of ferritin. Deficiency of ferritin significantly reduces iron accumulation in the cells of A. tumefaciens, but the effect of Bfr deficiency on iron accumulation is severer than Dps deficiency and the double mutant ΔbdF has the least intracellular iron content. All three ferritin-deficient mutants showed a decreased tolerance to 3 mM H2 O2 in comparison with the wild type. The tumour induced by each of three ferritin-deficient mutants is less than that of the wild type. Complementation reversed the effects of ferritin deficiency on the growth, iron homeostasis, oxidative stress resistance, and tumorigenicity of A. tumefaciens. Therefore, ferritin plays an important role in the pathogenesis of A. tumefaciens through regulating iron homeostasis and oxidative stress survival.
Collapse
Affiliation(s)
- Jing Yang
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Xiaoyue Pan
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Yujuan Xu
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Yuan Li
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Nan Xu
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Zhiwei Huang
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Jingyang Ye
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Dawei Gao
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| | - Minliang Guo
- College of Bioscience and BiotechnologyYangzhou UniversityJiangsu ProvinceYangzhou CityChina
| |
Collapse
|
24
|
Sampaio de Oliveira KB, Leite ML, Rodrigues GR, Duque HM, da Costa RA, Cunha VA, de Loiola Costa LS, da Cunha NB, Franco OL, Dias SC. Strategies for recombinant production of antimicrobial peptides with pharmacological potential. Expert Rev Clin Pharmacol 2020; 13:367-390. [PMID: 32357080 DOI: 10.1080/17512433.2020.1764347] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION The need to develop new drugs for the control of pathogenic microorganisms has redoubled efforts to prospect for antimicrobial peptides (AMPs) from natural sources and to characterize its structure and function. These molecules present a broad spectrum of action against different microorganisms and frequently present promiscuous action, with anticancer and immunomodulatory activities. Furthermore, AMPs can be used as biopharmaceuticals in the treatment of hospital-acquired infections and other serious diseases with relevant social and economic impacts.Areas covered: The low yield and the therefore difficult extraction and purification process in AMPs are problems that limit their industrial application and scientific research. Thus, optimized heterologous expression systems were developed to significantly boost AMP yields, allow high efficiency in purification and structural optimization for the increase of therapeutic activity.Expert opinion: This review provides an update on recent developments in the recombinant production of ribosomal and non-ribosomal synthesis of AMPs and on strategies to increase the expression of genes encoding AMPs at the transcriptional and translational levels and regulation of the post-translational modifications. Moreover, there are detailed reports of AMPs that have already reached marketable status or are in the pipeline under advanced stages of preclinical testing.
Collapse
Affiliation(s)
- Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Michel Lopes Leite
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Gisele Regina Rodrigues
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Harry Morales Duque
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Rosiane Andrade da Costa
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Victor Albuquerque Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Lorena Sousa de Loiola Costa
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Nicolau Brito da Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Octavio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil.,Universidade de Brasília, Pós-graduação em Patologia Molecular, Campus Darcy Ribeiro , Brasília, Brazil.,S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco , Campo Grande, Mato Grosso do Sul, Brazil
| | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil.,Universidade de Brasília, Pós-graduação em Biologia Animal, Campus Darcy Ribeiro , Brasília, Brazil
| |
Collapse
|
25
|
Li G, Hu S, Yang J, Zhao X, Kimura S, Schultz EA, Hou H. Establishment of an Agrobacterium mediated transformation protocol for the detection of cytokinin in the heterophyllous plant Hygrophila difformis (Acanthaceae). PLANT CELL REPORTS 2020; 39:737-750. [PMID: 32146519 DOI: 10.1007/s00299-020-02527-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/21/2020] [Indexed: 05/09/2023]
Abstract
This is the first report of a highly efficient Agrobacterium tumefaciens-mediated transformation protocol for Acanthaceae and its utilization in revealing important roles of cytokinin in regulating heterophylly in Hygrophila difformis. Plants show amazing morphological differences in leaf form in response to changes in the surrounding environment, which is a phenomenon called heterophylly. Previous studies have shown that the aquatic plant Hygrophila difformis (Acanthaceae) is an ideal model for heterophylly study. However, low efficiency and poor reproducibility of genetic transformation restricted H. difformis as a model plant. In this study, we reported successful induction of callus, shoots and the establishment of an efficient stable transformation protocol as mediated by Agrobacterium tumefaciens LBA4404. We found that the highest callus induction efficiency was achieved with 1 mg/L 1-Naphthaleneacetic acid (NAA) and 2 mg/L 6-benzyladenine (6-BA), that efficient shoot induction required 0.1 mg/L NAA and 0.1 mg/L 6-BA and that high transformation efficiency required 100 µM acetosyringone. Due to the importance of phytohormones in the regulation of heterophylly and the inadequate knowledge about the function of cytokinin (CK) in this process, we analyzed the function of CK in the regulation of heterophylly by exogenous CK application and endogenous CK detection. By using our newly developed transformation system to detect CK signals, contents and distribution in H. difformis, we revealed an important role of CK in environmental mediated heterophylly.
Collapse
Affiliation(s)
- Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Shiqi Hu
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto-shi, Kyoto, 603-8555, Japan
- Center for Ecological Evolutionary Developmental Biology, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto-shi, Kyoto, 603-8555, Japan
| | - Elizabeth A Schultz
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
| |
Collapse
|
26
|
Ramkumar TR, Lenka SK, Arya SS, Bansal KC. A Short History and Perspectives on Plant Genetic Transformation. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2020; 2124:39-68. [PMID: 32277448 DOI: 10.1007/978-1-0716-0356-7_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plant genetic transformation is an important technological advancement in modern science, which has not only facilitated gaining fundamental insights into plant biology but also started a new era in crop improvement and commercial farming. However, for many crop plants, efficient transformation and regeneration still remain a challenge even after more than 30 years of technical developments in this field. Recently, FokI endonuclease-based genome editing applications in plants offered an exciting avenue for augmenting crop productivity but it is mainly dependent on efficient genetic transformation and regeneration, which is a major roadblock for implementing genome editing technology in plants. In this chapter, we have outlined the major historical developments in plant genetic transformation for developing biotech crops. Overall, this field needs innovations in plant tissue culture methods for simplification of operational steps for enhancing the transformation efficiency. Similarly, discovering genes controlling developmental reprogramming and homologous recombination need considerable attention, followed by understanding their role in enhancing genetic transformation efficiency in plants. Further, there is an urgent need for exploring new and low-cost universal delivery systems for DNA/RNA and protein into plants. The advancements in synthetic biology, novel vector systems for precision genome editing and gene integration could potentially bring revolution in crop-genetic potential enhancement for a sustainable future. Therefore, efficient plant transformation system standardization across species holds the key for translating advances in plant molecular biology to crop improvement.
Collapse
Affiliation(s)
- Thakku R Ramkumar
- Agronomy Department, IFAS, University of Florida, Gainesville, FL, USA
| | - Sangram K Lenka
- TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, India
| | - Sagar S Arya
- TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, India
| | - Kailash C Bansal
- TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, India.
| |
Collapse
|
27
|
Santos CM, Romeiro D, Silva JP, Basso MF, Molinari HBC, Centeno DC. An improved protocol for efficient transformation and regeneration of Setaria italica. PLANT CELL REPORTS 2020; 39:501-510. [PMID: 31915913 DOI: 10.1007/s00299-019-02505-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
An efficient and improved transformation method for functional genetics studies in S. italica, being a boon for the Setaria scientific community and for crop improvement. Foxtail millet (Setaria italica) is a short life cycle C4 plant, with sequenced genome, and a potential model plant for C4 species. S. italica is also important on a global food security and healthiness context due to its importance in arid and semi-arid areas. However, despite its importance, there are just few transformation protocols directed to this species. The current protocols reached about 5.5-9% of efficiency, which do not make it a valuable model organism. Different types of explants were used in the above mentioned methods, such as immature and mature inflorescence and shoot apex. However, these techniques have many limitations, such as unavailability of explants throughout the year and a crucial, laborious and considerable time-consuming selection. Aiming a simplified and efficient methodology, we adopted dry mature seeds as explants, which are available in abundance, are constant along the year and well responsive to tissue culture, in addition to a differentiated approach that reaches on an average 19.2% transformation efficiency of S. italica. Thus, we propose a protocol that optimizes the transformation efficiency of this cereal crop allowing a high increase on transformation and regeneration rates. Our transformation protocol provides an interesting tool for Setaria community research as well as enables new strategies for breeding enhanced productivity in the species.
Collapse
Affiliation(s)
- C M Santos
- Universidade Federal Do ABC, São Bernardo Do Campo, SP, Brazil
| | - D Romeiro
- Universidade Federal Do ABC, São Bernardo Do Campo, SP, Brazil
| | - J P Silva
- Universidade Federal Do ABC, São Bernardo Do Campo, SP, Brazil
| | - M F Basso
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasília, DF, Brazil
| | - H B C Molinari
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasília, DF, Brazil
| | - D C Centeno
- Universidade Federal Do ABC, São Bernardo Do Campo, SP, Brazil.
| |
Collapse
|
28
|
Abstract
Single chain variable fragments (scFvs) are generated by joining together the variable heavy and light chain of a monoclonal antibody (mAb) via a peptide linker. They offer some advantages over the parental mAb such as low molecular weight, heterologous production, multimeric form, and multivalency. The scFvs were produced against more than 50 antigens till date using 10 different plant species as the expression system. There were considerable improvements in the expression and purification strategies of scFv in the last 24 years. With the growing demand of scFv in therapeutic and diagnostic fields, its biosynthesis needs to be increased. The easiness in development, maintenance, and multiplication of transgenic plants make them an attractive expression platform for scFv production. The review intends to provide comprehensive information about the use of plant expression system to produce scFv. The developments, advantages, pitfalls, and possible prospects of improvement for the exploitation of plants in the industrial level are discussed.
Collapse
Affiliation(s)
- Padikara Kutty Satheeshkumar
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP, 221005, India.
| |
Collapse
|
29
|
Martignago D, Rico-Medina A, Blasco-Escámez D, Fontanet-Manzaneque JB, Caño-Delgado AI. Drought Resistance by Engineering Plant Tissue-Specific Responses. FRONTIERS IN PLANT SCIENCE 2020; 10:1676. [PMID: 32038670 PMCID: PMC6987726 DOI: 10.3389/fpls.2019.01676] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/28/2019] [Indexed: 05/18/2023]
Abstract
Drought is the primary cause of agricultural loss globally, and represents a major threat to food security. Currently, plant biotechnology stands as one of the most promising fields when it comes to developing crops that are able to produce high yields in water-limited conditions. From studies of Arabidopsis thaliana whole plants, the main response mechanisms to drought stress have been uncovered, and multiple drought resistance genes have already been engineered into crops. So far, most plants with enhanced drought resistance have displayed reduced crop yield, meaning that there is still a need to search for novel approaches that can uncouple drought resistance from plant growth. Our laboratory has recently shown that the receptors of brassinosteroid (BR) hormones use tissue-specific pathways to mediate different developmental responses during root growth. In Arabidopsis, we found that increasing BR receptors in the vascular plant tissues confers resistance to drought without penalizing growth, opening up an exceptional opportunity to investigate the mechanisms that confer drought resistance with cellular specificity in plants. In this review, we provide an overview of the most promising phenotypical drought traits that could be improved biotechnologically to obtain drought-tolerant cereals. In addition, we discuss how current genome editing technologies could help to identify and manipulate novel genes that might grant resistance to drought stress. In the upcoming years, we expect that sustainable solutions for enhancing crop production in water-limited environments will be identified through joint efforts.
Collapse
Affiliation(s)
| | | | | | | | - Ana I. Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| |
Collapse
|
30
|
Li CX, Fan YF, Luan W, Dai Y, Wang MX, Wei CM, Wang Y, Tao X, Mao P, Ma XR. Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity. MICROBIAL ECOLOGY 2019; 77:967-979. [PMID: 30357425 DOI: 10.1007/s00248-018-1273-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/08/2018] [Indexed: 06/08/2023]
Abstract
Titanium ions significantly promote plant growth, but the mechanism is still unclear. Cut flowers are ideal materials for the study of plant growth and senescence. In this study, freshly cut Gerbera jamesonii were used to study the effects of titanium ions (8 mg/L) on the flower longevity. Flowering observation showed that the gerbera vase life was significantly prolonged in the presence of titanium ions. Plate colony counts showed that the amounts of bacteria in the vase solution of the control group were approximately 1700 times more than that of titanium ion treatment group. High-throughput sequencing was used to determine the sequences of 16S rRNA gene V3-V4 variable regions of the vase solutions to analyze bacterial species, their average proportions, and absolute abundance. The results showed that the titanium ions reduced the entire bacterial counts as well as altered the absolute abundance of different bacterial species in the vase solution. The most prevalent bacteria were mainly Enterobacteriaceae, Pseudomonas veronii, Pseudomonas sp., Delftia sp., Agrobacterium sp., Sphingobacterium multivorum, Acinetobacter johnsonii, and Clostridiaceae. In combination with plate colony counts, we demonstrated that all the bacterial growths were significantly inhibited by titanium ions, regardless of their average proportions increased or decreased. These results showed that titanium ions could extend effectively the longevity of gerberas and possess the broad-spectrum antibacterial properties. This study provides a basis for further mechanism exploration of titanium ions action and its applications in cut flower preservation and agricultural production.
Collapse
Affiliation(s)
- Cai-Xia Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yan-Fen Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Luan
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ya Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming-Xiu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun-Mei Wei
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Ping Mao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xin-Rong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China.
| |
Collapse
|
31
|
He B, Tu Y, Jiang C, Zhang Z, Li Y, Zeng B. Functional Genomics of Aspergillus oryzae: Strategies and Progress. Microorganisms 2019; 7:E103. [PMID: 30974907 PMCID: PMC6518170 DOI: 10.3390/microorganisms7040103] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/01/2019] [Accepted: 04/06/2019] [Indexed: 11/25/2022] Open
Abstract
Aspergillus oryzae has been used for the production of traditional fermentation and has promising potential to produce primary and secondary metabolites. Due to the tough cell walls and high drug resistance of A. oryzae, functional genomic characterization studies are relatively limited. The exploitation of selection markers and genetic transformation methods are critical for improving A. oryzae fermentative strains. In this review, we describe the genome sequencing of various A. oryzae strains. Recently developed selection markers and transformation strategies are also described in detail, and the advantages and disadvantages of transformation methods are presented. Lastly, we introduce the recent progress on highlighted topics in A. oryzae functional genomics including conidiation, protein secretion and expression, and secondary metabolites, which will be beneficial for improving the application of A. oryzae to industrial production.
Collapse
Affiliation(s)
- Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China.
| | - Yayi Tu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China.
| | - Chunmiao Jiang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China.
| | - Zhe Zhang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China.
| | - Yongkai Li
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China.
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China.
| |
Collapse
|
32
|
Muthamilarasan M, Singh NK, Prasad M. Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective. ADVANCES IN GENETICS 2019; 103:1-38. [PMID: 30904092 DOI: 10.1016/bs.adgen.2019.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
For several decades, researchers are working toward improving the "major" crops for better adaptability and tolerance to environmental stresses. However, little or no research attention is given toward neglected and underutilized crop species (NUCS) which hold the potential to ensure food and nutritional security among the ever-growing global population. NUCS are predominantly climate resilient, but their yield and quality are compromised due to selective breeding. In this context, the importance of omics technologies namely genomics, transcriptomics, proteomics, phenomics and ionomics in delineating the complex molecular machinery governing growth, development and stress responses of NUCS is underlined. However, gaining insights through individual omics approaches will not be sufficient to address the research questions, whereas integrating these technologies could be an effective strategy to decipher the gene function, genome structures, biological pathways, metabolic and regulatory networks underlying complex traits. Given this, the chapter enlists the importance of NUCS in food and nutritional security and provides an overview of deploying omics approaches to study the NUCS. Also, the chapter enumerates the status of crop improvement programs in NUCS and suggests implementing "integrating omics" for gaining a better understanding of crops' response to abiotic and biotic stresses.
Collapse
Affiliation(s)
- Mehanathan Muthamilarasan
- National Institute of Plant Genome Research, New Delhi, India; ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India.
| |
Collapse
|
33
|
Agrobacterium-mediated horizontal gene transfer: Mechanism, biotechnological application, potential risk and forestalling strategy. Biotechnol Adv 2018; 37:259-270. [PMID: 30579929 DOI: 10.1016/j.biotechadv.2018.12.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 11/20/2022]
Abstract
The extraordinary capacity of Agrobacterium to transfer its genetic material to host cell makes it evolve from phytopathogen to a powerful transgenic vector. Agrobacterium-mediated stable transformation is widely used as the preferred method to create transgenic plants for molecular plant biology research and crop breeding. Recent years, both mechanism and application of Agrobacterium-mediated horizontal gene transfer have made significant progresses, especially Agrobacterium-mediated transient transformation was developed for plant biotechnology industry to produce recombinant proteins. Agrobacterium strains are almost used and saved not only by each of microbiology and molecular plant labs, but also by many of plant biotechnology manufacturers. Agrobacterium is able to transfer its genetic material to a broad range of hosts, including plant and non-plant hosts. As a consequence, the concern of environmental risk associated with the accidental release of genetically modified Agrobacterium arises. In this article, we outline the recent progress in the molecular mechanism of Agrobacterium-meditated gene transfer, focus on the application of Agrobacterium-mediated horizontal gene transfer, and review the potential risk associated with Agrobacterium-meditated gene transfer. Based on the comparison between the infecting process of Agrobacterium as a pathogen and the transgenic process of Agrobacterium as a transgenic vector, we realize that chemotaxis is the distinct difference between these two biological processes and thus discuss the possible role of chemotaxis in forestalling the potential risk of Agrobacterium-meditated horizontal gene transfer to non-target plant species.
Collapse
|
34
|
Pathogenicity, Phylogenetic relationship and NGS based identification and assembly of tumorigenic Agrobacterium radiabacter plasmidic and chromosomic reads isolated from Prunus duclcis. Genomics 2018; 111:1423-1430. [PMID: 30287402 DOI: 10.1016/j.ygeno.2018.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/25/2018] [Indexed: 11/22/2022]
Abstract
Although many Agrobacterium radiobacter strains have already been identified, only a few genomes of strains belonging to genomovar G4 have been sequenced so far. In this study, we report the first virulent genome sequence of Agrobacterium radiobacter strain tun 183, which is highly virulent to almond specie. The genome size was estimated to be 5.53 Mb, with 57.9%GC content. In total, 6486 genes encoding proteins and 61 genes encoding RNAs were identified in this genome. Comparisons with the available sequenced genomes of genomovar G4 as well as with other A. sp. were conducted, revealing a hexapartite genome containing circular and linear chromosomes in addition to two accessory plasmids and a tumor inducing plasmid (pTi) in strain tun 183. The phylogenetic analysis of recA gene clearly showed the clustering of tun 183 strain within genomovar G4, supporting the monophyly within this genomovar.
Collapse
|
35
|
Lozoya-Pérez NE, Casas-Flores S, Martínez-Álvarez JA, López-Ramírez LA, Lopes-Bezerra LM, Franco B, Mora-Montes HM. Generation of Sporothrix schenckii mutants expressing the green fluorescent protein suitable for the study of host-fungus interactions. Fungal Biol 2018; 122:1023-1030. [PMID: 30227928 DOI: 10.1016/j.funbio.2018.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/11/2018] [Indexed: 01/10/2023]
Abstract
Sporotrichosis is an infection caused by members of the Sporothrix genus, and among them, Sporothrix schenckii is one of the etiological agents. Both, the disease and the causative agent have gained interest in the recent years, because of the report of epidemic outbreaks, and the description of the disease transmission from animals to human beings. Despite the relevance of S. schenckii in the clinical field, there are basic aspects of its biology poorly explored. So far, Agrobacterium tumefaciens-mediated transformation has been reported as an alternative for genetic manipulation of this fungal pathogen. Here, we report the optimization of the transformation method and used this to generate insertional mutants that express the green fluorescent protein in S. schenckii. We obtained five mutant strains that showed mitotic stability and expression of the reporter gene. The strains displayed normal cell wall composition, and a similar ability to interact ex vivo with human monocytes and monocyte-derived macrophages. Moreover, the virulence in larvae of Galleria mellonella was similar to that obtained with the wild-type control strains. These data indicate that these fluorescent mutants with normal ability to interact with the host could be used in bioimaging to track the host-Sporothrix interaction in vivo.
Collapse
Affiliation(s)
- Nancy E Lozoya-Pérez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, Col. Noria Alta, C.P. 36050, Guanajuato, Gto, Mexico
| | - Sergio Casas-Flores
- División de Biología Molecular, IPICYT, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | - José A Martínez-Álvarez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, Col. Noria Alta, C.P. 36050, Guanajuato, Gto, Mexico
| | - Luz A López-Ramírez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, Col. Noria Alta, C.P. 36050, Guanajuato, Gto, Mexico
| | - Leila M Lopes-Bezerra
- Laboratory of Cellular Mycology and Proteomics, Universidade do Estado do Rio de Janeiro, Brazil; Faculdade de Farmácia, Universidade de São Paulo, Brazil
| | - Bernardo Franco
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, Col. Noria Alta, C.P. 36050, Guanajuato, Gto, Mexico
| | - Héctor M Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, Col. Noria Alta, C.P. 36050, Guanajuato, Gto, Mexico.
| |
Collapse
|
36
|
Horvath M, Steinbiss HH, Reiss B. Gene Targeting Without DSB Induction Is Inefficient in Barley. FRONTIERS IN PLANT SCIENCE 2017; 7:1973. [PMID: 28105032 PMCID: PMC5214849 DOI: 10.3389/fpls.2016.01973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/13/2016] [Indexed: 05/29/2023]
Abstract
Double strand-break (DSB) induction allowed efficient gene targeting in barley (Hordeum vulgare), but little is known about efficiencies in its absence. To obtain such data, an assay system based on the acetolactate synthase (ALS) gene was established, a target gene which had been used previously in rice and Arabidopsis thaliana. Expression of recombinases RAD51 and RAD54 had been shown to improve gene targeting in A. thaliana and positive-negative (P-N) selection allows the routine production of targeted mutants without DSB induction in rice. We implemented these approaches in barley and analysed gene targeting with the ALS gene in wild type and RAD51 and RAD54 transgenic lines. In addition, P-N selection was tested. In contrast to the high gene targeting efficiencies obtained in the absence of DSB induction in A. thaliana or rice, not one single gene targeting event was obtained in barley. These data suggest that gene targeting efficiencies are very low in barley and can substantially differ between different plants, even at the same target locus. They also suggest that the amount of labour and time would become unreasonably high to use these methods as a tool in routine applications. This is particularly true since DSB induction offers efficient alternatives. Barley, unlike rice and A. thaliana has a large, complex genome, suggesting that genome size or complexity could be the reason for the low efficiencies. We discuss to what extent transformation methods, genome size or genome complexity could contribute to the striking differences in the gene targeting efficiencies between barley, rice and A. thaliana.
Collapse
Affiliation(s)
| | | | - Bernd Reiss
- Plant DNA Recombination Group, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| |
Collapse
|
37
|
Aguilar A, Peralta H, Mora Y, Díaz R, Vargas-Lagunas C, Girard L, Mora J. Genomic Comparison of Agrobacterium pusense Strains Isolated from Bean Nodules. Front Microbiol 2016; 7:1720. [PMID: 27833604 PMCID: PMC5081363 DOI: 10.3389/fmicb.2016.01720] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/13/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alejandro Aguilar
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Humberto Peralta
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Yolanda Mora
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Rafael Díaz
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Carmen Vargas-Lagunas
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Lourdes Girard
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Jaime Mora
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| |
Collapse
|