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Chandra T, Jaiswal S, Tomar RS, Iquebal MA, Kumar D. Realizing visionary goals for the International Year of Millet (IYoM): accelerating interventions through advances in molecular breeding and multiomics resources. PLANTA 2024; 260:103. [PMID: 39304579 DOI: 10.1007/s00425-024-04520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024]
Abstract
MAIN CONCLUSION Leveraging advanced breeding and multi-omics resources is vital to position millet as an essential "nutricereal resource," aligning with IYoM goals, alleviating strain on global cereal production, boosting resilience to climate change, and advancing sustainable crop improvement and biodiversity. The global challenges of food security, nutrition, climate change, and agrarian sustainability demand the adoption of climate-resilient, nutrient-rich crops to support a growing population amidst shifting environmental conditions. Millets, also referred to as "Shree Anna," emerge as a promising solution to address these issues by bolstering food production, improving nutrient security, and fostering biodiversity conservation. Their resilience to harsh environments, nutritional density, cultural significance, and potential to enhance dietary quality index made them valuable assets in global agriculture. Recognizing their pivotal role, the United Nations designated 2023 as the "International Year of Millets (IYoM 2023)," emphasizing their contribution to climate-resilient agriculture and nutritional enhancement. Scientific progress has invigorated efforts to enhance millet production through genetic and genomic interventions, yielding a wealth of advanced molecular breeding technologies and multi-omics resources. These advancements offer opportunities to tackle prevailing challenges in millet, such as anti-nutritional factors, sensory acceptability issues, toxin contamination, and ancillary crop improvements. This review provides a comprehensive overview of molecular breeding and multi-omics resources for nine major millet species, focusing on their potential impact within the framework of IYoM. These resources include whole and pan-genome, elucidating adaptive responses to abiotic stressors, organelle-based studies revealing evolutionary resilience, markers linked to desirable traits for efficient breeding, QTL analysis facilitating trait selection, functional gene discovery for biotechnological interventions, regulatory ncRNAs for trait modulation, web-based platforms for stakeholder communication, tissue culture techniques for genetic modification, and integrated omics approaches enabled by precise application of CRISPR/Cas9 technology. Aligning these resources with the seven thematic areas outlined by IYoM catalyzes transformative changes in millet production and utilization, thereby contributing to global food security, sustainable agriculture, and enhanced nutritional consequences.
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Affiliation(s)
- Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Rukam Singh Tomar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, 110012, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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Zhang Z, Shi W, Gu J, Song S, Xiao M, Yao J, Liu Y, Jiang J, Miao M. Short day promotes gall swelling by a CONSTANS-FLOWERING LOCUS T pathway in Zizania latifolia. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39292875 DOI: 10.1111/tpj.17033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/24/2024] [Accepted: 09/03/2024] [Indexed: 09/20/2024]
Abstract
"Jiaobai" is a symbiont of Zizania latifolia and Ustilago esculenta, producing fleshy galls as a popular vegetable in South and East Asia. Current "Jiaobai" cultivars exhibit abundant variation in their gall formation date; however, the underlying mechanism is not clear. In this study, a strict short-day (SD) "Jiaobai" line "YD-3" was used. Plants were treated with two day-length regimes [14 h/10 h (day/night) (control) and 8 h/16 h (day/night) (SD)] from 100 to 130 days after planting. The gall swelling rate of the two treatments and another early SD treatment (from 60 to 90 days after planting), together with the contingent flowering plants in the experiment population, revealed that SD can improve both gall enlargement and flowering of "Jiaobai" plants. Comparison of RNA sequencing data among control, SD swelling, and SD flowering treatments of leaves and meristems indicated that SD promotion of "Jiaobai" swelling is conducted by the CONSTANS (CO)-FLOWERING LOCUS T (FT) pathway, similar but not identical to the SD-induced flowering pathway in Z latifolia and rice. "Virus-induced gene silencing", "Yeast one-hybrid assay" and "Dual-luciferase assay" showed that a FT gene, ZlGsd1, is critical in SD promotion of gall formation and is positively regulated by a CO gene, ZlCOL1. Our study elucidated how photoperiod affects the formation of a unique organ produced by plant-fungus symbiosis. The difference in SD response between "Jiaobai" and rice, as well as their potential applications in breeding of "Jiaobai" and rice, were also discussed.
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Affiliation(s)
- Zhiping Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Wangjie Shi
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Jiawen Gu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Sixiao Song
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Meng Xiao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Junchi Yao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Yancheng Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Jiezeng Jiang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Minmin Miao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu, 225009, China
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3
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Zhao Y, Wang T, Wan S, Tong Y, Wei Y, Li P, Hu N, Liu Y, Chen H, Pan X, Zhang B, Peng R, Hu S. Genome-wide identification and functional analysis of the SiCIN gene family in foxtail millet (Setaria italica L.). Gene 2024; 921:148499. [PMID: 38718970 DOI: 10.1016/j.gene.2024.148499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Cell wall invertase (CIN) is a vital member of plant invertase (INV) and plays a key role in the breakdown of sucrose. This enzyme facilitates the hydrolysis of sucrose into glucose and fructose, which is crucial for various aspects of plant growth and development. However, the function of CIN genes in foxtail millet (Setaria italica) is less studied. In this research, we used the blast-p of NCBI and TBtools for bidirectional comparison, and a total of 13 CIN genes (named SiCINs) were identified from foxtail millet by using Arabidopsis and rice CIN sequences as reference sequences. The phylogenetic tree analysis revealed that the CIN genes can be categorized into three subfamilies: group 1, group 2, and group 3. Furthermore, upon conducting chromosomal localization analysis, it was observed that the 13 SiCINs were distributed unevenly across five chromosomes. Cis-acting elements of SiCIN genes can be classified into three categories: plant growth and development, stress response, and hormone response. The largest number of cis-acting elements were those related to light response (G-box) and the cis-acting elements related to seed-specific regulation (RY-element). qRT-PCR analysis further confirmed that the expression of SiCIN7 and SiCIN8 in the grain was higher than that in any other tissues. The overexpression of SiCIN7 in Arabidopsis improved the grain size and thousand-grain weight, suggesting that SiCIN7 could positively regulate grain development. Our findings will help to further understand the grain-filling mechanism of SiCIN and elucidate the biological mechanism underlying the grain development of SiCIN.
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Affiliation(s)
- Yongqing Zhao
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China
| | - Tao Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Sumei Wan
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China
| | - Yan Tong
- Anyang Academy of Agriculture Sciences, Anyang 455000, Henan, China
| | - Yangyang Wei
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Pengtao Li
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Nan Hu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Yuling Liu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Hongqi Chen
- Anyang Academy of Agriculture Sciences, Anyang 455000, Henan, China
| | - Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC 27858, United States
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, United States.
| | - Renhai Peng
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China.
| | - Shoulin Hu
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China.
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4
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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.
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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
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5
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Kalia D, Jose-Santhi J, Sheikh FR, Singh D, Singh RK. Tobacco rattle virus-based virus-induced gene silencing (VIGS) as an aid for functional genomics in Saffron ( Crocus sativus L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:749-755. [PMID: 38846460 PMCID: PMC11150356 DOI: 10.1007/s12298-024-01459-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 06/09/2024]
Abstract
Several limitations in genetic engineering interventions in saffron exist, hindering the development of genetically modified varieties and the widespread application of genetic engineering in this crop. Lack of genome sequence information, the complexity of genetic makeup, and lack of well-established genetic transformation protocols limit its in planta functional validation of genes that would eventually lead toward crop optimization. In this study, we demonstrate agro infiltration in leaves of adult plants and whole corm before sprouting are suitable for transient gene silencing in saffron using Tobacco Rattle Virus (TRV) based virus-induced gene silencing (VIGS) targeting phytoene desaturase (PDS). Silencing of PDS resulted in bleached phenotype in leaves in both methods. TRV-mediated VIGS could be attained in saffron leaves and corms, providing an opportunity for functional genomics studies in this expensive spice crop. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01459-0.
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Affiliation(s)
- Diksha Kalia
- Plant Adaptation and Developmental Biology Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, H.P. 176061 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Joel Jose-Santhi
- Plant Adaptation and Developmental Biology Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, H.P. 176061 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Firdous Rasool Sheikh
- Plant Adaptation and Developmental Biology Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, H.P. 176061 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Deepika Singh
- Plant Adaptation and Developmental Biology Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, H.P. 176061 India
| | - Rajesh Kumar Singh
- Plant Adaptation and Developmental Biology Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, H.P. 176061 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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6
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Zhang K, Wang X, Chen X, Zhang R, Guo J, Wang Q, Li D, Shao L, Shi X, Han J, Liu Z, Xia Y, Zhang J. Establishment of a Homologous Silencing System with Intact-Plant Infiltration and Minimized Operation for Studying Gene Function in Herbaceous Peonies. Int J Mol Sci 2024; 25:4412. [PMID: 38673996 PMCID: PMC11050706 DOI: 10.3390/ijms25084412] [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: 01/29/2024] [Revised: 04/04/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Gene function verification is a crucial step in studying the molecular mechanisms regulating various plant life activities. However, a stable and efficient homologous genetic transgenic system for herbaceous peonies has not been established. In this study, using virus-induced gene silencing technology (VIGS), a highly efficient homologous transient verification system with distinctive advantages was proposed, which not only achieves true "intact-plant" infiltration but also minimizes the operation. One-year-old roots of the representative species, Paeonia lactiflora Pall., were used as the materials; prechilling (4 °C) treatment for 3-5 weeks was applied as a critical precondition for P. lactiflora to acquire a certain chilling accumulation. A dormancy-related gene named HOMEOBOX PROTEIN 31 (PlHB31), believed to negatively regulate bud endodormancy release (BER), was chosen as the target gene in this study. GFP fluorescence was detected in directly infiltrated and newly developed roots and buds; the transgenic plantlets exhibited remarkably earlier budbreak, and PlHB31 was significantly downregulated in silenced plantlets. This study established a homologous transient silencing system featuring intact-plant infiltration and minimized manipulation for gene function research, and also offers technical support and serves as a theoretical basis for gene function discovery in numerous other geophytes.
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Affiliation(s)
- Kaijing Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Xiaobin Wang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Xiaoxuan Chen
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Runlong Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Junhong Guo
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Qiyao Wang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Danqing Li
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Lingmei Shao
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Xiaohua Shi
- Zhejiang Institute of Landscape Plants and Flowers, Hangzhou 311251, China;
| | - Jingtong Han
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Zhiyang Liu
- Harbin Academy of Agricultural Sciences, Harbin 150029, China;
| | - Yiping Xia
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Jiaping Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
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Prusty A, Panchal A, Singh RK, Prasad M. Major transcription factor families at the nexus of regulating abiotic stress response in millets: a comprehensive review. PLANTA 2024; 259:118. [PMID: 38592589 DOI: 10.1007/s00425-024-04394-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/17/2024] [Indexed: 04/10/2024]
Abstract
Millets stand out as a sustainable crop with the potential to address the issues of food insecurity and malnutrition. These small-seeded, drought-resistant cereals have adapted to survive a broad spectrum of abiotic stresses. Researchers are keen on unravelling the regulatory mechanisms that empower millets to withstand environmental adversities. The aim is to leverage these identified genetic determinants from millets for enhancing the stress tolerance of major cereal crops through genetic engineering or breeding. This review sheds light on transcription factors (TFs) that govern diverse abiotic stress responses and play role in conferring tolerance to various abiotic stresses in millets. Specifically, the molecular functions and expression patterns of investigated TFs from various families, including bHLH, bZIP, DREB, HSF, MYB, NAC, NF-Y and WRKY, are comprehensively discussed. It also explores the potential of TFs in developing stress-tolerant crops, presenting a comprehensive discussion on diverse strategies for their integration.
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Affiliation(s)
- Ankita Prusty
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Panchal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Roshan Kumar Singh
- Department of Botany, Mahishadal Raj College, Purba Medinipur, Garh Kamalpur, West Bengal, 721628, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Department of Genetics, University of Delhi, South Campus, Benito-Juarez Road, New Delhi, 110021, India.
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Wu J, Zhang Y, Li F, Zhang X, Ye J, Wei T, Li Z, Tao X, Cui F, Wang X, Zhang L, Yan F, Li S, Liu Y, Li D, Zhou X, Li Y. Plant virology in the 21st century in China: Recent advances and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:579-622. [PMID: 37924266 DOI: 10.1111/jipb.13580] [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: 09/12/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023]
Abstract
Plant viruses are a group of intracellular pathogens that persistently threaten global food security. Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years, including basic research and technologies for preventing and controlling plant viral diseases. Here, we review these milestones and advances, including the identification of new crop-infecting viruses, dissection of pathogenic mechanisms of multiple viruses, examination of multilayered interactions among viruses, their host plants, and virus-transmitting arthropod vectors, and in-depth interrogation of plant-encoded resistance and susceptibility determinants. Notably, various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants. We also recommend future plant virology studies in China.
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Affiliation(s)
- Jianguo Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Ye
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Taiyun Wei
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaorong Tao
- Department of Plant Pathology, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianbing Wang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lili Zhang
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dawei Li
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yi Li
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
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Nihranz CT, Guzchenko IA, Casteel CL. Silencing ZmPP2C-A10 with a foxtail mosaic virus (FoMV) derived vector benefits maize growth and development following water limitation. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:956-964. [PMID: 37658795 DOI: 10.1111/plb.13568] [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: 06/21/2023] [Accepted: 07/23/2023] [Indexed: 09/05/2023]
Abstract
Global climate change is causing more frequent and severe droughts, which can have negative impacts on plant growth and crop productivity. Under drought conditions, plants produce the hormone ABA (abscisic acid), which regulates adaptive responses, such as stomatal closure and root elongation. Plant viruses have been used in the lab to convey new traits to plants and could also be used to increase production of ABA or to enhance downstream plant drought resistance responses. In this study, foxtail mosaic virus (FoMV) was used to silence ZmPP2C-A10, a negative regulator of ABA signalling, in maize (Zea mays L.). Both silenced and control plants were exposed to an 8-day drought treatment, followed by a 30-day period of rewatering, after which indicators of drought resistance were measured. After drought treatment, we observed a nearly twofold increase in expression of a stress-mitigation gene, ZmRAB17, reduced chlorophyll fluorescence changes (indicator of stress), and increased plant biomass and development in the ZmPP2C-A10-silenced maize compared to controls. These results demonstrate that the FoMV system can be used to silence endogenous expression of ZmPP2C-A10 and increase maize tolerance to drought. This could offer a useful tool to improve crop traits and reduce yield loss during the growing season.
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Affiliation(s)
- C T Nihranz
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - I A Guzchenko
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - C L Casteel
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
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10
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Tuo D, Yao Y, Yan P, Chen X, Qu F, Xue W, Liu J, Kong H, Guo J, Cui H, Dai Z, Shen W. Development of cassava common mosaic virus-based vector for protein expression and gene editing in cassava. PLANT METHODS 2023; 19:78. [PMID: 37537660 PMCID: PMC10399001 DOI: 10.1186/s13007-023-01055-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/15/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Plant virus vectors designed for virus-mediated protein overexpression (VOX), virus-induced gene silencing (VIGS), and genome editing (VIGE) provide rapid and cost-effective tools for functional genomics studies, biotechnology applications and genome modification in plants. We previously reported that a cassava common mosaic virus (CsCMV, genus Potexvirus)-based VIGS vector was used for rapid gene function analysis in cassava. However, there are no VOX and VIGE vectors available in cassava. RESULTS In this study, we developed an efficient VOX vector (CsCMV2-NC) for cassava by modifying the CsCMV-based VIGS vector. Specifically, the length of the duplicated putative subgenomic promoter (SGP1) of the CsCMV CP gene was increased to improve heterologous protein expression in cassava plants. The modified CsCMV2-NC-based VOX vector was engineered to express genes encoding green fluorescent protein (GFP), bacterial phytoene synthase (crtB), and Xanthomonas axonopodis pv. manihotis (Xam) type III effector XopAO1 for viral infection tracking, carotenoid biofortification and Xam virulence effector identification in cassava. In addition, we used CsCMV2-NC to deliver single guide RNAs (gMePDS1/2) targeting two loci of the cassava phytoene desaturase gene (MePDS) in Cas9-overexpressing transgenic cassava lines. The CsCMV-gMePDS1/2 efficiently induced deletion mutations of the targeted MePDS with the albino phenotypes in systemically infected cassava leaves. CONCLUSIONS Our results provide a useful tool for rapid and efficient heterologous protein expression and guide RNA delivery in cassava. This expands the potential applications of CsCMV-based vector in gene function studies, biotechnology research, and precision breeding for cassava.
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Affiliation(s)
- Decai Tuo
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Yuan Yao
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Pu Yan
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Xin Chen
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Feihong Qu
- School of Tropical Agriculture and Forestry, Sanya Nanfan Research Institute, Hainan University, Haikou & Sanya, Hainan, China
| | - Weiqian Xue
- School of Tropical Agriculture and Forestry, Sanya Nanfan Research Institute, Hainan University, Haikou & Sanya, Hainan, China
| | - Jinping Liu
- School of Tropical Agriculture and Forestry, Sanya Nanfan Research Institute, Hainan University, Haikou & Sanya, Hainan, China
| | - Hua Kong
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Jianchun Guo
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Hongguang Cui
- School of Tropical Agriculture and Forestry, Sanya Nanfan Research Institute, Hainan University, Haikou & Sanya, Hainan, China
| | - Zhaoji Dai
- School of Tropical Agriculture and Forestry, Sanya Nanfan Research Institute, Hainan University, Haikou & Sanya, Hainan, China
| | - Wentao Shen
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China.
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11
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Gull I, Jander G. Inoculation of Maize with Sugarcane Mosaic Virus Constructs and Application for RNA Interference in Fall Armyworms. Bio Protoc 2023; 13:e4760. [PMID: 37497451 PMCID: PMC10367001 DOI: 10.21769/bioprotoc.4760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/21/2023] [Accepted: 05/29/2023] [Indexed: 07/28/2023] Open
Abstract
Virus-mediated transient gene overexpression and gene expression silencing can be used to screen gene functions in plants. Sugarcane mosaic virus (SCMV) is a positive strand RNA virus in the Potyviridae family that has been modified to be used as vector to infect monocots, including maize (Zea mays), for transient gene overexpression and gene expression silencing. Relative to stable transformation, SCMV-mediated transient expression in maize has the advantages of being faster and less expensive. Here, we describe a protocol for cloning constructs into the plasmid vector pSCMV-CS3. After maize seedlings are transformed with pSCMV-CS3 constructs by particle bombardment, the virus replicates and spreads systemically in the plants. Subsequent infections of maize seedlings can be accomplished by rub inoculation with sap from SCMV-infested plants. As an example of a practical application of the method, we also describe virus-induced gene silencing (VIGS) of fall armyworm (Spodoptera frugiperda) gene expression. Transgenic viruses are created by cloning a segment of the fall armyworm target gene into pSCMV-CS3 prior to maize transformation. Caterpillars are fed on the virus-infected maize plants, which make dsRNA to silence the expression of the fall armyworm target gene after ingestion. This use of SCMV for plant-mediated VIGS in insects allows rapid screening of gene functions when caterpillars are feeding on their host plants. Graphical overview.
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Affiliation(s)
- Iram Gull
- Boyce Thompson Institute, Ithaca, NY 14853, USA
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12
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Beernink BM, Whitham SA. Foxtail mosaic virus: A tool for gene function analysis in maize and other monocots. MOLECULAR PLANT PATHOLOGY 2023; 24:811-822. [PMID: 37036421 PMCID: PMC10257046 DOI: 10.1111/mpp.13330] [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: 10/31/2022] [Revised: 02/20/2023] [Accepted: 03/08/2023] [Indexed: 06/11/2023]
Abstract
Many plant viruses have been engineered into vectors for use in functional genomics studies, expression of heterologous proteins, and, most recently, gene editing applications. The use of viral vectors overcomes bottlenecks associated with mutagenesis and transgenesis approaches often implemented for analysis of gene function. There are several engineered viruses that are demonstrated or suggested to be useful in maize through proof-of-concept studies. However, foxtail mosaic virus (FoMV), which has a relatively broad host range, is emerging as a particularly useful virus for gene function studies in maize and other monocot crop or weed species. A few clones of FoMV have been independently engineered, and they have different features and capabilities for virus-induced gene silencing (VIGS) and virus-mediated overexpression (VOX) of proteins. In addition, FoMV can be used to deliver functional guide RNAs in maize and other plants expressing the Cas9 protein, demonstrating its potential utility in virus-induced gene editing applications. There is a growing number of studies in which FoMV vectors are being applied for VIGS or VOX in maize and the vast majority of these are related to maize-microbe interactions. In this review, we highlight the biology and engineering of FoMV as well as its applications in maize-microbe interactions and more broadly in the context of the monocot functional genomics toolbox.
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Affiliation(s)
- Bliss M. Beernink
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
- Department of BiologyUniversity of ManitobaWinnipegManitobaCanada
| | - Steven A. Whitham
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
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13
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Jiang J, Yu E, Nihranz CT, Prakash V, Varsani S, Casteel CL. Engineering aphid transmission of foxtail mosaic virus in the presence of potyvirus helper component proteinase through coat protein modifications. J Gen Virol 2023; 104. [PMID: 37053090 DOI: 10.1099/jgv.0.001844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Biotechnologies that use plant viruses as plant enhancement tools have shown great potential to flexibly engineer crop traits, but field applications of these technologies are still limited by efficient dissemination methods. Potyviruses can be rapidly inoculated into plants by aphid vectors due to the presence of the potyviral helper component proteinase (HC-Pro), which binds to the DAG motif of the coat protein (CP) of the virion. Previously it was determined that a naturally occurring DAG motif in the non-aphid-transmissible potexvirus, potato aucuba mosaic virus (PAMV), is functional when a potyviral HC-Pro is provided to aphids in plants. The DAG motif of PAMV was successfully transferred to the CP of another non-aphid-transmissible potexvirus, potato virus X, to convey aphid transmission capabilities in the presence of HC-Pro. Here, we demonstrate that DAG-containing segments of the CP from two different potyviruses (sugarcane mosaic virus and turnip mosaic virus), and from the previously used potexvirus, PAMV, can make the potexvirus, foxtail mosaic virus (FoMV), aphid-transmissible when fused with the FoMV CP. We show that DAG-containing FoMVs are transmissible by aphids that have prior access to HC-Pro through potyvirus-infected plants or ectopic expression of HC-Pro. The transmission efficiency of the DAG-containing FoMVs varied from less than 10 % to over 70 % depending on the length and composition of the surrounding amino acid sequences of the DAG-containing segment, as well as due to the recipient plant species. Finally, we show that the engineered aphid-transmissible FoMV is still functional as a plant enhancement resource, as endogenous host target genes were silenced in FoMV-infected plants after aphid transmission. These results suggest that aphid transmission could be engineered into non-aphid-transmissible plant enhancement viral resources to facilitate their field applications.
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Affiliation(s)
- Jun Jiang
- Department of Plant Pathology, University of California, Davis, CA, USA
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, PR China
| | - Eric Yu
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Chad T Nihranz
- School of Integrative Plant Science, Plant-Microbe Biology and Plant Pathology Section, Cornell University, Ithaca, NY, USA
| | - Ved Prakash
- School of Integrative Plant Science, Plant-Microbe Biology and Plant Pathology Section, Cornell University, Ithaca, NY, USA
| | - Suresh Varsani
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Clare L Casteel
- Department of Plant Pathology, University of California, Davis, CA, USA
- School of Integrative Plant Science, Plant-Microbe Biology and Plant Pathology Section, Cornell University, Ithaca, NY, USA
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14
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Virus-Induced Gene Silencing (VIGS): A Powerful Tool for Crop Improvement and Its Advancement towards Epigenetics. Int J Mol Sci 2023; 24:ijms24065608. [PMID: 36982682 PMCID: PMC10057534 DOI: 10.3390/ijms24065608] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/17/2023] Open
Abstract
Virus-induced gene silencing (VIGS) is an RNA-mediated reverse genetics technology that has evolved into an indispensable approach for analyzing the function of genes. It downregulates endogenous genes by utilizing the posttranscriptional gene silencing (PTGS) machinery of plants to prevent systemic viral infections. Based on recent advances, VIGS can now be used as a high-throughput tool that induces heritable epigenetic modifications in plants through the viral genome by transiently knocking down targeted gene expression. As a result of the progression of DNA methylation induced by VIGS, new stable genotypes with desired traits are being developed in plants. In plants, RNA-directed DNA methylation (RdDM) is a mechanism where epigenetic modifiers are guided to target loci by small RNAs, which play a major role in the silencing of the target gene. In this review, we described the molecular mechanisms of DNA and RNA-based viral vectors and the knowledge obtained through altering the genes in the studied plants that are not usually accessible to transgenic techniques. We showed how VIGS-induced gene silencing can be used to characterize transgenerational gene function(s) and altered epigenetic marks, which can improve future plant breeding programs.
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15
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Prakash V, Nihranz CT, Casteel CL. The Potyviral Protein 6K2 from Turnip Mosaic Virus Increases Plant Resilience to Drought. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:189-197. [PMID: 36534062 DOI: 10.1094/mpmi-09-22-0183-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Virus infection can increase drought tolerance of infected plants compared with noninfected plants; however, the mechanisms mediating virus-induced drought tolerance remain unclear. In this study, we demonstrate turnip mosaic virus (TuMV) infection increases Arabidopsis thaliana survival under drought compared with uninfected plants. To determine if specific TuMV proteins mediate drought tolerance, we cloned the coding sequence for each of the major viral proteins and generated transgenic A. thaliana that constitutively express each protein. Three TuMV proteins, 6K1, 6K2, and NIa-Pro, enhanced drought tolerance of A. thaliana when expressed constitutively in plants compared with controls. While in the control plant, transcripts related to abscisic acid (ABA) biosynthesis and ABA levels were induced under drought, there were no changes in ABA or related transcripts in plants expressing 6K2 under drought compared with well-watered conditions. Expression of 6K2 also conveyed drought tolerance in another host plant, Nicotiana benthamiana, when expressed using a virus overexpression construct. In contrast to ABA, 6K2 expression enhanced salicylic acid (SA) accumulation in both Arabidopsis and N. benthamiana. These results suggest 6K2-induced drought tolerance is mediated through increased SA levels and SA-dependent induction of plant secondary metabolites, osmolytes, and antioxidants that convey drought tolerance. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Ved Prakash
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, U.S.A
| | - Chad T Nihranz
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, U.S.A
| | - Clare L Casteel
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, U.S.A
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16
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Bredow M, Natukunda MI, Beernink BM, Chicowski AS, Salas‐Fernandez MG, Whitham SA. Characterization of a foxtail mosaic virus vector for gene silencing and analysis of innate immune responses in Sorghum bicolor. MOLECULAR PLANT PATHOLOGY 2023; 24:71-79. [PMID: 36088637 PMCID: PMC9742499 DOI: 10.1111/mpp.13270] [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: 07/12/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 05/08/2023]
Abstract
Sorghum is vulnerable to many biotic and abiotic stresses, which cause considerable yield losses globally. Efforts to genetically characterize beneficial sorghum traits, including disease resistance, plant architecture, and tolerance to abiotic stresses, are ongoing. One challenge faced by sorghum researchers is its recalcitrance to transformation, which has slowed gene validation efforts and utilization for cultivar development. Here, we characterize the use of a foxtail mosaic virus (FoMV) vector for virus-induced gene silencing (VIGS) by targeting two previously tested marker genes: phytoene desaturase (PDS) and ubiquitin (Ub). We additionally demonstrate VIGS of a subgroup of receptor-like cytoplasmic kinases (RLCKs) and report the role of these genes as positive regulators of early defence signalling. Silencing of subgroup 8 RLCKs also resulted in higher susceptibility to the bacterial pathogens Pseudomonas syringae pv. syringae (B728a) and Xanthomonas vasicola pv. holcicola, demonstrating the role of these genes in host defence against bacterial pathogens. Together, this work highlights the utility of FoMV-induced gene silencing in the characterization of genes mediating defence responses in sorghum. Moreover, FoMV was able to systemically infect six diverse sorghum genotypes with high efficiency at optimal temperatures for sorghum growth and therefore could be extrapolated to study additional traits of economic importance.
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Affiliation(s)
- Melissa Bredow
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Martha Ibore Natukunda
- Department of AgronomyIowa State UniversityAmesIowaUSA
- Present address:
Department of BiologyAugustana UniversitySioux FallsSouth DakotaUSA.
| | - Bliss M. Beernink
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
- Present address:
Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada.
| | - Aline Sartor Chicowski
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
| | | | - Steven A. Whitham
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
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17
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Rhee SJ, Jang YJ, Park JY, Ryu J, Lee GP. Virus-induced gene silencing for in planta validation of gene function in cucurbits. PLANT PHYSIOLOGY 2022; 190:2366-2379. [PMID: 35944218 PMCID: PMC9706489 DOI: 10.1093/plphys/kiac363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Virus-induced gene silencing (VIGS) is a powerful tool for high-throughput analysis of gene function. Here, we developed the VIGS vector pCF93, from which expression of the cucumber fruit mottle mosaic virus genome is driven by the cauliflower mosaic virus 35S promoter to produce viral transcripts in inoculated plants. To test the utility of the pCF93 vector, we identified candidate genes related to male sterility (MS) in watermelon (Citrullus lanatus), which is recalcitrant to genetic transformation. Specifically, we exploited previously reported reference-based and de novo transcriptome data to define 38 differentially expressed genes between a male-sterile line and its fertile near-isogenic line in the watermelon cultivar DAH. We amplified 200- to 300-bp fragments of these genes, cloned them into pCF93, and inoculated DAH with the resulting VIGS clones. The small watermelon cultivar DAH enabled high-throughput screening using a small cultivation area. We simultaneously characterized the phenotypes associated with each of the 38 candidate genes in plants grown in a greenhouse. Silencing of 8 of the 38 candidate genes produced male-sterile flowers with abnormal stamens and no pollen. We confirmed the extent of gene silencing in inoculated flowers using reverse transcription-qPCR. Histological analysis of stamens from male-fertile and male-sterile floral buds and mature flowers revealed developmental defects and shrunken pollen sacs. Based on these findings, we propose that the pCF93 vector and our VIGS system will facilitate high-throughput analysis for the study of gene function in watermelons.
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Affiliation(s)
- Sun-Ju Rhee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Yoon Jeong Jang
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Jun-Young Park
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Jisu Ryu
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Gung Pyo Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
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18
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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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Dangol A, Shavit R, Yaakov B, Strickler SR, Jander G, Tzin V. Characterizing serotonin biosynthesis in Setaria viridis leaves and its effect on aphids. PLANT MOLECULAR BIOLOGY 2022; 109:533-549. [PMID: 35020104 DOI: 10.1007/s11103-021-01239-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
A combined transcriptomic and metabolic analysis of Setaria viridis leaves responding to aphid infestation was used to identify genes related to serotonin biosynthesis. Setaria viridis (green foxtail), a short life-cycle C4 plant in the Poaceae family, is the wild ancestor of Setaria italica (foxtail millet), a resilient crop that provides good yields in dry and marginal land. Although S. viridis has been studied extensively in the last decade, the molecular mechanisms of insect resistance in this species remain under-investigated. To address this issue, we performed a metabolic analysis of S. viridis and discovered that these plants accumulate the tryptophan-derived compounds tryptamine and serotonin. To elucidate the defensive functions of serotonin, Rhophalosiphum padi (bird cherry-oat aphids) were exposed to this compound, either by exogenous application to the plant medium or with artificial diet bioassays. In both cases, exposure to serotonin increased aphid mortality. To identify genes that are involved in serotonin biosynthesis, we conducted a transcriptome analysis and identified several predicted S. viridis tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) genes. Two candidate genes were ectopically expressed in Nicotiana tabacum, where SvTDC1 (Sevir.6G066200) had tryptophan decarboxylase activity, and SvT5H1 (Sevir.8G219600) had tryptamine hydroxylase activity. Moreover, the function of the SvTDC1 gene was validated using virus-induced gene silencing in S. italica, which caused a reduction in serotonin levels. This study provides the first evidence of serotonin biosynthesis in Setaria leaves. The biosynthesis of serotonin may play an important role in defense responses and could prove to be useful for developing more pest-tolerant Setaria italica cultivars.
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Affiliation(s)
- Anuma Dangol
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Reut Shavit
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Beery Yaakov
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | | | - Georg Jander
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel.
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20
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Beernink BM, Lappe RR, Bredow M, Whitham SA. Impacts of RNA Mobility Signals on Virus Induced Somatic and Germline Gene Editing. Front Genome Ed 2022; 4:925088. [PMID: 35755451 PMCID: PMC9219249 DOI: 10.3389/fgeed.2022.925088] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Viral vectors are being engineered to deliver CRISPR/Cas9 components systemically in plants to induce somatic or heritable site-specific mutations. It is hypothesized that RNA mobility signals facilitate entry of viruses or single guide RNAs (sgRNAs) into the shoot apical meristem where germline mutations can occur. Our objective was to understand the impact of RNA mobility signals on virus-induced somatic and germline gene editing in Nicotiana benthamiana and Zea mays. Previously, we showed that foxtail mosaic virus (FoMV) expressing sgRNA induced somatic mutations in N. benthamiana and Z. mays expressing Cas9. Here, we fused RNA mobility signals to sgRNAs targeting the genes encoding either N. benthamiana phytoene desaturase (PDS) or Z. mays high affinity potassium transporter 1 (HKT1). Addition of Arabidopsis thaliana Flowering Locus T (AtFT) and A. thaliana tRNA-Isoleucine (AttRNAIle) did not improve FoMV-induced somatic editing, and neither were sufficient to facilitate germline mutations in N. benthamiana. Maize FT homologs, Centroradialus 16 (ZCN16) and ZCN19, as well as AttRNAIle were found to aid somatic editing in maize but did not enable sgRNAs delivered by FoMV to induce germline mutations. Additional viral guide RNA delivery systems were assessed for somatic and germline mutations in N. benthamiana with the intention of gaining a better understanding of the specificity of mobile signal-facilitated germline editing. Potato virus X (PVX), barley stripe mosaic virus (BSMV), and tobacco rattle virus (TRV) were included in this comparative study, and all three of these viruses delivering sgRNA were able to induce somatic and germline mutations. Unexpectedly, PVX, a potexvirus closely related to FoMV, expressing sgRNA alone induced biallelic edited progeny, indicating that mobility signals are dispensable in virus-induced germline editing. These results show that PVX, BSMV, and TRV expressing sgRNA all have an innate ability to induce mutations in the germline. Our results indicate that mobility signals alone may not be sufficient to enable virus-based delivery of sgRNAs using the viruses, FoMV, PVX, BSMV, and TRV into cell types that result in germline mutations.
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Affiliation(s)
| | | | | | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
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21
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Xu XJ, Geng C, Jiang SY, Zhu Q, Yan ZY, Tian YP, Li XD. A maize triacylglycerol lipase inhibits sugarcane mosaic virus infection. PLANT PHYSIOLOGY 2022; 189:754-771. [PMID: 35294544 PMCID: PMC9157127 DOI: 10.1093/plphys/kiac126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 05/13/2023]
Abstract
Triacylglycerol lipase (TGL) plays critical roles in providing energy for seed germination and plant development. However, the role of TGL in regulating plant virus infection is largely unknown. In this study, we adopted affinity purification coupled with mass spectrometry and identified that a maize (Zea mays) pathogenesis-related lipase protein Z. mays TGL (ZmTGL) interacted with helper component-proteinase (HC-Pro) of sugarcane mosaic virus (SCMV). Yeast two-hybrid, luciferase complementation imaging, and bimolecular fluorescence complementation assays confirmed that ZmTGL directly interacted with SCMV HC-Pro in vitro and in vivo. The 101-460 residues of SCMV HC-Pro were important for its interaction with ZmTGL. ZmTGL and SCMV HC-Pro co-localized at the mitochondria. Silencing of ZmTGL facilitated SCMV infection, and over-expression of ZmTGL reduced the RNA silencing suppression activity, most likely through reducing HC-Pro accumulation. Our results provided evidence that the lipase hydrolase activity of ZmTGL was associated with reducing HC-Pro accumulation, activation of salicylic acid (SA)-mediated defense response, and inhibition of SCMV infection. We show that ZmTGL inhibits SCMV infection by reducing HC-Pro accumulation and activating the SA pathway.
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Affiliation(s)
- Xiao-Jie Xu
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Chao Geng
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Shao-Yan Jiang
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Qing Zhu
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Zhi-Yong Yan
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Yan-Ping Tian
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
- Author for correspondence:
| | - Xiang-Dong Li
- Department of Plant Pathology, College of Plant Protection, Laboratory of Plant Virology, Shandong Agricultural University, Tai’an, Shandong 271018, China
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22
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Tiedge K, Destremps J, Solano-Sanchez J, Arce-Rodriguez ML, Zerbe P. Foxtail mosaic virus-induced gene silencing (VIGS) in switchgrass (Panicum virgatum L.). PLANT METHODS 2022; 18:71. [PMID: 35644680 PMCID: PMC9150325 DOI: 10.1186/s13007-022-00903-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/07/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Although the genome for the allotetraploid bioenergy crop switchgrass (Panicum virgatum) has been established, limitations in mutant resources have hampered in planta gene function studies toward crop optimization. Virus-induced gene silencing (VIGS) is a versatile technique for transient genetic studies. Here we report the implementation of foxtail mosaic virus (FoMV)-mediated gene silencing in switchgrass in above- and below-ground tissues and at different developmental stages. RESULTS The study demonstrated that leaf rub-inoculation is a suitable method for systemic gene silencing in switchgrass. For all three visual marker genes, Magnesium chelatase subunit D (ChlD) and I (ChlI) as well as phytoene desaturase (PDS), phenotypic changes were observed in leaves, albeit at different intensities. Gene silencing efficiency was verified by RT-PCR for all tested genes. Notably, systemic gene silencing was also observed in roots, although silencing efficiency was stronger in leaves (~ 63-94%) as compared to roots (~ 48-78%). Plants at a later developmental stage were moderately less amenable to VIGS than younger plants, but also less perturbed by the viral infection. CONCLUSIONS Using FoMV-mediated VIGS could be achieved in switchgrass leaves and roots, providing an alternative approach for studying gene functions and physiological traits in this important bioenergy crop.
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Affiliation(s)
- Kira Tiedge
- Department of Plant Biology, University of California, Davis, USA.
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.
| | | | | | | | - Philipp Zerbe
- Department of Plant Biology, University of California, Davis, USA
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23
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Lee YJ, Kim JK, Baek SA, Yu JS, You MK, Ha SH. Differential Regulation of an OsIspH1, the Functional 4-Hydroxy-3-Methylbut-2-Enyl Diphosphate Reductase, for Photosynthetic Pigment Biosynthesis in Rice Leaves and Seeds. FRONTIERS IN PLANT SCIENCE 2022; 13:861036. [PMID: 35498655 PMCID: PMC9044040 DOI: 10.3389/fpls.2022.861036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/10/2022] [Indexed: 06/02/2023]
Abstract
The methylerythritol 4-phosphate (MEP) pathway is responsible for providing common precursors for the biosynthesis of diverse plastidial terpenoids, including chlorophylls, carotenoids, and phytohormones, in plants. In rice (Oryza sativa), the last-step genes encoding 4-hydroxy-3-methylbut-2-enyl diphosphate reductase [HDR/isoprenoid synthesis H (IspH)] have been annotated in two genes (OsIspH1 and OsIspH2) in the rice genome. The spatial transcript levels indicated that OsIspH1 is highly expressed in all tissues at different developmental stages, whereas OsIspH2 is barely expressed due to an early stop in exon 1 caused by splicing error. OsIspH1 localized into plastids and osisph1, a T-DNA inserted knockout mutant, showed an albino phenotype, indicating that OsIspH1 is the only functional gene. To elucidate the role of OsIspH1 in the MEP pathway, we created two single (H145P and K407R) and double (H145P/K407R) mutations and performed complementation tests in two hdr mutants, including Escherichia coli DLYT1 strains and osisph1 rice plants. The results showed that every single mutation retained HDR function, but a double mutation lost it, proposing that the complementary relations of two residues might be important for enzyme activity but not each residue. When overexpressed in rice plants, the double-mutated gene, OsIspH1MUT , reduced chlorophyll and carotenoid biosynthesis in the leaves and seeds. It confirmed the crucial role of OsIspH1 in plastidic terpenoid biosynthesis, revealing organ-specific differential regulation of OsIspH1 in rice plants.
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Affiliation(s)
- Yeo Jin Lee
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
| | - Jae Kwang Kim
- Division of Life Sciences, Bio-Resource and Environmental Center, Incheon National University, Incheon, South Korea
| | - Seung-A Baek
- Division of Life Sciences, Bio-Resource and Environmental Center, Incheon National University, Incheon, South Korea
| | - Ji-Su Yu
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
| | - Min Kyoung You
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
| | - Sun-Hwa Ha
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
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24
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Osorio CE, Till BJ. A Bitter-Sweet Story: Unraveling the Genes Involved in Quinolizidine Alkaloid Synthesis in Lupinus albus. FRONTIERS IN PLANT SCIENCE 2022; 12:795091. [PMID: 35154186 PMCID: PMC8826574 DOI: 10.3389/fpls.2021.795091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/30/2021] [Indexed: 05/05/2023]
Abstract
Alkaloids are part of a structurally diverse group of over 21,000 cyclic nitrogen-containing secondary metabolites that are found in over 20% of plant species. Lupinus albus are naturally containing quinolizidine alkaloid (QA) legumes, with wild accessions containing up to 11% of QA in seeds. Notwithstanding their clear advantages as a natural protecting system, lupin-breeding programs have selected against QA content without proper understanding of quinolizidine alkaloid biosynthetic pathway. This review summarizes the current status in this field, with focus on the utilization of natural mutations such as the one contained in pauper locus, and more recently the development of molecular markers, which along with the advent of sequencing technology, have facilitated the identification of candidate genes located in the pauper region. New insights for future research are provided, including the utilization of differentially expressed genes located on the pauper locus, as candidates for genome editing. Identification of the main genes involved in the biosynthesis of QA will enable precision breeding of low-alkaloid, high nutrition white lupin. This is important as plant based high quality protein for food and feed is an essential for sustainable agricultural productivity.
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Affiliation(s)
- Claudia E. Osorio
- Instituto de Investigaciones Agropecuarias, INIA Carillanca, Temuco, Chile
| | - Bradley J. Till
- Veterinary Genetics Laboratory, University of California, Davis, Davis, CA, United States
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25
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Kanyuka K. Virus-Mediated Protein Overexpression (VOX) in Monocots to Identify and Functionally Characterize Fungal Effectors. Methods Mol Biol 2022; 2523:93-112. [PMID: 35759193 DOI: 10.1007/978-1-0716-2449-4_7] [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] [Indexed: 06/15/2023]
Abstract
One of the important armories that pathogens utilize to successfully colonize the plants is small secreted effector proteins, which could perform a variety of functions from suppression of plant innate immunity to manipulation of plant physiology in favor of the disease. Plants, on the other hand, evolved disease resistance genes that recognize some of the effectors or avirulence (Avr) proteins. Both, identification of the Avr proteins and understanding of the mechanisms of action of other effectors, are important areas of research in the molecular plant-pathogen interactions field as this knowledge is critical for the development of new effective pathogen control measures. To enable functional analysis of the effectors, it is desirable to be able to overexpress them readily in the host plants. Here we describe detailed experimental protocols for transient effector overexpression in wheat and other monocots using binary Barley stripe mosaic virus (BSMV)- and Foxtail mosaic virus (FoMV)-derived vectors. This functional genomics tool, better known as VOX (Virus-mediated protein OvereXpression), is rapid and relatively simple and inexpensive.
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Affiliation(s)
- Kostya Kanyuka
- Plant Pathology and Entomology, NIAB, Cambridge, UK.
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.
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26
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Panwar V, Kanyuka K. Virus-Induced Gene Silencing in Wheat and Related Monocot Species. Methods Mol Biol 2022; 2408:95-107. [PMID: 35325418 DOI: 10.1007/978-1-0716-1875-2_6] [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] [Indexed: 06/14/2023]
Abstract
Advances made in genome sequencing projects and structural genomics are generating large repertoire of candidate genes in plants associated with specific agronomic traits. Rapid and high-throughput functional genomics approaches are therefore needed to validate the biological function of these genes especially for agronomically important crops beyond the few model plant species. This can be achieved by utilizing available gene knockout or transgenic methodologies, but these can take considerable time and effort particularly in crops with large and complex genomes such as wheat. Therefore, any tool that expedites the validation of gene function is of particular benefit especially in cereal crop plants that are genetically difficult to transform. One such reverse genetics tool is virus-induced gene silencing (VIGS) which relies on the plants' natural antiviral RNA silencing defence mechanism. VIGS is used to downregulate target gene expression in a transient manner which persists long enough to determine its effect on a specific trait. VIGS based on Barley stripe mosaic virus (BSMV) is rapid, powerful, efficient, and relatively inexpensive tool for the analysis of gene function in cereal species. Here we present detailed protocols for BSMV-mediated VIGS for robust gene silencing in bread wheat and related species.
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Affiliation(s)
- Vinay Panwar
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Kostya Kanyuka
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.
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27
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Zhou T, Dong L, Jiang T, Fan Z. Silencing Specific Genes in Plants Using Virus-Induced Gene Silencing (VIGS) Vectors. Methods Mol Biol 2022; 2400:149-161. [PMID: 34905199 DOI: 10.1007/978-1-0716-1835-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
As an efficient tool for functional genomics, VIGS (virus-induced gene silencing) has been widely used in reverse and forward genetics to identify genes involved in various biology processes in many plant species. Up to now, at least 50 VIGS vectors based on RNA viruses, DNA viruses or satellites have been developed for either dicots or monocots or both. Silencing specific genes using VIGS vector involves five major steps including, first, choosing an appropriate VIGS vector for the plant; second, selecting a fragment of targeted host gene; third, cloning the fragment into viral VIGS vector; forth, inoculating and infecting the appropriate plant; and fifth, quantifying silencing effects including recording silencing phenotypes and determining silencing efficiency of the target gene. In this chapter, we introduce these steps for VIGS assay in dicots and monocots, by taking a cucumber mosaic virus-based VIGS vector for Nicotiana benthamiana and maize plants as an example. Moreover, we list available VIGS vectors for monocots.
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Affiliation(s)
- Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China.
| | - Laihua Dong
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Tong Jiang
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zaifeng Fan
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China
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28
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Li H, Zhang D, Xie K, Wang Y, Liao Q, Hong Y, Liu Y. Efficient and high-throughput pseudorecombinant-chimeric Cucumber mosaic virus-based VIGS in maize. PLANT PHYSIOLOGY 2021; 187:2865-2876. [PMID: 34606612 PMCID: PMC8644855 DOI: 10.1093/plphys/kiab443] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/23/2021] [Indexed: 05/04/2023]
Abstract
Virus-induced gene silencing (VIGS) is a versatile and attractive approach for functional gene characterization in plants. Although several VIGS vectors for maize (Zea mays) have been previously developed, their utilities are limited due to low viral infection efficiency, insert instability, short maintenance of silencing, inadequate inoculation method, or abnormal requirement of growth temperature. Here, we established a Cucumber mosaic virus (CMV)-based VIGS system for efficient maize gene silencing that overcomes many limitations of VIGS currently available for maize. Using two distinct strains, CMV-ZMBJ and CMV-Fny, we generated a pseudorecombinant-chimeric (Pr) CMV. Pr CMV showed high infection efficacy but mild viral symptoms in maize. We then constructed Pr CMV-based vectors for VIGS, dubbed Pr CMV VIGS. Pr CMV VIGS is simply performed by mechanical inoculation of young maize leaves with saps of Pr CMV-infected Nicotiana benthamiana under normal growth conditions. Indeed, suppression of isopentenyl/dimethylallyl diphosphate synthase (ZmIspH) expression by Pr CMV VIGS resulted in non-inoculated leaf bleaching as early as 5 d post-inoculation (dpi) and exhibited constant and efficient systemic silencing over the whole maize growth period up to 105 dpi. Furthermore, utilizing a ligation-independent cloning (LIC) strategy, we developed a modified Pr CMV-LIC VIGS vector, allowing easy gene cloning for high-throughput silencing in maize. Thus, our Pr CMV VIGS system provides a much-improved toolbox to facilitate efficient and long-duration gene silencing for large-scale functional genomics in maize, and our pseudorecombination-chimera combination strategy provides an approach to construct efficient VIGS systems in plants.
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Affiliation(s)
- Huangai Li
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Danfeng Zhang
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Ke Xie
- Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
| | - Yan Wang
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qiansheng Liao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, Zhejiang, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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29
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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.
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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
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30
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Fei Y, Pyott DE, Molnar A. Temperature modulates virus-induced transcriptional gene silencing via secondary small RNAs. THE NEW PHYTOLOGIST 2021; 232:356-371. [PMID: 34185326 DOI: 10.1111/nph.17586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/17/2021] [Indexed: 05/08/2023]
Abstract
Virus-induced gene silencing (VIGS) can be harnessed to sequence-specifically degrade host transcripts and induce heritable epigenetic modifications referred to as virus-induced post-transcriptional gene silencing (ViPTGS) and virus-induced transcriptional gene silencing (ViTGS), respectively. Both ViPTGS and ViTGS enable manipulation of endogenous gene expression without the need for transgenesis. Although VIGS has been widely used in many plant species, it is not always uniform or highly efficient. The efficiency of VIGS is affected by developmental, physiological and environmental factors. Here, we use recombinant Tobacco rattle viruses (TRV) to study the effect of temperature on ViPTGS and ViTGS using GFP as a reporter gene of silencing in N. benthamiana 16c plants. We found that unlike ViPTGS, ViTGS was impaired at high temperature. Using a novel mismatch-small interfering RNA (siRNA) tool, which precisely distinguishes virus-derived (primary) from target-generated (secondary) siRNAs, we demonstrated that the lack of secondary siRNA production/amplification was responsible for inefficient ViTGS at 29°C. Moreover, inefficient ViTGS at 29°C inhibited the transmission of epigenetic gene silencing to the subsequent generations. Our finding contributes to understanding the impact of environmental conditions on primary and secondary siRNA production and may pave the way to design/optimize ViTGS for transgene-free crop improvement.
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Affiliation(s)
- Yue Fei
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Douglas E Pyott
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
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31
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Tuo D, Zhou P, Yan P, Cui H, Liu Y, Wang H, Yang X, Liao W, Sun D, Li X, Shen W. A cassava common mosaic virus vector for virus-induced gene silencing in cassava. PLANT METHODS 2021; 17:74. [PMID: 34247636 PMCID: PMC8273954 DOI: 10.1186/s13007-021-00775-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/01/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cassava is an important crop for food security and industry in the least-developed and developing countries. The completion of the cassava genome sequence and identification of large numbers of candidate genes by next-generation sequencing provide extensive resources for cassava molecular breeding and increase the need for rapid and efficient gene function analysis systems in cassava. Several plant virus-induced gene silencing (VIGS) systems have been developed as reverse genetic tools for rapid gene function analysis in cassava. However, these VIGS vectors could cause severe viral symptoms or inefficient gene silencing. RESULTS In this study, we constructed agroinfection-compatible infectious cDNA clones of cassava common mosaic virus isolate CM (CsCMV-CM, genus Potexvirus, family Alphaflexiviridae) that causes systemic infection with mild symptoms in cassava. CsCMV-CM was then modified to a viral vector carrying the Nimble cloning frame, which facilitates the rapid and high-throughput cloning of silencing fragments into the viral genome. The CsCMV-based vector successfully silenced phytoene desaturase (PDS) and magnesium chelatase subunit I (ChlI) in different cassava varieties and Nicotiana benthamiana. The silencing of the ChlI gene could persist for more than two months. CONCLUSIONS This CsCMV-based VIGS system provides a new tool for rapid and efficient gene function studies in cassava.
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Affiliation(s)
- Decai Tuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Peng Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Pu Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hongguang Cui
- College of Plant Protection, Hainan University, Haikou, 570228, China
| | - Yang Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- College of Horticulture, Hainan University, Haikou, 570228, China
| | - He Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- College of Horticulture, Hainan University, Haikou, 570228, China
| | - Xiukun Yang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- College of Horticulture, Hainan University, Haikou, 570228, China
| | - Wenbin Liao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Di Sun
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- College of Horticulture, Hainan University, Haikou, 570228, China
| | - Xiaoying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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Wang Y, Chai C, Khatabi B, Scheible WR, Udvardi MK, Saha MC, Kang Y, Nelson RS. An Efficient Brome mosaic virus-Based Gene Silencing Protocol for Hexaploid Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:685187. [PMID: 34220905 PMCID: PMC8253535 DOI: 10.3389/fpls.2021.685187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/07/2021] [Indexed: 05/09/2023]
Abstract
Virus-induced gene silencing (VIGS) is a rapid and powerful method to evaluate gene function, especially for species like hexaploid wheat that have large, redundant genomes and are difficult and time-consuming to transform. The Brome mosaic virus (BMV)-based VIGS vector is widely used in monocotyledonous species but not wheat. Here we report the establishment of a simple and effective VIGS procedure in bread wheat using BMVCP5, the most recently improved BMV silencing vector, and wheat genes PHYTOENE DESATURASE (TaPDS) and PHOSPHATE2 (TaPHO2) as targets. Time-course experiments revealed that smaller inserts (~100 nucleotides, nt) were more stable in BMVCP5 and conferred higher silencing efficiency and longer silencing duration, compared with larger inserts. When using a 100-nt insert and a novel coleoptile inoculation method, BMVCP5 induced extensive silencing of TaPDS transcript and a visible bleaching phenotype in the 2nd to 5th systemically-infected leaves from nine to at least 28 days post inoculation (dpi). For TaPHO2, the ability of BMVCP5 to simultaneously silence all three homoeologs was demonstrated. To investigate the feasibility of BMV VIGS in wheat roots, ectopically expressed enhanced GREEN FLUORESCENT PROTEIN (eGFP) in a transgenic wheat line was targeted for silencing. Silencing of eGFP fluorescence was observed in both the maturation and elongation zones of roots. BMVCP5 mediated significant silencing of eGFP and TaPHO2 mRNA expression in roots at 14 and 21 dpi, and TaPHO2 silencing led to the doubling of inorganic phosphate concentration in the 2nd through 4th systemic leaves. All 54 wheat cultivars screened were susceptible to BMV infection. BMVCP5-mediated TaPDS silencing resulted in the expected bleaching phenotype in all eight cultivars examined, and decreased TaPDS transcript was detected in all three cultivars examined. This BMVCP5 VIGS technology may serve as a rapid and effective functional genomics tool for high-throughput gene function studies in aerial and root tissues and in many wheat cultivars.
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33
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Genome-Wide Identification and Expression Analysis of the Histone Deacetylase Gene Family in Wheat ( Triticum aestivum L.). PLANTS 2020; 10:plants10010019. [PMID: 33374252 PMCID: PMC7823868 DOI: 10.3390/plants10010019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/20/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022]
Abstract
Histone acetylation is a dynamic modification process co-regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Although HDACs play vital roles in abiotic or biotic stress responses, their members in Triticumaestivum and their response to plant viruses remain unknown. Here, we identified and characterized 49 T. aestivumHDACs (TaHDACs) at the whole-genome level. Based on phylogenetic analyses, TaHDACs could be divided into 5 clades, and their protein spatial structure was integral and conserved. Chromosomal location and synteny analyses showed that TaHDACs were widely distributed on wheat chromosomes, and gene duplication has accelerated the TaHDAC gene family evolution. The cis-acting element analysis indicated that TaHDACs were involved in hormone response, light response, abiotic stress, growth, and development. Heatmaps analysis of RNA-sequencing data showed that TaHDAC genes were involved in biotic or abiotic stress response. Selected TaHDACs were differentially expressed in diverse tissues or under varying temperature conditions. All selected TaHDACs were significantly upregulated following infection with the barley stripe mosaic virus (BSMV), Chinese wheat mosaic virus (CWMV), and wheat yellow mosaic virus (WYMV), suggesting their involvement in response to viral infections. Furthermore, TaSRT1-silenced contributed to increasing wheat resistance against CWMV infection. In summary, these findings could help deepen the understanding of the structure and characteristics of the HDAC gene family in wheat and lay the foundation for exploring the function of TaHDACs in plants resistant to viral infections.
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Murphree C, Kim S, Karre S, Samira R, Balint‐Kurti P. Use of virus-induced gene silencing to characterize genes involved in modulating hypersensitive cell death in maize. MOLECULAR PLANT PATHOLOGY 2020; 21:1662-1676. [PMID: 33037769 PMCID: PMC7694674 DOI: 10.1111/mpp.12999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/28/2020] [Accepted: 09/04/2020] [Indexed: 05/22/2023]
Abstract
Plant disease resistance proteins (R-proteins) detect specific pathogen-derived molecules, triggering a defence response often including a rapid localized cell death at the point of pathogen penetration called the hypersensitive response (HR). The maize Rp1-D21 gene encodes a protein that triggers a spontaneous HR causing spots on leaves in the absence of any pathogen. Previously, we used fine mapping and functional analysis in a Nicotiana benthamiana transient expression system to identify and characterize a number of genes associated with variation in Rp1-D21-induced HR. Here we describe a system for characterizing genes mediating HR, using virus-induced gene silencing (VIGS) in a maize line carrying Rp1-D21. We assess the roles of 12 candidate genes. Three of these genes, SGT1, RAR1, and HSP90, are required for HR induced by a number of R-proteins across several plant-pathogen systems. We confirmed that maize HSP90 was required for full Rp1-D21-induced HR. However, suppression of SGT1 expression unexpectedly increased the severity of Rp1-D21-induced HR while suppression of RAR1 expression had no measurable effect. We confirmed the effects on HR of two genes we had previously validated in the N. benthamiana system, hydroxycinnamoyltransferase and caffeoyl CoA O-methyltransferase. We further showed the suppression the expression of two previously uncharacterized, candidate genes, IQ calmodulin binding protein (IQM3) and vacuolar protein sorting protein 37, suppressed Rp1-D21-induced HR. This approach is an efficient way to characterize the roles of genes modulating the hypersensitive defence response and other dominant lesion phenotypes in maize.
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Affiliation(s)
- Colin Murphree
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Saet‐Byul Kim
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Shailesh Karre
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Rozalynne Samira
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
- Fiber and Biopolymer Research Institute (FBRI)Department of Plant and Soil ScienceTexas Tech UniversityTexasUSA
| | - Peter Balint‐Kurti
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
- Plant Science Research UnitUSDA‐ARSRaleighNorth CarolinaUSA
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35
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Wang M, Gao S, Zeng W, Yang Y, Ma J, Wang Y. Plant Virology Delivers Diverse Toolsets for Biotechnology. Viruses 2020; 12:E1338. [PMID: 33238421 PMCID: PMC7700544 DOI: 10.3390/v12111338] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023] Open
Abstract
Over a hundred years of research on plant viruses has led to a detailed understanding of viral replication, movement, and host-virus interactions. The functions of vast viral genes have also been annotated. With an increased understanding of plant viruses and plant-virus interactions, various viruses have been developed as vectors to modulate gene expressions for functional studies as well as for fulfilling the needs in biotechnology. These approaches are invaluable not only for molecular breeding and functional genomics studies related to pivotal agronomic traits, but also for the production of vaccines and health-promoting carotenoids. This review summarizes the latest progress in these forefronts as well as the available viral vectors for economically important crops and beyond.
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Affiliation(s)
- Mo Wang
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Shilei Gao
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Wenzhi Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yongqing Yang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Junfei Ma
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39759, USA;
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39759, USA;
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36
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Zhang X, Kang L, Zhang Q, Meng Q, Pan Y, Yu Z, Shi N, Jackson S, Zhang X, Wang H, Tor M, Hong Y. An RNAi suppressor activates in planta virus-mediated gene editing. Funct Integr Genomics 2020; 20:471-477. [PMID: 31848794 DOI: 10.1007/s10142-019-00730-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/10/2019] [Accepted: 11/05/2019] [Indexed: 11/30/2022]
Abstract
RNA-guided CRISPR/Cas9 technology has been developed for gene/genome editing (GE) in organisms across kingdoms. However, in planta delivery of the two core GE components, Cas9 and small guide RNA (sgRNA), often involves time-consuming and labor-intensive production of transgenic plants. Here we show that Foxtail mosaic virus, a monocot- and dicot-infecting potexvirus, can simultaneously express Cas9, sgRNA, and an RNAi suppressor to efficiently induce GE in Nicotiana benthamiana through a transgenic plant-free manner.
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Affiliation(s)
- Xian Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Lihua Kang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Qi Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Qiqi Meng
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Yafei Pan
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Zhiming Yu
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Stephen Jackson
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK
| | - Xinlian Zhang
- Department of Family Medicine and Public Health, Division of Biostatistics & Bioinformatics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Mahmut Tor
- Department of Biology, School of Science and the Environment, Worcester-Hangzhou Joint Molecular Plant Health Laboratory, University of Worcester, Worcester, WR2 6AJ, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China.
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK.
- Department of Biology, School of Science and the Environment, Worcester-Hangzhou Joint Molecular Plant Health Laboratory, University of Worcester, Worcester, WR2 6AJ, UK.
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37
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Abstract
Virus-induced gene silencing (VIGS) is a powerful tool for rapidly knocking down the expression of plant genes to elucidate functional genomics. We have established a VIGS vector for monocot plants derived from Foxtail mosaic virus (FoMV), a positive-sense single-stranded RNA virus. For silencing a targeted gene, plant gene fragment was inserted into the vector between open reading frame 4 (ORF4) and ORF5 under the control of a duplicated coat protein promoter. Plants of different monocot species were infected by mechanical inoculation with sap from FoMV derivative-infected Chenopodium quinoa leaves. Gene silencing was typically observed within 2-3 weeks after inoculation. In this chapter, we describe the detailed protocol for silencing a target gene in various Poaceae plants by using FoMV-based vectors.
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38
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Abrahamian P, Hammond RW, Hammond J. Plant Virus-Derived Vectors: Applications in Agricultural and Medical Biotechnology. Annu Rev Virol 2020; 7:513-535. [PMID: 32520661 DOI: 10.1146/annurev-virology-010720-054958] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Major advances in our understanding of plant viral genome expression strategies and the interaction of a virus with its host for replication and movement, induction of disease, and resistance responses have been made through the generation of infectious molecules from cloned viral sequences. Autonomously replicating viral vectors derived from infectious clones have been exploited to express foreign genes in plants. Applications of virus-based vectors include the production of human/animal therapeutic proteins in plant cells and the specific study of plant biochemical processes, including those that confer resistance to pathogens. Additionally, virus-induced gene silencing, which is RNA mediated and triggered through homology-dependent RNA degradation mechanisms, has been exploited as an efficient method to study the functions of host genes in plants and to deliver small RNAs to insects. New and exciting strategies for vector engineering, delivery, and applications of plant virus-based vectors are the subject of this review.
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Affiliation(s)
- Peter Abrahamian
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705, USA
| | - Rosemarie W Hammond
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705, USA
| | - John Hammond
- Floral and Nursery Plants Research Unit, United States National Arboretum, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705, USA;
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39
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Mellado-Sánchez M, McDiarmid F, Cardoso V, Kanyuka K, MacGregor DR. Virus-Mediated Transient Expression Techniques Enable Gene Function Studies in Black-Grass. PLANT PHYSIOLOGY 2020; 183:455-459. [PMID: 32238443 PMCID: PMC7271810 DOI: 10.1104/pp.20.00205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/26/2020] [Indexed: 05/05/2023]
Abstract
Virus-mediated transient expression techniques create loss- and gain-of-function mutations in black-grass with genotype specificity and measurable changes in herbicide resistance.
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Affiliation(s)
- Macarena Mellado-Sánchez
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Faye McDiarmid
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Victor Cardoso
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Kostya Kanyuka
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Dana R MacGregor
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
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40
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Tiedge K, Muchlinski A, Zerbe P. Genomics-enabled analysis of specialized metabolism in bioenergy crops: current progress and challenges. Synth Biol (Oxf) 2020; 5:ysaa005. [PMID: 32995549 PMCID: PMC7445794 DOI: 10.1093/synbio/ysaa005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/03/2020] [Accepted: 05/25/2020] [Indexed: 11/25/2022] Open
Abstract
Plants produce a staggering diversity of specialized small molecule metabolites that play vital roles in mediating environmental interactions and stress adaptation. This chemical diversity derives from dynamic biosynthetic pathway networks that are often species-specific and operate under tight spatiotemporal and environmental control. A growing divide between demand and environmental challenges in food and bioenergy crop production has intensified research on these complex metabolite networks and their contribution to crop fitness. High-throughput omics technologies provide access to ever-increasing data resources for investigating plant metabolism. However, the efficiency of using such system-wide data to decode the gene and enzyme functions controlling specialized metabolism has remained limited; due largely to the recalcitrance of many plants to genetic approaches and the lack of 'user-friendly' biochemical tools for studying the diverse enzyme classes involved in specialized metabolism. With emphasis on terpenoid metabolism in the bioenergy crop switchgrass as an example, this review aims to illustrate current advances and challenges in the application of DNA synthesis and synthetic biology tools for accelerating the functional discovery of genes, enzymes and pathways in plant specialized metabolism. These technologies have accelerated knowledge development on the biosynthesis and physiological roles of diverse metabolite networks across many ecologically and economically important plant species and can provide resources for application to precision breeding and natural product metabolic engineering.
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Affiliation(s)
- Kira Tiedge
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
| | - Andrew Muchlinski
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
| | - Philipp Zerbe
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
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41
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Ahmed RI, Ren A, Yang D, Ding A, Kong Y. Identification and characterization of pectin related gene NbGAE6 through virus-induced gene silencing in Nicotiana benthamiana. Gene 2020; 741:144522. [PMID: 32145329 DOI: 10.1016/j.gene.2020.144522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 11/18/2022]
Abstract
Virus-induced gene silencing (VIGS) is a transient based reverse genetic tool used to elucidate the function of novel gene in N. benthamiana. In current study, 14 UDP-D-glucuronate 4-epimerase (GAE) family members were identified and their gene structure, phylogeny and expression pattern were analyzed. VIGS system was optimized for the functional characterization of NbGAE6 homologous genes in N. benthamiana. Whilst the GAE family is well-known for the interconversion of UDP-D-GlcA and UDP-D-GalA during pectin synthesis. Our results revealed that the downregulation of these genes significantly reduced the amount of GalA in the homogalacturunan which is the major component of pectin found in primary cell wall. Biphenyl assay and high performance liquid chromatography analysis (HPLC) depicted that the level of 'GalA' monosaccharide reduced to 40-51% in VIGS plants as compared to the wild type plants. Moreover, qRT-PCR also confirmed the downregulation of the NbGAE6 mRNA in VIGS plants. In all, this is the first comprehensive study of the optimization of VIGS system for the provision of rapid silencing of GAE family members in N. benthamiana, eliminating the need of stable transformants.
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Affiliation(s)
- Rana Imtiaz Ahmed
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Angyan Ren
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Dahai Yang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Kunming 650021, China
| | - Anming Ding
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Yingzhen Kong
- College of Agronomy, Qingdao Agricultural University, Qingdao 266108, China.
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42
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Ayre BG, El-Gebaly FE, McGarry RC. Virus-induced flowering-a tool for cereals. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2839-2841. [PMID: 32472691 DOI: 10.1093/jxb/eraa153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This article comments on:
Yuan C, Li H, Qin C, Zhang X, Chen Q, Zhang P, Xu X, He M, Zhang X, Tör M, Xue Dawei, Wang H, Jackson S, He Y, Liu Y, Shi N, Hong Y. 2020. Foxtail mosaic virus-induced flowering assays in monocot crops. Journal of Experimental Botany 71, 3012–3023.
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Affiliation(s)
- Brian G Ayre
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Fathy E El-Gebaly
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Roisin C McGarry
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA
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43
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Yuan C, Li H, Qin C, Zhang X, Chen Q, Zhang P, Xu X, He M, Zhang X, Tör M, Xue D, Wang H, Jackson S, He Y, Liu Y, Shi N, Hong Y. Foxtail mosaic virus-induced flowering assays in monocot crops. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3012-3023. [PMID: 32061090 DOI: 10.1093/jxb/eraa080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/11/2020] [Indexed: 05/04/2023]
Abstract
Virus-induced flowering (VIF) exploits RNA or DNA viruses to express flowering time genes to induce flowering in plants. Such plant virus-based tools have recently attracted widespread attention for their fundamental and applied uses in flowering physiology and in accelerating breeding in dicotyledonous crops and woody fruit-trees. We now extend this technology to a monocot grass and a cereal crop. Using a Foxtail mosaic virus (FoMV)-based VIF system, dubbed FoMViF, we showed that expression of florigenic Flowering Locus T (FT) genes can promote early flowering and spikelet development in proso millet, a C4 grass species with potential as a nutritional food and biofuel resource, and in non-vernalized C3 wheat, a major food crop worldwide. Floral and spikelet/grain induction in the two monocot plants was caused by the virally expressed untagged or FLAG-tagged FT orthologs, and the florigenic activity of rice Hd3a was more pronounced than its dicotyledonous counterparts in proso millet. The FoMViF system is easy to use and its efficacy to induce flowering and early spikelet/grain production is high. In addition to proso millet and wheat, we envisage that FoMViF will be also applicable to many economically important monocotyledonous food and biofuel crops.
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Affiliation(s)
- Chen Yuan
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Hongmei Li
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Cheng Qin
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xian Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qianqian Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaorui Xu
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Meiling He
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xinlian Zhang
- Department of Family Medicine and Public Health, Division of Biostatistics & Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Mahmut Tör
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
| | - Dawei Xue
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Stephen Jackson
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Yuehui He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yule Liu
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
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Sood P, Singh RK, Prasad M. An efficient Agrobacterium-mediated genetic transformation method for foxtail millet (Setaria italica L.). PLANT CELL REPORTS 2020; 39:511-525. [PMID: 31938834 DOI: 10.1007/s00299-019-02507-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/30/2019] [Indexed: 05/25/2023]
Abstract
A simple and robust Agrobacterium-mediated gene expression system in the C4 panicoid model crop, foxtail millet has been developed with up to 27 % transformation efficiency. Foxtail millet (Setaria italica L.) is a model crop to study C4 photosynthesis, abiotic stress tolerance, and bioenergy traits. Advances in molecular genetics and genomics had identified several potential genes in this crop that would serve as candidates for imparting climate-resilient traits in related millets, cereals, and biofuel crops. However, the lack of an efficient genetic transformation system has been impeding the functional characterization of these genes in foxtail millet per se. Given this, an easy and efficient regeneration and transformation protocol was optimized using mature seeds as a choicest explant. The suitability of secondary embryogenic calli over primary calli is underlined due to their high competence. The use of perfect combinations of plant growth regulators together with the ionic strength of organic and inorganics salts was found to influence regeneration and genetic transformation. We studied and optimized various crucial factors that affect the genetic transformation of foxtail millet calli using Agrobacterium tumefaciens-mediated approach. Secondary embryogenic calli and LBA44404 strain were found to be the best targets for transformation. The use of high sucrose and glucose, together with freshly prepared tobacco leaves extract, Silwet L-77 and acetosyringone, improved the efficiency of the genetic transformation of foxtail millet. Moreover, the use of an in vitro regeneration system with 84% callusing efficiency and 70-74% regeneration frequency led to a high recovery of transformants. Altogether, the present study reports a highly efficient (~ 27%) transformation system in foxtail millet that will expedite forward and reverse genetic studies in this important crop.
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Affiliation(s)
- Priyanka Sood
- 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
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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45
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Liu M, Liang Z, Aranda MA, Hong N, Liu L, Kang B, Gu Q. A cucumber green mottle mosaic virus vector for virus-induced gene silencing in cucurbit plants. PLANT METHODS 2020; 16:9. [PMID: 32025236 PMCID: PMC6996188 DOI: 10.1186/s13007-020-0560-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/23/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND Cucurbits produce fruits or vegetables that have great dietary importance and economic significance worldwide. The published genomes of at least 11 cucurbit species are boosting gene mining and novel breeding strategies, however genetic transformation in cucurbits is impractical as a tool for gene function validation due to low transformation efficiency. Virus-induced gene silencing (VIGS) is a potential alternative tool. So far, very few ideal VIGS vectors are available for cucurbits. RESULTS Here, we describe a new VIGS vector derived from cucumber green mottle mosaic virus (CGMMV), a monopartite virus that infects cucurbits naturally. We show that the CGMMV vector is competent to induce efficient silencing of the phytoene desaturase (PDS) gene in the model plant Nicotiana benthamiana and in cucurbits, including watermelon, melon, cucumber and bottle gourd. Infection with the CGMMV vector harboring PDS sequences of 69-300 bp in length in the form of sense-oriented or hairpin cDNAs resulted in photobleaching phenotypes in N. benthamiana and cucurbits by PDS silencing. Additional results reflect that silencing of the PDS gene could persist for over two months and the silencing effect of CGMMV-based vectors could be passaged. CONCLUSIONS These results demonstrate that CGMMV vector could serve as a powerful and easy-to-use tool for characterizing gene function, controlling viral pathogens or even performing resistance breeding in cucurbits. Moreover, this study will possess considerable important reference value for developing different viral vectors.
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Affiliation(s)
- Mei Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
- Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Zhiling Liang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
| | - Miguel A. Aranda
- Centro de Edafologia y Biologia Aplicada del Segura (CEBAS)-CSIC, Apdo. Correos 164, Espinardo, 30100 Murcia, Spain
| | - Ni Hong
- Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Liming Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
| | - Baoshan Kang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
| | - Qinsheng Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
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46
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Bomzan DP, Shilpashree HB, Anjali P, Kumar SR, Nagegowda DA. Virus-Induced Gene Silencing for Functional Genomics in Withania somnifera, an Important Indian Medicinal Plant. Methods Mol Biol 2020; 2172:139-154. [PMID: 32557367 DOI: 10.1007/978-1-0716-0751-0_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Virus-induced gene silencing (VIGS) has emerged as a fast and efficient reverse and forward genetics tool to study gene function in model plants as well as in agriculturally important plants. In addition, VIGS approach has been successfully used to provide insights into the role of several genes and regulators involved in plant secondary metabolism. Ashwagandha (Withania somnifera) is an important Indian medicinal plant that accumulates pharmacologically important triterpenoid steroidal lactones, which are collectively termed as withanolides. W. somnifera being a highly recalcitrant plant for genetic transformation, Tobacco rattle virus (TRV)-mediated VIGS was established by our group to facilitate understanding of withanolides' pathway. Here, we describe a detailed procedure to carry out VIGS for gene function studies in W. somnifera.
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Affiliation(s)
- Dikki Pedenla Bomzan
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants Research Centre, Bengaluru, India
| | - H B Shilpashree
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants Research Centre, Bengaluru, India
| | - P Anjali
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants Research Centre, Bengaluru, India
| | - Sarma Rajeev Kumar
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants Research Centre, Bengaluru, India
| | - Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants Research Centre, Bengaluru, India.
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47
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Li Z, Jiang Z, Yang X, Yue N, Wang X, Zhang K, Jackson AO, Li D, Zhang Y. Construction of an Infectious Poa semilatent virus cDNA Clone and Comparisons of Hordeivirus Cytopathology and Pathogenicity. PHYTOPATHOLOGY 2020; 110:215-227. [PMID: 31483225 DOI: 10.1094/phyto-06-19-0221-fi] [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] [Indexed: 06/10/2023]
Abstract
Poa semilatent virus (PSLV), Lychnis ringspot virus (LRSV), and Barley stripe mosaic virus (BSMV) are members of the genus Hordeivirus in the family Virgaviridae. However, the biological properties and molecular genetics of PSLV have not been compared with other hordeiviruses. Here, we have constructed an infectious cDNA clone of the PSLV Canadian strain and provided evidence that PSLV differs from BSMV and LRSV. First, unlike the other two hordeiviruses that replicate in chloroplasts, PSLV induces dramatic structural changes in peroxisome during its infection in barley. The αa replication protein also localizes to peroxisomes, suggesting that PSLV replication occurs in peroxisomes. Second, PSLV encodes a γb protein that shares 19 to 23% identity with those of other hordeiviruses, and its activity as a viral suppressor of RNA (VSR) silencing is distinct from those of BSMV and LRSV. Substitution of the BSMV γb protein with that of PSLV or LRSV revealed a negative correlation between VSR activity and symptom severity of the recombinant BSMV derivatives. Intriguingly, the Ser-Lys-Leu (SKL) peroxisome-targeting signals differ among γb proteins of various hordeiviruses, including some BSMV strains. The presence of the C-terminal SKL motif in the γb protein impairs its silencing suppressor activity and influences symptoms. Finally, we developed a PSLV-based virus-induced gene silencing vector that induced strong and effective silencing phenotypes of endogenous genes in barley, wheat, and millet. Our results shed new light on hordeivirus pathogenesis and evolution, and provide an alternative tool for genomics studies of model hosts and economically important monocots.
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Affiliation(s)
- Zhaolei Li
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhihao Jiang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xinxin Yang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ning Yue
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xueting Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Kun Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Andrew O Jackson
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, U.S.A
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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48
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Schachtsiek J, Hussain T, Azzouhri K, Kayser O, Stehle F. Virus-induced gene silencing (VIGS) in Cannabis sativa L. PLANT METHODS 2019; 15:157. [PMID: 31889981 PMCID: PMC6931244 DOI: 10.1186/s13007-019-0542-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/05/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND The raised demand of cannabis as a medicinal plant in recent years led to an increased interest in understanding the biosynthetic routes of cannabis metabolites. Since there is no established protocol to generate stable gene knockouts in cannabis, the use of a virus-induced gene silencing (VIGS) method, resulting in a gene knockdown, to study gene functions is desirable. RESULTS For this, a computational approach was employed to analyze the Cannabis sativa L. transcriptomic and genomic resources. Reporter genes expected to give rise to easily scorable phenotypes upon silencing, i.e. the phytoene desaturase (PDS) and magnesium chelatase subunit I (ChlI), were identified in C. sativa. Subsequently, the targets of specific small interfering RNAs (siRNAs) and silencing fragments were predicted and tested in a post-transcriptional gene silencing (PTGS) approach. Here we show for the first time a gene knockdown in C. sativa using the Cotton leaf crumple virus (CLCrV) in a silencing vector system. Plants transiently transformed with the Agrobacterium tumefaciens strain AGL1, carrying the VIGS-vectors, showed the desired phenotypes, spotted bleaching of the leaves. The successful knockdown of the genes was additionally validated by quantitative PCR resulting in reduced expression of transcripts from 70 to 73% for ChlI and PDS, respectively. This is accompanied with the reduction of the chlorophyll a and carotenoid content, respectively. In summary, the data clearly demonstrate the potential for functional gene studies in cannabis using the CLCrV-based vector system. CONCLUSIONS The applied VIGS-method can be used for reverse genetic studies in C. sativa to identify unknown gene functions. This will gain deeper inside into unknown biosynthetic routes and will help to close the gap between available genomic data and biochemical information of this important medicinal plant.
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Affiliation(s)
- Julia Schachtsiek
- Laboratory of Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Tajammul Hussain
- Laboratory of Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Khadija Azzouhri
- Laboratory of Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Oliver Kayser
- Laboratory of Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Felix Stehle
- Laboratory of Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
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49
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Mei Y, Beernink BM, Ellison EE, Konečná E, Neelakandan AK, Voytas DF, Whitham SA. Protein expression and gene editing in monocots using foxtail mosaic virus vectors. PLANT DIRECT 2019; 3:e00181. [PMID: 31768497 PMCID: PMC6874699 DOI: 10.1002/pld3.181] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/08/2019] [Accepted: 10/24/2019] [Indexed: 05/03/2023]
Abstract
Plant viruses can be engineered to carry sequences that direct silencing of target host genes, expression of heterologous proteins, or editing of host genes. A set of foxtail mosaic virus (FoMV) vectors was developed that can be used for transient gene expression and single guide RNA delivery for Cas9-mediated gene editing in maize, Setaria viridis, and Nicotiana benthamiana. This was accomplished by duplicating the FoMV capsid protein subgenomic promoter, abolishing the unnecessary open reading frame 5A, and inserting a cloning site containing unique restriction endonuclease cleavage sites immediately after the duplicated promoter. The modified FoMV vectors transiently expressed green fluorescent protein (GFP) and bialaphos resistance (BAR) protein in leaves of systemically infected maize seedlings. GFP was detected in epidermal and mesophyll cells by epifluorescence microscopy, and expression was confirmed by Western blot analyses. Plants infected with FoMV carrying the bar gene were temporarily protected from a glufosinate herbicide, and expression was confirmed using a rapid antibody-based BAR strip test. Expression of these proteins was stabilized by nucleotide substitutions in the sequence of the duplicated promoter region. Single guide RNAs expressed from the duplicated promoter mediated edits in the N. benthamiana Phytoene desaturase gene, the S. viridis Carbonic anhydrase 2 gene, and the maize HKT1 gene encoding a potassium transporter. The efficiency of editing was enhanced in the presence of synergistic viruses and a viral silencing suppressor. This work expands the utility of FoMV for virus-induced gene silencing (VIGS), virus-mediated overexpression (VOX), and virus-enabled gene editing (VEdGE) in monocots.
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Affiliation(s)
- Yu Mei
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Bliss M. Beernink
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Evan E. Ellison
- Department of Genetics, Cell Biology and DevelopmentCenter for Genome EngineeringCenter for Precision Plant GenomicsUniversity of MinnesotaSt. PaulMNUSA
| | - Eva Konečná
- Department of Genetics, Cell Biology and DevelopmentCenter for Genome EngineeringCenter for Precision Plant GenomicsUniversity of MinnesotaSt. PaulMNUSA
| | | | - Daniel F. Voytas
- Department of Genetics, Cell Biology and DevelopmentCenter for Genome EngineeringCenter for Precision Plant GenomicsUniversity of MinnesotaSt. PaulMNUSA
| | - Steven A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
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50
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Kant R, Dasgupta I. Gene silencing approaches through virus-based vectors: speeding up functional genomics in monocots. PLANT MOLECULAR BIOLOGY 2019; 100:3-18. [PMID: 30850930 DOI: 10.1007/s11103-019-00854-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 03/02/2019] [Indexed: 05/20/2023]
Abstract
The design and use of existing VIGS vectors for revealing monocot gene functions are described and potential new vectors are discussed, which may expand their repertoire. Virus induced gene silencing (VIGS) is a method of transient gene silencing in plants, triggered by the use of modified viral vectors. VIGS has found widespread use in deciphering the functions of plant genes, mainly for dicots. In the last decade, however, its use in monocots has increased noticeably, involving not only previously described viruses for monocots, but also those described for dicots. Additional viruses have been modified for VIGS to bring a larger collection of monocots under the ambit of this method. For monocots, new methods of inoculation have been tried to obtain increased silencing efficiency. The issue of insert stability and duration of silencing have also been addressed by various research groups. VIGS has been used to unravel the functions of a fairly large collection of monocot genes. This review summarizes the above developments, bringing out some of the gaps in our understanding and identifies directions to develop this technology further in the coming years.
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Affiliation(s)
- Ravi Kant
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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