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Li JW, Zeng T, Xu ZZ, Li JJ, Hu H, Yu Q, Zhou L, Zheng RR, Luo J, Wang CY. Ribozyme-mediated CRISPR/Cas9 gene editing in pyrethrum (Tanacetum cinerariifolium) hairy roots using a RNA polymerase II-dependent promoter. PLANT METHODS 2022; 18:32. [PMID: 35292048 PMCID: PMC8925089 DOI: 10.1186/s13007-022-00863-5] [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: 11/24/2021] [Accepted: 02/24/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Traditional CRISPR/Cas9 systems that rely on U6 or U3 snRNA promoters (RNA polymerase III-dependent promoters) can only achieve constitutive gene editing in plants, hampering the functional analysis of specifically expressed genes. Ribozyme-mediated CRISPR/Cas9 systems increase the types of promoters which can be used to transcribe sgRNA. Therefore, such systems allow specific gene editing; for example, transcription of the artificial gene Ribozyme-sgRNA-Ribozyme (RGR) is initiated by an RNA polymerase II-dependent promoter. Genetic transformation is indispensable for editing plant genes. In certain plant species, including pyrethrum, genetic transformation remains challenging to do, limiting the functional verification of novel CRISPR/Cas9 systems. Thus, this study's aim was to develop a simple Agrobacterium rhizogenes-mediated hairy root transformation system to analyze the function of a ribozyme-mediated CRISPR/Cas9 system in pyrethrum. RESULTS A hairy root transformation system for pyrethrum is described, with a mean transformation frequency of 7%. Transgenic hairy roots transformed with the pBI121 vector exhibited significantly increased beta-glucuronidase staining as a visual marker of transgene expression. Further, a ribozyme-based CRISPR/Cas9 vector was constructed to edit the TcEbFS gene, which catalyzes synthesis of the defense-related compound (E)-β-farnesene in pyrethrum. The vector was transferred into the hairy roots of pyrethrum and two stably transformed hairy root transgenic lines obtained. Editing of the TcEbFS gene in the hairy roots was evaluated by gene sequencing, demonstrating that both hairy root transgenic lines had DNA base loss at the editing target site. Gas chromatography-mass spectrometry showed that the (E)-β-farnesene content was significantly decreased in both hairy root transgenic lines compared with the empty vector control group. Altogether, these results show that RGR can be driven by the CaMV35S promoter to realize TcEbFS gene editing in pyrethrum hairy roots. CONCLUSION An A. rhizogenes-mediated hairy root transformation and ribozyme-mediated CRISPR/Cas9 gene editing system in pyrethrum was established, thereby facilitating gene editing in specific organs or at a particular developmental stage in future pyrethrum research.
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Affiliation(s)
- Jia-Wen Li
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tuo Zeng
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Zhi-Zhuo Xu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin-Jin Li
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Hu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin Yu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Zhou
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ri-Ru Zheng
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Luo
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Cai-Yun Wang
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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Multiple mutations across the succinate dehydrogenase gene complex are associated with boscalid resistance in Didymella tanaceti in pyrethrum. PLoS One 2019; 14:e0218569. [PMID: 31220147 PMCID: PMC6586343 DOI: 10.1371/journal.pone.0218569] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/04/2019] [Indexed: 11/19/2022] Open
Abstract
Failures in control of tan spot of pyrethrum, caused by Didymella tanaceti, has been associated with decreased sensitivity within the pathogen population to the succinate dehydrogenase inhibitor (SDHI) fungicide boscalid. Sequencing the SdhB, SdhC, and SdhD subunits of isolates with resistant and sensitive phenotypes identified 15 mutations, resulting in three amino acid substitutions in the SdhB (H277Y/R, I279V), six in the SdhC (S73P, G79R, H134R, H134Q, S135R and combined H134Q/S135R), and two in the SdhD (D112E, H122R). In vitro testing of their boscalid response and estimation of resistance factors (RF) identified isolates with wild-type (WT) Sdh genotypes were sensitive to boscalid. Isolates with SdhB-I279V, SdhC-H134Q and SdhD-D112E exhibited moderate resistance phenotypes (10 ≥ RF < 100) and isolates with SdhC-H134R exhibited very high resistance phenotypes (RF ≥ 1000). All other substitutions were associated with high resistance phenotypes (100 ≥ RF < 1000). High-resolution melt assays were designed and used to estimate the frequencies of substitutions in four field populations (n = 774) collected in August (pre-boscalid application) and November (post-boscalid application) 2012. The SdhB-H277Y, SdhC-H134R and SdhB-H277R genotypes were most frequently observed across populations at 56.7, 19.0, and 10.3%, respectively. In August 92.9% of D. tanaceti contained a substitution associated with decreased sensitivity. Following boscalid application, this increased to 98.9%, with no WT isolates detected in three fields. Overlaying previously obtained microsatellite and mating-type data revealed that all ten recurrent substitutions were associated with multiple genotypes. Thus, boscalid insensitivity in D. tanaceti appears widespread and not associated with clonal spread of a limited pool of individuals.
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Scott JB, Gent DH, Pearce TL, Pethybridge SJ, Pilkington SJ, Hay FS. Mycoflora Associated With Pyrethrum Seed and the Integration of Seed Steam Treatment Into Foliar Disease Management Strategies. PLANT DISEASE 2017; 101:1874-1884. [PMID: 30677321 DOI: 10.1094/pdis-03-17-0309-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A complex of foliar diseases can affect pyrethrum in Australia, but those of greatest importance are ray blight, caused by Stagonosporopsis tanaceti, and tan spot, caused primarily by Didymella tanaceti. Isolation of fungi from pyrethrum seed lots produced over 15 years resulted in recovery of six known pathogens: S. tanaceti, D. tanaceti, Alternaria tenuissima, Colletotrichum tanaceti, Stemphylium botryosum, and Botrytis cinerea. The incidence of S. tanaceti and D. tanaceti isolated from seed varied between 0.9 and 19.5% (mean = 7.7%) and 0 and 24.1% (mean = 5.3%) among years, respectively. Commercial heat treatment of pyrethrum seed via steaming reduced the incidence of D. tanaceti from 10.9 to 0.06% and the incidence of S. tanaceti from 24.6% to nondetectable levels (<0.18%). In a second experiment, both species were reduced to nondetectable levels (<0.20%) from their initial incidences of 22.4 and 2.4%, respectively. In a field study in 2013, colonization of pyrethrum foliage by S. tanaceti was reduced from 21.1 to 14.3% in early winter when heat-treated seed was planted. However, isolation frequency of D. tanaceti was not affected significantly by seed treatment in this year. In a related experiment in 2015, the isolation frequency of D. tanaceti in plots planted from heat-treated seed depended on both prior application of an industry-standard fungicide program and proximity to another pyrethrum field in autumn. The fungus was recovered at a similar frequency in fungicide-treated and nontreated plots located near other pyrethrum fields (13.8 versus 16.3%, respectively), whereas recovery of the pathogen was reduced by fungicide applications in geographically remote pyrethrum fields (6.7 versus 1.4%, respectively). However, these differences in isolation frequency of D. tanaceti in autumn did not obviate the need for later fungicide applications to suppress foliar disease intensity in spring or flower yield in summer, independent of the proximity to other pyrethrum fields. This study suggests that steam treatment of seed can delay development of the foliar disease complex on pyrethrum, although an extremely low level of remaining infected seed or exogenous sources of inoculum necessitates the use of foliar fungicide applications in spring.
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Affiliation(s)
- Jason B Scott
- Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, Tasmania 7320, Australia
| | - David H Gent
- United States Department of Agriculture - Agricultural Research Services (USDA-ARS), Forage Seed and Cereal Research Unit, and Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - Tamieka L Pearce
- Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, Tasmania 7320, Australia
| | - Sarah J Pethybridge
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Stacey J Pilkington
- Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, Tasmania 7320, Australia
| | - Frank S Hay
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
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Hay FS, Gent DH, Pilkington SJ, Pearce TL, Scott JB, Pethybridge SJ. Changes in Distribution and Frequency of Fungi Associated With a Foliar Disease Complex of Pyrethrum in Australia. PLANT DISEASE 2015; 99:1227-1235. [PMID: 30695926 DOI: 10.1094/pdis-12-14-1357-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In Australia, pyrethrum (Tanacetum cinerariifolium) is affected by a foliar disease complex that can substantially reduce green leaf area and yield. Historically, the most important foliar disease of pyrethrum in Australia has been ray blight, caused by Stagonosporopsis tanaceti, and other fungi generally of minor importance. Temporal fluctuations in the frequency of fungi associated with foliar disease were quantified in each of 83 fields in northern Tasmania, Australia, during 2012 and 2013. Sampling was conducted throughout winter (April to July), spring (August to September), and summer (November) representing different phenological stages. Microsphaeropsis tanaceti, the cause of tan spot, was the pathogen most prevalent and isolated at the highest frequency, irrespective of sampling period. The next most common species was S. tanaceti, whose isolation frequency was low in winter and increased in spring and summer. Known pathogens of pyrethrum, Alternaria tenuissima, Colletotrichum tanaceti, and Stemphylium botryosum were recovered sporadically and at low frequency. Two species of potential importance, Paraphoma chrysanthemicola and Itersonilia perplexans, were also found at low frequency. This finding suggests a substantial shift in the dominant pathogen associated with foliar disease, from S. tanaceti to M. tanaceti, and coincides with an increase in defoliation severity in winter, and control failures of the spring fungicide program. Factors associated with this finding were also investigated. Sensitivity of M. tanaceti and S. tanaceti populations to the fungicides boscalid and cyprodinil collected prior to and following disease control failures in the field were tested under in vitro conditions. A high proportion (60%) of the M. tanaceti isolates obtained from fields in which no response to the spring fungicide program was found were insensitive to 50 µg a.i./ml boscalid. This represented a 4.2-fold increase in the frequency of this phenotype within the M. tanaceti population over 2 years. No shifts in sensitivities to cyprodinil of M. tanaceti and S. tanaceti, or S. tanaceti to boscalid, were observed. Considering the increase in defoliation severity over winter, the benefits of applying fungicides in autumn, in addition to the commercial standard (spring only), were quantified in 14 individual field trials conducted in 2011 and 2012. Mixed-model analysis suggested fungicide application in autumn may improve pyrethrum growth during late winter and early spring, although effects on defoliation and yield were minimal. The increasing prevalence and isolation frequency of M. tanaceti and boscalid resistance within the population is of concern and highlights the urgent need for adoption of nonchemical methods for disease management in Australian pyrethrum fields.
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Affiliation(s)
- Frank S Hay
- Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, 7320, Australia
| | - David H Gent
- United States Department of Agriculture - Agricultural Research Services (USDA-ARS), Forage Seed and Cereal Research Unit, and Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - Stacey J Pilkington
- Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, 7320, Australia
| | - Tamieka L Pearce
- Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, 7320, Australia
| | - Jason B Scott
- Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, 7320, Australia
| | - Sarah J Pethybridge
- Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Geneva, NY 14456
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Vaghefi N, Hay FS, Ades PK, Pethybridge SJ, Ford R, Taylor PWJ. Rapid Changes in the Genetic Composition of Stagonosporopsis tanaceti Population in Australian Pyrethrum Fields. PHYTOPATHOLOGY 2015; 105:358-369. [PMID: 25226524 DOI: 10.1094/phyto-08-14-0212-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A novel set of microsatellite markers were developed and employed for geographical and temporal population analyses of Stagonosporopsis tanaceti, the cause of ray blight of pyrethrum in Australia. Genotyping of 407 isolates, using 13 markers, suggested an asexual mode of reproduction with significant linkage disequilibrium and high levels of clonality. Low geographical differentiation and widespread distribution of a few multilocus genotypes (MLGs), in the absence of airborne ascospores, suggested the role of human-mediated movement of seed as a major means of long-distance pathogen dispersal. The genetic composition of S. tanaceti was stable for a decade then changed rapidly in only 2 years. Bayesian clustering analyses and minimum spanning networks determined only two major clonal lineages in and prior to 2010. However, in 2012, a previously unobserved cluster of MLGs was detected, which significantly increased in frequency and displaced the historically dominant MLGs by 2013. This rapid change in the genetic composition of S. tanaceti could indicate a second introduction then a selective sweep, or strong selection pressures from recently introduced fungicides or pyrethrum varieties. These results may have serious implications for durability of management strategies for this disease.
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Scott JB, Gent DH, Pethybridge SJ, Groom T, Hay FS. Crop Damage from Sclerotinia Crown Rot and Risk Factors in Pyrethrum. PLANT DISEASE 2014; 98:103-111. [PMID: 30708595 DOI: 10.1094/pdis-06-13-0599-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sclerotinia crown rot, caused by Sclerotinia sclerotiorum and S. minor, is a prevalent disease in pyrethrum fields in Australia. Management involves fungicide applications during the rosette stage of plant development from autumn to early spring in fields approaching first harvest. However, estimates of crop damage and the efficacy of these tactics are poorly understood; therefore, plots were established in 86 pyrethrum fields in Tasmania, Australia during 2010 to 2012 to quantify these and to identify risk factors for disease outbreaks. On average, commercial management for Sclerotinia crown rot reduced disease incidence 43 to 67% compared with nontreated plots. There was a weak but significant relationship between relative increase in flower yield when fungicides were applied and the incidence of crown rot (R2 = 0.09, P = 0.006), although the mean number of flowers produced was similar regardless of fungicide applications. Flower yield was positively associated with canopy density in spring (S = 0.39, P = 0.001). Moreover, canopy density in spring was linked by both direct and indirect effects to canopy density during autumn and winter which, in turn, were associated with planting date and previous rain events. Modeling canopy density and disease incidence in autumn correctly categorized disease incidence in spring relative to a threshold of 2% in 72% of fields. In a subset of 22 fields monitored over 2 years, canopy density in the autumn following the first harvest had a negative relationship with Sclerotinia crown rot incidence the preceding year (R2 = 0.23, P = 0.006). On average, however, current commercial management efforts provided only small increases in flower yield in the current season and appear best targeted to fields with well-developed plant canopies and Sclerotinia crown rot present during early autumn.
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Affiliation(s)
- Jason B Scott
- Tasmanian Institute of Agriculture (TIA), University of Tasmania-Cradle Coast Campus, Burnie, Tasmania, 7320, Australia
| | - David H Gent
- United States Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331
| | - Sarah J Pethybridge
- The New Zealand Institute of Plant and Food Research Ltd., Private Bag 4704, Lincoln, Christchurch, New Zealand
| | - Tim Groom
- Botanical Resources Australia-Agricultural Services Pty. Ltd., Ulverstone, Tasmania, Australia
| | - Frank S Hay
- TIA, University of Tasmania-Cradle Coast Campus
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