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Zhao N, Yuan R, Usman B, Qin J, Yang J, Peng L, Mackon E, Liu F, Qin B, Li R. Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice ( Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1. Biomolecules 2022; 12:biom12121850. [PMID: 36551278 PMCID: PMC9775987 DOI: 10.3390/biom12121850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient's genetic background. CSSLs are an ideal genetic population for mapping quantitative traits loci (QTLs). In this study, 59 CSSLs from the common wild rice (Oryza rufipogon Griff.) accession DP15 under the indica rice cultivar (O. sativa L. ssp. indica) variety 93-11 background were constructed through multiple backcrosses and marker-assisted selection (MAS). Through high-throughput whole genome re-sequencing (WGRS) of parental lines, 12,565 mapped InDels were identified and designed for polymorphic molecular markers. The 59 CSSLs library covered 91.72% of the genome of common wild rice accession DP15. The DP15-CSSLs displayed variation in six economic traits including grain length (GL), grain width (GW), thousand-grain weight (TGW), grain length-width ratio (GLWR), plant height (PH), and leaf margin color (LMC), which were finally attributed to 22 QTLs. A homozygous CSSL line and a purple leave margin CSSL line were selected to construct two secondary genetic populations for the QTLs mapping. Thus, the PH-controlling QTL qPH1.1 was mapped to a region of 4.31-Mb on chromosome 1, and the LMC-controlling QTL qLMC6.1 was mapped to a region of 370-kb on chromosome 6. Taken together, these identified novel QTLs/genes from common wild rice can potentially promote theoretical knowledge and genetic applications to rice breeders worldwide.
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Affiliation(s)
- Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ruizhi Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Babar Usman
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jiaming Qin
- Maize Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China
| | - Jinlian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Liyun Peng
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- Correspondence:
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Liu X, Strelkov SE, Sun R, Hwang SF, Fredua-Agyeman R, Li F, Zhang S, Li G, Zhang S, Zhang H. Histopathology of the Plasmodiophora brassicae-Chinese Cabbage Interaction in Hosts Carrying Different Sources of Resistance. FRONTIERS IN PLANT SCIENCE 2022; 12:783550. [PMID: 35095958 PMCID: PMC8792839 DOI: 10.3389/fpls.2021.783550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/14/2021] [Indexed: 05/07/2023]
Abstract
Clubroot is a serious soil-borne disease of crucifers caused by the obligate parasite Plasmodiophora brassicae. The genetic basis and histopathology of clubroot resistance in two Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines Bap055 and Bap246, challenged with pathotype 4 of P. brassicae, was evaluated. The Chinese cabbage cultivar "Juxin" served as a susceptible check. The resistance in Bap055 was found to be controlled by the CRa gene, while resistance in Bap246 fit a model of control by unknown recessive gene. Infection of the roots by P. brassicae was examined by inverted microscopy. Despite their resistance, primary and secondary infection were observed to occur in Bap055 and Bap246. Primary infection was detected at 2 days post-inoculation (DPI) in "Juxin," at 4 DPI in Bap055, and at 6 DPI in Bap246. Infection occurred most quickly on "Juxin," with 60% of the root hairs infected at 10 DPI, followed by Bap055 (31% of the root hairs infected at 12 DPI) and Bap246 (20% of the root hairs infected at 14 DPI). Secondary infection of "Juxin" was first observed at 8 DPI, while in Bap055 and Bap246, secondary infection was first observed at 10 DPI. At 14 DPI, the percentage of cortical infection in "Juxin," Bap055 and Bap246 was 93.3, 20.0, and 11.1%, respectively. Although cortical infection was more widespread in Bap055 than in Bap246, secondary infection in both of these hosts was restricted relative to the susceptible check, and the vascular system remained intact. A large number of binucleate secondary plasmodia were observed in "Juxin" and the vascular system was disrupted at 16 DPI; in Bap055 and Bap246, only a few secondary plasmodia were visible, with no binucleate secondary plasmodia. The defense mechanisms and expression of resistance appears to differ between Chinese cabbage cultivars carrying different sources of resistance.
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Affiliation(s)
- Xitong Liu
- Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Stephen E. Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Rifei Sun
- Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sheau-Fang Hwang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Rudolph Fredua-Agyeman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Fei Li
- Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shifan Zhang
- Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoliang Li
- Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shujiang Zhang
- Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhang
- Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing, China
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Song T, Zhou M, Yuan Y, Yu J, Cai H, Li J, Chen Y, Bai Y, Zhou G, Cui G. Chromosome-Scale Reference Genome of Amphicarpaea edgeworthii: A New Resource for Amphicarpic Plants Research and Complex Flowering Pattern. FRONTIERS IN PLANT SCIENCE 2021; 12:770660. [PMID: 34868169 PMCID: PMC8637744 DOI: 10.3389/fpls.2021.770660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Amphicarpaea edgeworthii, an annual twining herb, is a widely distributed species and an attractive model for studying complex flowering types and evolutionary mechanisms of species. Herein, we have generated a high-quality assembly of A. edgeworthii by using a combination of PacBio, 10× Genomics libraries, and Hi-C mapping technologies. The final 11 chromosome-level scaffolds covered 90.61% of the estimated genome (343.78Mb), which is a chromosome-scale assembled genome of an amphicarpic plant. Subsequently, we characterized the genetic diversity and population structure of A. edgeworthii species by resequencing individuals collected from their natural area of distribution. Using transcriptome profiling, we observed that specific phenotypes are regulated by a complex network of light, hormones, and MADS-box gene families. These data are beneficial for the discovery of genes that control major agronomic traits and spur genetic improvement of and functional genetic studies in legumes, as well as supply comparative genetic resources for other amphicarpic plants.
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Affiliation(s)
- Tingting Song
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Yuying Yuan
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jinqiu Yu
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hua Cai
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jiawei Li
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yajun Chen
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yan Bai
- Novogene Bioinformatics Institute, Beijing, China
| | - Gang Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Guowen Cui
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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Hariharan G, Prasannath K. Recent Advances in Molecular Diagnostics of Fungal Plant Pathogens: A Mini Review. Front Cell Infect Microbiol 2021; 10:600234. [PMID: 33505921 PMCID: PMC7829251 DOI: 10.3389/fcimb.2020.600234] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/25/2020] [Indexed: 12/18/2022] Open
Abstract
Phytopathogenic fungal species can cause enormous losses in quantity and quality of crop yields and this is a major economic issue in the global agricultural sector. Precise and rapid detection and identification of plant infecting fungi are essential to facilitate effective management of disease. DNA-based methods have become popular methods for accurate plant disease diagnostics. Recent developments in standard and variant polymerase chain reaction (PCR) assays including nested, multiplex, quantitative, bio and magnetic-capture hybridization PCR techniques, post and isothermal amplification methods, DNA and RNA based probe development, and next-generation sequencing provide novel tools in molecular diagnostics in fungal detection and differentiation fields. These molecular based detection techniques are effective in detecting symptomatic and asymptomatic diseases of both culturable and unculturable fungal pathogens in sole and co-infections. Even though the molecular diagnostic approaches have expanded substantially in the recent past, there is a long way to go in the development and application of molecular diagnostics in plant diseases. Molecular techniques used in plant disease diagnostics need to be more reliable, faster, and easier than conventional methods. Now the challenges are with scientists to develop practical techniques to be used for molecular diagnostics of plant diseases. Recent advancement in the improvement and application of molecular methods for diagnosing the widespread and emerging plant pathogenic fungi are discussed in this review.
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Affiliation(s)
- Ganeshamoorthy Hariharan
- Department of Agricultural Biology, Faculty of Agriculture, Eastern University, Chenkalady, Sri Lanka
| | - Kandeeparoopan Prasannath
- Department of Agricultural Biology, Faculty of Agriculture, Eastern University, Chenkalady, Sri Lanka
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Li Q, Zhao T, Liang L, Hou S, Wang G, Ma Q. Molecular cloning and expression analysis of hybrid hazelnut (Corylus heterophylla × Corylus avellana) ChaSRK1/2 genes and their homologs from other cultivars and species. Gene 2020; 756:144917. [PMID: 32590104 DOI: 10.1016/j.gene.2020.144917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 05/22/2020] [Accepted: 06/17/2020] [Indexed: 12/01/2022]
Abstract
The self-incompatibility system of Corylus is a sporophytic type that is phenotypically similar to that of Brassica. While the molecular mechanism of sporophytic self-incompatibility (SSI) has been investigated extensively in Brassica (Brassicaceae), little is known about the corresponding mechanism in Corylus (Betulaceae). Here, we discuss the SSI mechanism with respect to S-locus receptor kinase (SRK) gene homologs. To obtain two SRK candidate unigenes, we compared all of the unigenes in a transcriptional protein database from our previous study with BnSRK-1 (AB270767) using BLASTX with a cutoff e-value of 10-5. We then cloned the full-length cDNA of ChaSRK1 and ChaSRK2 genes from Ping'ou hybrid hazelnut (Corylus heterophylla × Corylus avellana) using RACE techniques. Bioinformatics approaches were used to analyze the cDNA sequences, protein sequences, and domains of the encoded proteins. The full-length ChaSRK1 cDNA was 2883 base pairs (bp) with a coding sequence (CDS) of 2,547 bp encoding 849 amino acid residues. The full-length ChaSRK2 cDNA was 2,693 bp, with a CDS of 2,433 bp encoding 811 amino acids. The ChaSRK1/2 proteins contained an S-domain (extracellular domain), a transmembrane domain, a Ser/Thr protein kinase active site (kinase domain), and DUF3660 and/or DUF3403 domains. The lengths of 18 partial SRK homologs ranged from 1347 to 1451 bp, and they contained the same structural domains as ChaSRK1 and ChaSRK2. Phylogenetic analysis revealed that all SRK homologs could be divided into two categories that were similar to the classification of SRKs in Brassica. The expression patterns of ChaSRK1 and ChaSRK2 differed: ChaSRK2 was predominantly expressed in mature stigmatic styles, while ChaSRK1 was expressed in other tissues with the highest in the root tips of Corylus. Using dual-color fluorescence in situ hybridization, ChaSRK1/2 expression was found to be localized in papillar cells. Collectively, these results revealed that SRKs from Corylus had similar characteristics to SRKs from Brassica. We therefore speculated that the SSI mechanism in Corylus might be more similar to the Brassica mechanism than to other SSI types.
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Affiliation(s)
- Qing Li
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China
| | - Tiantian Zhao
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China
| | - Lisong Liang
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China
| | - Sihao Hou
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China
| | - Guixi Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China
| | - Qinghua Ma
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China.
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Shao J, Liu Z, Ding Y, Wang J, Li X, Yang Y. Biosynthesis of the starch is improved by the supplement of nickel (Ni 2+) in duckweed (Landoltia punctata). JOURNAL OF PLANT RESEARCH 2020; 133:587-596. [PMID: 32458160 DOI: 10.1007/s10265-020-01204-0] [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] [Received: 02/12/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Duckweed is a kind of floating aquatic plant and increasing its starch production is favorable for bioenergy. In this study, we found that starch biosynthesis was greatly promoted by the supplement of nickel ion (Ni2+) through the comparison of other different ions. The starch content in duckweed was increased by nearly eightfold when duckweed was treated with 20 µM Ni2+. The analysis of paraffin sections visually found that starch granules were more complete and dark blue in Ni2+ treated duckweed than the control. Quantitative real-time PCR demonstrated that the expressions of starch synthesis-related enzymes were up-regulated in Ni2+ treated duckweed. Further analysis revealed that the accumulation of Ni2+ in duckweed effectively increased the activity of urease, which compensated for the deficiency of certain decrease in biomass and accelerated biosynthesis of the starch. Thus, our results represent another strategy to improve starch production of duckweed.
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Affiliation(s)
- Jin Shao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhibin Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yongqiang Ding
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jianmei Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xufeng Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yi Yang
- College of Life Sciences, Sichuan University , Chengdu, 610064, China.
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Molecular Approaches for Analyzing Environmental Chaetomium Diversity and Exploitation of Chaetomium thermophilum for Biochemical Analyses. Fungal Biol 2020. [DOI: 10.1007/978-3-030-31612-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Li C, Hu S, Lei Q, Wang C, Yang Y, Yang Y, Sun X. Establishment and optimization of mRNA in situ hybridization system in turnip ( Brassica rapa var . rapa). PLANT METHODS 2019; 15:115. [PMID: 31636692 PMCID: PMC6794860 DOI: 10.1186/s13007-019-0499-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/09/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND In situ hybridization (ISH) is a general molecular biological technique used to determine the spatiotemporal expression of genes in many species. In the past few years, numerous ISH protocols have been established in many species. Turnip (Brassica rapa var. rapa) is an important crop in the world, especially in the Plateau area of China, and is a traditional Tibetan medicine. However, ISH protocol in turnip has not been established. RESULTS We explored and established an optimal workflow for mRNA ISH system for turnip which has been evaluated using BrrCLV3 and BrrWUSa. The optimal methods include: (1) fixation method, (2) protease K pretreatment time, (3) probe length and concentration, (4) washing temperature. We also provide advice on weakening background and improving the efficiency of RNA transcription in vitro. The expression of the BrrCLV3 gene in turnip was detected by the optimized system, and the applicability of the system was confirmed by using BrrWUSa. CONCLUSIONS In this study, we established and optimized the mRNA ISH system for turnip. We explored and found that (1) FAA fixative was the optimized fixation method, (2) 30 min was the optimized protease K pretreatment time, (3) 100 bp, 100 ng/ml probe had good hybridization signal, (4) the optimized washing temperature was 52 °C. It provides a powerful method to locate mRNA in the tissue, which can study the expression and function of turnip's genes. As such, it has considerable advantages in terms of time and cost.
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Affiliation(s)
- Cheng Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Simin Hu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qidong Lei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan China
| | - Chongde Wang
- College of Plant Protection, Yunnan Agriculture University, Kunming, 650201 China
| | - Yunqiang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Yongping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Xudong Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
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Salgado-Salazar C, Bauchan GR, Wallace EC, Crouch JA. Visualization of the impatiens downy mildew pathogen using fluorescence in situ hybridization (FISH). PLANT METHODS 2018; 14:92. [PMID: 30386410 PMCID: PMC6199785 DOI: 10.1186/s13007-018-0362-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/19/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plasmopara obducens is the biotrophic oomycete responsible for impatiens downy mildew, a destructive disease of Impatiens that causes high crop loss. Currently, there are no available methods for the microscopic detection of P. obducens from leaves of impatiens, which may be contributing to the spread of the disease. Fluorescence in situ hybridization (FISH) is a sensitive and robust method that uses sequence-specific, fluorescence-labeled oligonucleotide probes to detect target organisms from the environment. To study this important pathogen, we developed and standardized a FISH technique for the visualization of P. obducens from Impatiens walleriana tissues using a species-specific 24-mer oligonucleotide probe designed to target a region of the rRNA internal transcribed spacer 2 (ITS2). RESULTS Since P. obducens cannot be propagated in vitro, we developed a custom E. coli expression vector that transcribes the P. obducens rRNA-ITS target sequence (clone-FISH) for use as a control and to optimize hybridization conditions. The FISH assay could detect P. obducens sporangiophores, sporangia and oospores, and hyphae from naturally infected I. walleriana leaves and stems. Cross-reactivity was not observed from plant tissue, and the assay did not react when applied to E. coli with self-ligated plasmids and non-target oomycete species. CONCLUSIONS This FISH protocol may provide a valuable tool for the study of this disease and could potentially be used to improve early monitoring of P. obducens, substantially reducing the persistence and spread of this destructive plant pathogen.
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Affiliation(s)
- Catalina Salgado-Salazar
- Agriculture Research Service (ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, 10300 Baltimore Avenue, Beltsville, MD 20705 USA
- ARS Research Participation Program, Oak Ridge Institute for Science and Education, MC-100-44, P.O. Box 117, Oak Ridge, TN 37831 USA
| | - Gary R. Bauchan
- Agriculture Research Service, Electron and Confocal Microscopy Unit, U.S. Department of Agriculture, 10300 Baltimore Avenue, Beltsville, MD 20705 USA
| | - Emma C. Wallace
- Agriculture Research Service (ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, 10300 Baltimore Avenue, Beltsville, MD 20705 USA
- ARS Research Participation Program, Oak Ridge Institute for Science and Education, MC-100-44, P.O. Box 117, Oak Ridge, TN 37831 USA
- Present Address: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 120 Buckhout Lab, University Park, PA 16802 USA
| | - Jo Anne Crouch
- Agriculture Research Service (ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, 10300 Baltimore Avenue, Beltsville, MD 20705 USA
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