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Shah AP, Travadi T, Sharma S, Pandit R, Joshi C, Joshi M. Comprehensive analysis using DNA metabarcoding, SCAR marker based PCR assay, and HPLC unveils the adulteration in Brahmi herbal products. Mol Biol Rep 2023; 50:7605-7618. [PMID: 37532919 DOI: 10.1007/s11033-023-08653-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND Brahmi is one of the important nootropic botanicals, widely sold in the market, with the name "Brahmi'' being used to describe both Bacopa monnieri and Centella asiatica species. The Brahmi herbal products market is expanding; hence, economically motivated adulteration is highly prevalent. METHODS AND RESULTS This study aimed to develop DNA-based methods, including SCAR marker-based PCR and metabarcoding, to authenticate Brahmi herbal products and compare these methods with HPLC. These methods have been validated using mock controls (in-house blended formulations). All targeted plant species in mock controls were detected successfully with all three methods, whereas, in market samples, only 22.2%, 55.6%, and 50.0% were found positive for Brahmi by PCR assay, DNA metabarcoding, and HPLC, respectively. Metabarcoding can detect the presence of non-labeled plants together with targeted species, which is an advantage over PCR assay or HPLC. CONCLUSION SCAR marker-based PCR is a rapid and cost-effective method for detecting the presence of B. monnieri and C. asiatica. However, in this study, the success rate of PCR amplification was relatively low because the primers targeted either RAPD or ITS-based SCAR markers. HPLC assay, although an alternative, was unable to detect the presence of other botanicals, just like the SCAR marker-based PCR assay. On the other hand, metabarcoding can be utilized to identify the target plants, even in very small quantities, while also providing simulated identification of other botanicals. This study successfully addressed the need for quality control of Brahmi herbal products and provided the first-time report of DNA metabarcoding for such products.
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Affiliation(s)
- Abhi P Shah
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Tasnim Travadi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Sonal Sharma
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India.
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Ambreetha S, Balachandar D. SCAR marker: A potential tool for authentication of agriculturally important microorganisms. J Basic Microbiol 2023; 63:4-16. [PMID: 35916264 DOI: 10.1002/jobm.202200419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/23/2022] [Indexed: 01/04/2023]
Abstract
Microbial inoculants are globally recommended for plant growth promotion and control of plant pathogens. These inoculants require stringent quality checks for sustainable field efficacy. Questionable regulatory frameworks constantly deteriorate the reliability of bio-inoculant technology. Existing global regulations do not involve any rapid molecular technique for the routine inspection of microbial preparations. Sequence characterized amplified region (SCAR) marker offers rapid and precise strain-level authentication of target microbes. Such advanced molecular techniques must be exploited to accurately validate the microbial formulations. Besides, the global dissemination of plant pathogenic microbes has always been an alarming threat to food security. SCAR markers could be used at the plant quarantine centers to rapidly detect catastrophic pathogens, thereby circumventing the import and export of contagious plant materials. The current review is focused on promoting the SCAR marker technology to validate commercial bio-inoculants and predict plant pandemics.
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Affiliation(s)
- Sakthivel Ambreetha
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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3
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Ren Z, Chen R, Muhae-Ud-Din G, Fang M, Li T, Yang Y, Chen W, Gao L. Development of real-time PCR and droplet digital PCR based marker for the detection of Tilletia caries inciting common bunt of wheat. Front Plant Sci 2022; 13:1031611. [PMID: 36507438 PMCID: PMC9732894 DOI: 10.3389/fpls.2022.1031611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/18/2022] [Indexed: 06/17/2023]
Abstract
This is the first study reporting droplet digital PCR and quantitative real time PCR for detection of Tilletia caries (syn. T. tritici), which causes common bunt of wheat and leads to yield losses of 80% in many wheat growing areas worldwide. To establish an accurate, rapid and quantifiable detection method, we tested 100 inter simple sequence repeats (ISSR) primers and obtained a species-specific fragment (515 bp) generated by ISSR 827. Then, a specific 266 bp band for the sequence characterized amplified region (SCAR) marker was produced from T. caries. The detection limit reached 50 pg/μL. Based on the SCAR marker, we further developed a higher sensitivity of quantitative real time-polymerase chain reaction (qRT-PCR) with a detection limit of 2.4 fg/μL, and droplet digital PCR (ddPCR) with a detection limit of 0.24 fg/μL. Both methods greatly improved the detection sensitivity of T. caries, which will be contribute a lot for quickly and accurately detection of T. caries, which causes wheat common bunt.
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Affiliation(s)
- Zhaoyu Ren
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rongzhen Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Plant Protection, Shenyang Agricultural University, Liaoning, China
| | - Ghulam Muhae-Ud-Din
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingke Fang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Sciences, Yangtze University, Jingzhou, China
| | - Tianya Li
- Department of Plant Protection, Shenyang Agricultural University, Liaoning, China
| | - Yazheng Yang
- College of Life Sciences, Yangtze University, Jingzhou, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Murali P, Hilda K, Ramakrishnan M, Ganesh A, Bhuvaragavan S, Janarthanan S. Molecular genotypic diversity of populations of brinjal shoot and fruit borer, Leucinodes orbonalis and development of SCAR marker for pesticide resistance. Mol Biol Rep 2021; 48:7787-800. [PMID: 34655405 DOI: 10.1007/s11033-021-06791-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND The brinjal shoot and fruit borer, Leucinodes orbonalis is a destructive pest of Solanum melongena. The control of L. orbonalis with extensive application of synthetic chemical insecticides resulted in the development of resistance with known genetic heterogeneity among populations. Understanding the genetic diversity of their populations is important in developing strategies for their management. The present investigation was performed to characterize populations of L. orbonalis for their genetic diversity in the entire region of Tamil Nadu, South India using random amplified polymorphic DNA (RAPD) primers as a tool of the molecular marker. METHODS AND RESULTS Among 60 random 10-mer primers, only ten primers generated reproducible and scorable banding profile. Among the ten different random primers, the primers namely OPG 7, OPG 8, OPS 2 and OPS 7 generated the highest genetic variation with over 80% genetic polymorphism. Phylogram analysis produced 18 clusters with eight major and ten minor clusters. Cluster analysis, statistical fitness, population structure and analysis of molecular variance confirmed the significant genetic variation among different populations. A trait specific marker obtained through RAPD was cloned, sequenced and used to develop a stable diagnostic SCAR marker for DNA fingerprinting to distinguish the populations. Amplification of this locus in the samples of 20 different populations indicated recognition of the trait for pesticide resistance in 12 populations. CONCLUSIONS The results suggest that the biochemical nature of host plant varieties of this insect pest and variation in the application of different insecticides are essential contributing factors for the genotypic variations observed among populations of L. orbonalis.
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Zheng K, Cai Y, Chen W, Gao Y, Jin J, Wang H, Feng S, Lu J. Development, Identification, and Application of a Germplasm Specific SCAR Marker for Dendrobium officinale Kimura et Migo. Front Plant Sci 2021; 12:669458. [PMID: 34054907 PMCID: PMC8160518 DOI: 10.3389/fpls.2021.669458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/20/2021] [Indexed: 05/27/2023]
Abstract
The stems of Dendrobium officinale have been used as a rare and valuable Chinese tonic medicine, known as "Tiepi Fengdou", since the Qing dynasty. Because of the increased market demand and continued exploitation of this plant, the reserves of wild D. officinale resources have been depleted, and D. officinale products on the market are being increasingly adulterated. Such changes have strongly affected the sustainable utilization of this valuable medicinal plant resource and the development of related industries. In this study, a species-specific DNA marker was developed for the rapid and accurate authentication of D. officinale. In total, 36 start codon-targeted (SCoT) polymorphism primers were screened in 36 definite Dendrobium species, and a distinct species-specific DNA amplicon (SCoT13-215) for D. officinale was obtained. After the sequence was cloned and sequenced, a sequence-characterized amplified region marker was developed (named SHF/SHR) and validated through PCR amplification of all 38 Dendrobium samples. The marker's specificity for D. officinale was confirmed through the consistent amplification of a clear 197-bp band. This SCAR marker can be used to rapidly, effectively, and reliably identify D. officinale among various Dendrobium species and may play an important role in ensuring the quality of medicinal preparations and protecting the germplasm of this important medicinal species.
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Affiliation(s)
- Kaixin Zheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Yuchen Cai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Weijie Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yadi Gao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Jingjing Jin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Shangguo Feng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jiangjie Lu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
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Chen S, Yang X, Huang WG, Liu Y, Yu Y, Wu GW, Zhang SQ, Li TY, Cao YY. Development of a specific AFLP-based SCAR marker for Chinese Race 34MKG of Puccinia graminis f. sp. tritici. Mol Biol Rep 2020; 47:4303-9. [PMID: 32418113 DOI: 10.1007/s11033-020-05513-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a fungus that causes the devastating fungalwheat stem rust disease in wheat production. Rapid identification of the physiological races of Pgt are very importance for the prevention of wheat stem rust. In this paper we developed a molecular method to identify the most prevalent race of Pgt, as a supplement for traditionally used host-specific methods. Amplified fragment length polymorphism (AFLP) was employed as a means of analyzing DNA polymorphisms in six common physiological races of Pgt in China and Ug99. In total, 64 pairs of primers were used for AFLP screening of race-specific molecular markers. One primer pair-namely, E7/M7 (5'-GACTGCGTACCAATTCG G-3'/5'-GATGAGTCCTGAGTAACGG-3')-yielded a unique band for the race 34MKG that was purified and cloned into the pGEM-T vector for sequencing. We then designed a new primer pairs (sequence-characterized amplified region marker) to amplify the 171-bp fragment and confirmed that the marker was highly specific for 34MKG. These results provide a new tool for monitoring different races of Pgt for improved control of wheat stem rust in China.
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Gherbawy YA, El-Dawy EGAE. Conventional detection and quantification real-time PCR of the pks-1 gene of Chaetomium globosum. J Basic Microbiol 2020; 60:407-414. [PMID: 32124471 DOI: 10.1002/jobm.201900672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/12/2020] [Accepted: 02/15/2020] [Indexed: 11/09/2022]
Abstract
Chaetomium globosum is known as a potential biocontrol indicator against various soil and seedborne pathogens. Precise data are necessary for population monitoring of C. globosum for its effective use in agriculture. A sequence-characterized amplified region marker has been applied for the detection of this biocontrol agent, which will help to detect C. globosum at the site of its application. Out of 17 isolates of C. globosum, only 8 isolates of C. globosum amplified a monomorphic band of 1,900 bp. C. globosum is known for producing chaetoglobosin A. The pks-1 gene is unique in C. globosum in that it is involved in chaetoglobosin A production, melanin formation, and sporulation. Real-time PCR of pks-1 was used to compare the expressions of the pks-1 gene and chaetoglobosin A biosynthesis and sporulation. It was found that the sporulation of C. globosum was associated with the levels of pks-1 gene expression; Cg2 isolate showed high expression of the pks-1 gene, 41.21%, and also produced a great number of spores and perithecia. The association between the pks-1 gene expression and chaetoglobosin A production was estimated. The Pks-1 gene was expressed by all C. globosum isolates except one isolate, C1, which is another species of Chaetomium. In addition, all C. globosum isolates produced chaetoglobosin A with different concentrations and did not express the same levels of pks-1. This finding may be a result of the solvent type used in the extraction.
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Affiliation(s)
- Youssuf A Gherbawy
- Botany and Microbiology Department, Faculty of Science, South Valley University, Qena, Egypt
| | - Eman G A E El-Dawy
- Botany and Microbiology Department, Faculty of Science, South Valley University, Qena, Egypt
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Wang Y, Singh R, Tong E, Tang M, Zheng L, Fang H, Li R, Guo L, Song J, Srinivasan R, Sharma A, Lin L, Trujillo JA, Manshardt R, Chen LY, Ming R, Yu Q. Positional cloning and characterization of the papaya diminutive mutant reveal a truncating mutation in the CpMMS19 gene. New Phytol 2020; 225:2006-2021. [PMID: 31733154 DOI: 10.1111/nph.16325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
The papaya diminutive mutant exhibits miniature stature, retarded growth and reduced fertility. This undesirable mutation appeared in the variety 'Sunset', the progenitor of the transgenic line 'SunUp', and was accidentally carried forward into breeding populations. The diminutive mutation was mapped to chromosome 2 and fine mapped to scaffold 25. Sequencing of a bacterial artificial chromosome in the fine mapped region led to the identification of the target gene responsible for the diminutive mutant, a gene orthologous to MMS19 with a 36.8 kb deletion co-segregating with the diminutive mutant. The genomic sequence of CpMMS19 is 62 kb, consisting of 20 exons and 19 introns. It encodes a protein of 1143 amino acids while the diminutive allele encodes a truncated protein of 287 amino acids. Expression of the full-length CpMMS19 was able to complement the thermosensitive growth of the yeast mms19 deletion mutant while expression of the diminutive allele resulted in increased thermosensitivity. Over-expression of the diminutive allele in Arabidopsis met18 mutant results in a high frequency of seed abortion. The papaya diminutive phenotype is caused by an alteration in gene function rather than a loss-of-function mutation. SCAR (sequence characterized amplified region) markers were developed for rapid detection of the diminutive allele in breeding populations.
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Affiliation(s)
- Ying Wang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ratnesh Singh
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Eric Tong
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
| | - Min Tang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liwei Zheng
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Hongkun Fang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruoyu Li
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin Guo
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jinjin Song
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rajeswari Srinivasan
- Department of Tropical Plant & Soil Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Anupma Sharma
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Lianyu Lin
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jorge A Trujillo
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - Richard Manshardt
- Department of Tropical Plant & Soil Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Li-Yu Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
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Jha SR, Naz R, Asif A, Okla MK, Soufan W, Al-Ghamdi AA, Ahmad A. Development of an In Vitro Propagation Protocol and a Sequence Characterized Amplified Region (SCAR) Marker of Viola serpens Wall. ex Ging. Plants (Basel) 2020; 9:plants9020246. [PMID: 32074984 PMCID: PMC7076368 DOI: 10.3390/plants9020246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/30/2020] [Accepted: 02/10/2020] [Indexed: 11/22/2022]
Abstract
An efficient protocol of plant regeneration through indirect organogenesis in Viola serpens was developed in the present study. Culture of leaf explants on MS (Murashige and Skoog) medium supplemented with 2.0 mg/L 6-benzyladenine and 0.13 mg/L 2,4-dichloro phenoxy acetic acid. Adventitious shoot formation was observed when calli were transferred on to MS medium containing 0.5 mg/L α-naphthalene acetic acid and 2.25 mg/L kinetin, which showed the maximum 86% shoot regeneration frequency. The highest root frequency (80.92%) with the 5.6 roots per explant and 1.87 cm root length was observed on MS medium supplemented with 2 mg/L indole-3-butyric acid. The plantlets were transferred to the mixture of sand, coffee husk and soil in the ratio of 1:2:1 in a pot, and placed under 80% shade net for one month. It was then transferred to 30% shade net for another one month, prior to transplantation in the field. These plantlets successfully acclimatized under field conditions. A Sequence Characterized Amplified Region (SCAR) marker was also developed using a 1135 bp amplicon that was obtained from RAPD (Random Amplification of Polymorphic DNA) analysis of six accessions of V. serpens. Testing of several market samples of V. serpens using the SCAR marker revealed successful identification of the genuine samples of V. serpens. This study, therefore, provides a proficient in vitro propagation protocol of V. serpens using leaf explants and a SCAR marker for the authentic identification of V. serpens. This study will be helpful for conservation of authentic V. serpens.
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Affiliation(s)
- Shipra Rani Jha
- Department of Botany, Jamia Hamdard, New Delhi 110062, India;
| | - Ruphi Naz
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (R.N.); (A.A.)
| | - Ambreen Asif
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (R.N.); (A.A.)
| | - Mohammad K. Okla
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia; (M.K.O.); (A.A.A.-G.)
| | - Walid Soufan
- Plant Production Department, Faculty of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia;
| | - Abdullah A. Al-Ghamdi
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia; (M.K.O.); (A.A.A.-G.)
| | - Altaf Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (R.N.); (A.A.)
- Correspondence:
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Lee SH, Ali A, Ha B, Kim MK, Kong WS, Ryu JS. Development of a Molecular Marker Linked to the A4 Locus and the Structure of HD Genes in Pleurotus eryngii. Mycobiology 2019; 47:200-206. [PMID: 31448140 PMCID: PMC6691818 DOI: 10.1080/12298093.2019.1619989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/12/2019] [Indexed: 06/02/2023]
Abstract
Allelic differences in A and B mating-type loci are a prerequisite for the progression of mating in the genus Pleurotus eryngii; thus, the crossing is hampered by this biological barrier in inbreeding. Molecular markers linked to mating types of P. eryngii KNR2312 were investigated with randomly amplified polymorphic DNA to enhance crossing efficiency. An A4-linked sequence was identified and used to find the adjacent genomic region with the entire motif of the A locus from a contig sequenced by PacBio. The sequence-characterized amplified region marker 7-2299 distinguished A4 mating-type monokaryons from KNR2312 and other strains. A BLAST search of flanked sequences revealed that the A4 locus had a general feature consisting of the putative HD1 and HD2 genes. Both putative HD transcription factors contain a homeodomain sequence and a nuclear localization sequence; however, valid dimerization motifs were found only in the HD1 protein. The ACAAT motif, which was reported to have relevance to sex determination, was found in the intergenic region. The SCAR marker could be applicable in the classification of mating types in the P. eryngii breeding program, and the A4 locus could be the basis for a multi-allele detection marker.
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Affiliation(s)
- Song Hee Lee
- Department of Mushroom Science, Korea National College of Agriculture and Fisheries, Jeonju, Republic of Korea
| | - Asjad Ali
- Environment-Friendly Research Division, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju, Republic of Korea
| | - Byeongsuk Ha
- Environment-Friendly Research Division, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju, Republic of Korea
| | - Min-Keun Kim
- Environment-Friendly Research Division, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju, Republic of Korea
| | - Won-Sik Kong
- Mushroom Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Eumseong, Republic of Korea
| | - Jae-San Ryu
- Department of Mushroom Science, Korea National College of Agriculture and Fisheries, Jeonju, Republic of Korea
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Baite MS, Upadhyay BK, Dubey SC. Development of a sequence-characterized amplified region marker for detection of Ascochyta rabiei causing Ascochyta blight in chickpea. Folia Microbiol (Praha) 2019; 65:103-108. [PMID: 31049801 DOI: 10.1007/s12223-019-00711-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 04/22/2019] [Indexed: 11/29/2022]
Abstract
Ascochyta blight of chickpea is caused by Ascochyta rabiei (Pass.) Labr. which is primarily seedborne. For rapid detection and precise identification of A. rabiei, a sequence-characterized amplified region (SCAR) marker was developed for detection of genomic DNA and infected plant DNA. An SSR primer amplified monomorphic band was cloned in pGEM®-T easy vector and sequenced. The best primer pair was selected and validated on A. rabiei. The specificity and sensitivity of the SCAR-based marker designated as MBAR was evaluated using conventional PCR and real-time PCR. The marker produced consistently an amplicon size of 196 bp in all A. rabiei isolates tested. The sensitivity of the marker was 0.1 ng of genomic fungal DNA and 0.5 ng of plant DNA by conventional PCR and 0.5 pg of A. rabiei DNA and 1.0 pg of plant DNA by real-time PCR. This is the first SCAR marker having high specificity and sensitivity towards A. rabiei. The marker may be useful in detecting the pathogen before the disease appearance and in plant quarantine program to detect the pathogen in seed lots.
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Affiliation(s)
- Mathew S Baite
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Balendu K Upadhyay
- Division of Plant Pathology, ICAR- Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sunil C Dubey
- Division of Plant Quarantine, ICAR- National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
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Hiremani NS, Dubey SC. Phylogenetic relationship among Indian population of Fusarium oxysporum f. sp. lentis infecting lentil and development of specific SCAR markers for detection. 3 Biotech 2019; 9:196. [PMID: 31065496 DOI: 10.1007/s13205-019-1734-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/26/2019] [Indexed: 11/26/2022] Open
Abstract
The present study was taken up to understand the phylogenetic relationship using ITS and TEF markers among 22 isolates of Fusarium oxysporum f. sp. lentis (Fol) causing lentil wilt belonging to eight races isolated from different geographic locations of India and to develop specific markers for its detection. The nucleotide sequences of ITS region varied from 490 to 560 bp whereas, 670-725 bp for TEF 1α. The phylogeny analysis revealed that the isolates were more than 98% similar based on the neighbour joining analysis and were grouped into two major clusters in both ITS and TEF. The first major cluster of ITS had twenty isolates whereas for TEF, there were 15 isolates. Two sets of SCAR markers MS1 (162 bp) and MS2 (125 bp) were designed and synthesised. These markers were used against race representative Fol isolates for amplification. While, MS 1 marker was able to detect the genomic DNA up to 0.1 ng, MS 2 could detect the Fol genomic DNA up to 0.05 ng. The specificity of these two markers to detect Fol and their inability to amplify most common lentil pathogens (Rhizoctonia solani, R. bataticola, Sclerotium rolfsii, Sclerotinia sclerotiarum, and Aschochyta rabiei) makes them a reliable tool for detection. The phylogenetic analysis is helpful in the understanding of variability in Fol populations and the SCAR markers help in rapid and reliable detection of an important pathogen of lentil.
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Affiliation(s)
- Neelakanth S Hiremani
- 1Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- 2Present Address: Division of Crop Protection, ICAR- Central Institute for Cotton Research, Nagpur, 440010 India
| | - Sunil C Dubey
- 1Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- 3Present Address: Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012 India
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Kim WJ, Yang S, Choi G, Park I, Noh P, Seo C, Moon BC. Development of conventional PCR and real-time PCR assays to discriminate the origins of Chinese pepper oil and herbal materials from Zanthoxylum. J Sci Food Agric 2019; 99:2021-2029. [PMID: 30370936 PMCID: PMC6590328 DOI: 10.1002/jsfa.9458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/28/2018] [Accepted: 10/25/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND To ensure the safety, quality and therapeutic efficacy of processed foods and herbal medicines, it is important to identify and discriminate economically motivated adulterants. Zanthoxylum schinifolium is sold at a higher price than other Zanthoxylum species and is frequently adulterated with closely related Zanthoxylum species because of its high demand as a Korean food ingredient and medicinal material in markets. In addition, the pericarps of three Zanthoxylum species (Z. schinifolium, Z. bungeanum and Z. piperitum) are defined as herbal medicine Zanthoxyli Pericarpium in Korean pharmacopoeias, but not Z. piperitum in Chinese pharmacopoeias. Further confusion arises in the morphological similarity between Z. armatum (adulterant) and Z. bungeanum. Therefore, the aim of this study was to develop a sequence characterized amplified region (SCAR) marker for discrimination of four Zanthoxylum species. RESULTS With the goal of developing rapid and reliable tools for genetic discrimination of authentic Zanthoxyli Pericarpium, we designed species-specific SCAR markers, based on ITS2 sequences, that generate amplicons of less than 200 bp. Using these markers, we established both conventional and real-time PCR assay methods capable of differentiating samples at the species level. We validated the ability of SCAR markers to authenticate edible oil and herbal medicine, and confirmed that some herbal medicines contaminated with Z. armatum are being distributed as Zanthoxyli Pericarpium in Korean and Chinese markets. CONCLUSIONS The SCAR markers and PCR methods described represent powerful tools for protecting against adulteration and ensuring standardization of processed foods and herbal medicine. © 2018 The Authors. Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Wook Jin Kim
- Herbal Medicine Research DivisionKorea Institute of Oriental MedicineDaejeonRepublic of Korea
| | - Sungyu Yang
- Herbal Medicine Research DivisionKorea Institute of Oriental MedicineDaejeonRepublic of Korea
| | - Goya Choi
- Herbal Medicine Research DivisionKorea Institute of Oriental MedicineDaejeonRepublic of Korea
| | - Inkyu Park
- Herbal Medicine Research DivisionKorea Institute of Oriental MedicineDaejeonRepublic of Korea
| | - Pureum Noh
- Herbal Medicine Research DivisionKorea Institute of Oriental MedicineDaejeonRepublic of Korea
| | - Chang‐Seob Seo
- Herbal Medicine Research DivisionKorea Institute of Oriental MedicineDaejeonRepublic of Korea
| | - Byeong Cheol Moon
- Herbal Medicine Research DivisionKorea Institute of Oriental MedicineDaejeonRepublic of Korea
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Xu YX, Shen SY, Chen W, Chen L. Analysis of Genetic Diversity and Development of a SCAR Marker for Green Tea (Camellia sinensis) Cultivars in Zhejiang Province: The Most Famous Green Tea-Producing Area in China. Biochem Genet 2019; 57:555-570. [PMID: 30734883 DOI: 10.1007/s10528-019-09909-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/28/2019] [Indexed: 11/24/2022]
Abstract
Camellia sinensis (L.) O. Kuntze is one of the most important non-alcoholic beverage crops in Asian and African countries. In recent years, many green tea cultivars have been released and played an important role in improving the production and quality of tea trees. The objectives of this study were to assess the genetic diversity of the eighteen main green tea cultivars in Zhejiang Province-the most famous green tea-producing area of China-using start codon-targeted (SCoT) markers and to develop a specific sequence-characterized amplified region (SCAR) marker for application in cultivar diagnosis. Thirty-one SCoT primers produced 264 loci, 226 of which were polymorphic. The genetic similarity coefficients among these green tea cultivars ranged from 0.587 to 0.814, indicating that a high level of genetic diversity was present. Both a UPGMA dendrogram and a PCoA plot grouped the tea cultivars into three groups. The partitioning of groups in the UPGMA and PCoA was similar, and much of the clustering was highly consistent with the classification of tea cultivars according to their genetic backgrounds. A unique SCoT band, SCoT4-1649, specific to the tea cultivar 'Yingshuang,' was transformed into a SCAR marker. This SCAR marker is highly useful for the identification and germplasm conservation of green tea cultivars.
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Affiliation(s)
- Yan-Xia Xu
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Si-Yan Shen
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Wei Chen
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Liang Chen
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China.
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Kwon OC, Lee CS, Park YJ. SNP and SCAR Markers for Specific Discrimination of Antler-Shaped Ganoderma lucidum. Microorganisms 2019; 7:E12. [PMID: 30634458 DOI: 10.3390/microorganisms7010012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 12/31/2018] [Accepted: 01/08/2019] [Indexed: 11/17/2022] Open
Abstract
In this study we identified single nucleotide polymorphism (SNP) and sequence characteristic amplification region (SCAR) markers for specific identification of antler-shaped Ganoderma lucidum strains. When the partial mitochondrial SSU rDNA gene sequence of various antler- and kidney-shaped G. lucidum strains were analyzed and aligned, an SNP was found only in the antler-shaped G. lucidum strain at position 456 bp. In addition, this SNP of antler-shaped strains was digested by HinfI restriction enzyme. We further analyzed the polymorphism of various G. lucidum strains by random amplified polymorphic DNA (RAPD) analysis. In RAPD analysis, we isolated and sequenced a fragment, specific for antler-shaped G. lucidum strains. Based on this specific fragment sequence, two sets of specific primer pairs for antler-shaped G. lucidum strains were designed. PCR analysis revealed that two specific bands were observed only from antler-shaped strains. These two molecular markers will be helpful for identification of morphological characteristics of G. lucidum.
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Reddypriya P, Soumare A, Balachandar D. Multiplex and quantitative PCR targeting SCAR markers for strain-level detection and quantification of biofertilizers. J Basic Microbiol 2018; 59:111-119. [PMID: 30318739 DOI: 10.1002/jobm.201800318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/23/2018] [Accepted: 09/22/2018] [Indexed: 11/12/2022]
Abstract
Biofertilizers are the eco-friendly bio-input being used to sustain the agriculture by reducing the chemical inputs and improving the soil health. Quality is the major concern of biofertilizer technology which often leads to poor performance in the field and thereby loses the farmers' faith. To authenticate the strain as well as its presumed cell load of a commercial product, sequence characterized amplified region (SCAR) markers were developed for three biofertilizer strains viz., Azospirillum brasilense (Sp7), Bacillus megaterium (Pb1) and Azotobacter chroococcum (Ac1). We evaluated the feasibility of multiplex-PCR and quantitative real-time PCR for SCAR marker-based quality assessment of the product as well as the persistence of the strains during crop growth. We showed that multiplex PCR can concurrently discriminate the strains based on the amplicons' size and detects up to 104 cells per g or per ml of carrier-based or liquid formulation of biofertilizer, respectively. The detection limit of quantitative PCR targeting SCAR markers is 103 cells per g or ml of biofertilizer. Both the PCR methods detected and quantified them in the maize rhizosphere. Hence SCAR marker-based quality assessment would be a sensitive tool to monitor the biofertilizer production as well as its persistence in the inoculated crop rhizosphere.
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Affiliation(s)
- Pasupuleti Reddypriya
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Abdoulaye Soumare
- Laboratoire Commun de Microbiologie (LCM, IRD/ISRA/UCAD), Dakar, Senegal
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, India
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Zhang QC, Yu RC, Chen ZF, Qiu LM, Wang YF, Kong FZ, Geng HX, Zhao Y, Jiang P, Yan T, Zhou MJ. Genetic evidence in tracking the origin of Ulva prolifera blooms in the Yellow Sea, China. Harmful Algae 2018; 78:86-94. [PMID: 30196928 DOI: 10.1016/j.hal.2018.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 06/19/2018] [Accepted: 08/04/2018] [Indexed: 06/08/2023]
Abstract
Recurrent green tides have been recorded in the Yellow Sea for 11 consecutive years. The origin of floating green algae in the Yellow Sea, however, remains a subject of debate. Previous studies suggest that the major bloom-forming green alga Ulva prolifera represent a unique ecotype different from other attached populations of U. prolifera in China. In this study, 97 green algal samples collected during the 2012 green-tide event and from other locations along the coastline of China were analyzed. Based on the sequences of nuclear ribosomal RNA gene (rDNA) internal transcribed spacer (ITS) region and 5S rDNA spacer region, the green alga U. prolifera in the samples were identified. The intraspecific genetic diversity within U. prolifera was then examined using sequences of 5S rDNA spacer and a marker of sequence characterized amplified region (SCAR) highly specific for bloom-forming U. prolifera in the Yellow Sea. The screening results for SCAR marker demonstrated that U. prolifera attached to aquaculture rafts in Subei Shoal belong to the same ecotype of the bloom-forming U. prolifera in the Yellow Sea. These findings offer genetic evidence that aquaculture rafts in Subei Shoal are a major source of floating green algae in the Yellow Sea.
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Affiliation(s)
- Qing-Chun Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ren-Cheng Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Zhen-Fan Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Mei Qiu
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yun-Feng Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Fan-Zhou Kong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hui-Xia Geng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yue Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Jiang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Tian Yan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ming-Jiang Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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Dunlap CA, Mascarin GM, Romagnoli EM, Jackson MA. Rapid discrimination of Isaria javanica and Isaria poprawskii from Isaria spp. using high resolution DNA melting assays. J Invertebr Pathol 2017; 150:88-93. [PMID: 28939380 DOI: 10.1016/j.jip.2017.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 09/08/2017] [Accepted: 09/13/2017] [Indexed: 10/18/2022]
Abstract
The current study evaluates the potential of using high resolution DNA melting assays to discriminate species in the genus Isaria. The study utilizes a previously identified 103 base pair PCR amplicon, which was reported to be selective for Isaria fumosorosea. Our study finds the amplicon selective for Isaria javanica and Isaria poprawskii when assayed against all members of the genus. In addition, the high resolution melting profile of this amplicon can be used to discriminate between I. javanica, I. poprawskii and a 1:1 mixture of the two species. The practical application of this technique was confirmed using a bioassay on whitefly nymphs (Bemisia tabaci biotype B) inoculated with I. javanica, I. poprawskii or a 1:1 mixture of the two species. This assay provides a simple assay to identify these two species of entomopathogenic fungi.
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Affiliation(s)
- Christopher A Dunlap
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 North University Street, Peoria, IL 61604, USA.
| | - Gabriel M Mascarin
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 North University Street, Peoria, IL 61604, USA; Embrapa Rice and Beans, Rodovia GO-462, Km 12, Zona Rural, C.P. 179, 75375-000 Santo Antônio de Goiás, GO, Brazil
| | - Emiliana M Romagnoli
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 North University Street, Peoria, IL 61604, USA
| | - Mark A Jackson
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 North University Street, Peoria, IL 61604, USA
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Roy NS, Park KC, Lee SI, Im MJ, Ramekar RV, Kim NS. Development of CACTA transposon derived SCAR markers and their use in population structure analysis in Zea mays. Genetica 2018; 146:1-12. [PMID: 28916874 DOI: 10.1007/s10709-017-9985-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022]
Abstract
Molecular marker technologies have proven to be an important breakthrough for genetic studies, construction of linkage maps and population genetics analysis. Transposable elements (TEs) constitute major fractions of repetitive sequences in plants and offer a wide range of possible areas to be explored as molecular markers. Sequence characterized amplified region (SCAR) marker development provides us with a simple and time saving alternative approach for marker development. We employed the CACTA-TD to develop SCARs and then integrated them into linkage map and used them for population structure and genetic diversity analysis of corn inbred population. A total of 108 dominant SCAR markers were designed out of which, 32 were successfully integrated in to the linkage map of maize RIL population and the remaining were added to a physical map for references to check the distribution throughout all chromosomes. Moreover, 76 polymorphic SCARs were used for diversity analysis of corn accessions being used in Korean corn breeding program. The overall average polymorphic information content (PIC) was 0.34, expected heterozygosity was 0.324 and Shannon's information index was 0.491 with a percentage of polymorphism of 98.67%. Further analysis by associating with desirable traits may also provide some accurate trait specific tagged SCAR markers. TE linked SCARs can provide an added level of polymorphism as well as improved discriminating ability and therefore can be useful in further breeding programs to develop high yielding germplasm.
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Zhang J, Jiang Y, Xuan P, Guo Y, Deng G, Yu M, Long H. Isolation of two new retrotransposon sequences and development of molecular and cytological markers for Dasypyrum villosum (L.). Genetica 2017. [PMID: 28638972 DOI: 10.1007/s10709-017-9972-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dasypyrum villosum is a valuable genetic resource for wheat improvement. With the aim to efficiently monitor the D. villosum chromatin introduced into common wheat, two novel retrotransposon sequences were isolated by RAPD, and were successfully converted to D. villosum-specific SCAR markers. In addition, we constructed a chromosomal karyotype of D. villosum. Our results revealed that different accessions of D. villosum showed slightly different signal patterns, indicating that distribution of repeats did not diverge significantly among D. villosum accessions. The two SCAR markers and FISH karyotype of D. villosum could be used for efficient and precise identification of D. villosum chromatin in wheat breeding.
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Affiliation(s)
- Jie Zhang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture), Chengdu, 610066, Sichuan, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Pu Xuan
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Yuanlin Guo
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin South Road, Chengdu, 610041, Sichuan, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin South Road, Chengdu, 610041, Sichuan, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin South Road, Chengdu, 610041, Sichuan, China.
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Yamashita Y, Takeuchi T, Okuyama M, Sasaki J, Onodera K, Sato M, Souma C, Ebe S. Development and validation of DNA markers linked to Sdvy-1, a common bean gene conferring resistance to the yellowing strain of Soybean dwarf virus. Breed Sci 2014; 64:404-8. [PMID: 25914596 PMCID: PMC4267316 DOI: 10.1270/jsbbs.64.404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/29/2014] [Indexed: 06/04/2023]
Abstract
The yellowing strain of Soybean dwarf virus (SbDV-YS) causes yellowing and yield loss in common bean (Phaseolus vulgaris). The most effective control is achieved through breeding for resistance. An indeterminate climbing cultivar with a white seed coat, 'Oofuku', is resistant to SbDV-YS in inoculation tests. We crossed 'Oofuku' with an elite cultivar, 'Taisho-Kintoki', which is SbDV-YS-susceptible, determinate dwarf with a red-purple seed coat, and performed amplified-fragment-length polymorphism analysis of F3 lines. From nucleotide sequences of the resistant-specific fragments and their flanking regions, we developed five DNA markers, of which DV86, DV386, and DV398 were closely linked to Sdvy-1, a resistance gene. Using the markers, we developed 'Toiku-B79' and 'Toiku-B80', the near-isogenic lines (NILs) incorporating Sdvy-1 in the background of 'Taisho-Kintoki'. The NILs had similar growth habit, maturity date and seed shape to those of 'Taisho-Kintoki'. The quality of boiled beans was also similar, except that the NILs had more seed coat cracking than 'Taisho-Kintoki'. The NILs showed no SbDV-YS infection in inoculation tests. We suggest that Sdvy-1 is a useful source of SbDV-YS resistance in common bean.
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Affiliation(s)
- Yoko Yamashita
- Hokkaido Research Organization (HRO) Central Agricultural Experiment Station (AES),
Higashi 6 Kita 15, Naganuma, Hokkaido 069-1395,
Japan
| | - Toru Takeuchi
- Hokkaido Research Organization (HRO) Central Agricultural Experiment Station (AES),
Higashi 6 Kita 15, Naganuma, Hokkaido 069-1395,
Japan
| | | | - Jun Sasaki
- HRO Kitami AES,
52 Yayoi, Kunneppu, Hokkaido 099-1496,
Japan
| | | | - Mikako Sato
- Hokkaido Research Organization (HRO) Central Agricultural Experiment Station (AES),
Higashi 6 Kita 15, Naganuma, Hokkaido 069-1395,
Japan
| | - Chihiro Souma
- Hokkaido Research Organization (HRO) Central Agricultural Experiment Station (AES),
Higashi 6 Kita 15, Naganuma, Hokkaido 069-1395,
Japan
| | - Shigehiko Ebe
- HRO Tokachi AES,
S9-2 Shinsei, Memuro, Hokkaido 082-0071,
Japan
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Ryuk JA, Kim YS, Lee HW, Ko BS. Identification of Acorus gramineus, A. calamus, and A. tatarinowii using sequence characterized amplified regions (SCAR) primers for monitoring of Acori graminei rhizoma in Korean markets. Int J Clin Exp Med 2014; 7:2488-2496. [PMID: 25356101 PMCID: PMC4211751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/16/2014] [Indexed: 06/04/2023]
Abstract
Acori Graminei Rhizoma (AGR), widely used in traditional herbal medicine, is composed of the roots of Acorus gramineus Soland. The family Acoraceae includes A. gramineus, A. calamus, and A. tatarinowii, among others. We compared genomic DNA sequences of AGR for polymorphisms. The sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA, the rbcL region of chloroplast DNA from A. gramineus, A. calamus, and A. tatarinowii were compared. We designed primers specific to the ITS region of A. calamus and A. tatarinowii (A. cataF4/R4) and the internal primer Araceae Radix (IntAcoF2/R4). Random amplification of polymorphic DNA (RAPD) analysis showed a difference in A. calamus using the UBC 681 primer. A specific primer (Aca681-F/R) amplified 138 base pairs of A. calamus. The primers designed for this study (A. cataF4/R4, Aca681-F/R, and IntAcoF2/R2) can be used for multiplex PCR to distinguish the three species of Acorus. An allelic discrimination assay was conducted using commercially available AGR. We used sequence-characterized amplified region (SCAR) markers to confirm whether AGR purchased at a market was A. gramineus. Our study indicated the SCAR markers could be used as molecular evidence to distinguish Araceae Radix.
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Affiliation(s)
- Jin Ah Ryuk
- KM-Based Herbal Drug Research Group, Korea Institute of Oriental Medicine 1672 Yuseongdae-ro, Daejeon 305-811, Korea
| | - Young Seon Kim
- KM-Based Herbal Drug Research Group, Korea Institute of Oriental Medicine 1672 Yuseongdae-ro, Daejeon 305-811, Korea
| | - Hye Won Lee
- KM-Based Herbal Drug Research Group, Korea Institute of Oriental Medicine 1672 Yuseongdae-ro, Daejeon 305-811, Korea
| | - Byoung Seob Ko
- KM-Based Herbal Drug Research Group, Korea Institute of Oriental Medicine 1672 Yuseongdae-ro, Daejeon 305-811, Korea
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Amaradasa BS, Lakshman D, Horvath BJ, Amundsen KL. Development of SCAR markers and UP-PCR cross-hybridization method for specific detection of four major subgroups of Rhizoctonia from infected turfgrasses. Mycologia 2014; 106:163-72. [PMID: 24396105 DOI: 10.3852/13-006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A rapid identification assay for Waitea circinata (anamorph: Rhizoctonia spp.) varieties zeae and circinata causing patch diseases on turfgrasses was developed based on the universally primed PCR (UP-PCR) products cross-blot hybridization. Tester isolates belonging to the two varieties of W. circinata were amplified with a single UP primer L21, which generated multiple DNA fragments for each variety. Probes were prepared with UP-PCR products of each tester isolate by labeling with digoxigenin. Fieldcollected W. circinata isolates and representative isolates of different R. solani anastomosis groups (AG) and AG subgroups were amplified with L21, immobilized on nylon membrane and cross hybridized with the two probes. Isolates within a W. circinata variety cross-hybridized strongly, while non-homologous isolates did not cross-hybridize or did so weakly. Closely related W. circinata varieties zeae and circinata were clearly distinguished with this assay. Sequence-characterized amplified region (SCAR) markers also were developed from UP-PCR products to identify isolates of Thanatephorus cucumeris (anamorph: R. solani) AG 1-IB and AG 2-2IIIB. These two AGs are commonly isolated from diseased, cool-season turfgrasses. The specific SCAR markers that were developed could differentiate isolates of AG 1-IB or AG 2-2IIIB groups. These SCAR markers did not amplify a product from genomic DNA of nontarget isolates of Rhizoctonia. The specificities and sensitivities of the SCAR primers were tested on total DNA extracted from several field-grown, cool-season turf species having severe brown-patch symptoms. First, the leaf samples from diseased turf species were tested for the anastomosis groups of the causal pathogen, and thereafter the total DNA was amplified with the specific primers. The specific primers were sensitive and unique enough to produce a band from total DNA of diseased turfgrasses infected with either AG 1-IB or AG 2-2IIIB.
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Affiliation(s)
- Bimal S Amaradasa
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, Nebraska 68583
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Yang L, Fu S, Khan MA, Zeng W, Fu J. Molecular cloning and development of RAPD- SCAR markers for Dimocarpus longan variety authentication. Springerplus 2013; 2:501. [PMID: 24130961 PMCID: PMC3795202 DOI: 10.1186/2193-1801-2-501] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 09/18/2013] [Indexed: 11/10/2022]
Abstract
As an edible fruit and source of traditional medicine, D. longan is grown in most areas of Southern China. Identification of D. longan cultivars by using molecular markers is important genetically. In this study, we cloned fragments from improved randomly amplified polymorphic DNA (RAPD), and developed stably diagnostic sequence-characterized amplified region (SCAR) markers. The specific RAPD bands of D. longan cultivars from Guangxi, with size ranging from 500 bp to 900 bp were gel-purified, cloned and sequenced. Four clones named LY2-1, LY4-7, LY4-8 and LY5-2 were identified. In order to investigate whether the fragments were specific for the species, four pairs of SCAR primers were then designed. PCR amplifications were conducted to analyze 18 samples including different D. longan cultivars and other species. The specific bands with expected sizes were amplified in five D. longan samples but not in others. To identify and characterize the difference between D. longan and D. confinis, PCR amplifications were performed again. The specific bands with expected sizes were found in D. longan but not in D. confinis by SCAR markers LY2-1, LY4-7 and LY5-2, respectively. These results showed that our developed SCAR markers could be very useful as a specific D. longan variety authentication. Therefore, our study provides an effective and precise PCR-based diagnostic method and markers to identify D. longan species.
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Affiliation(s)
- Luquan Yang
- Research Center for Preclinical Medicine, Luzhou Medical College, Luzhou, Sichuan 646000 China
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Dutta SR, Kar PK, Srivastava AK, Sinha MK, Shankar J, Ghosh AK. Identification of RAPD and SCAR markers associated with yield traits in the Indian tropical tasar silkworm Antheraea mylitta drury. Genet Mol Biol 2012; 35:743-51. [PMID: 23271934 PMCID: PMC3526081 DOI: 10.1590/s1415-47572012005000059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 05/21/2012] [Indexed: 11/22/2022] Open
Abstract
The tropical tasar silkworm, Antheraea mylitta, is a semi-domesticated vanya silk-producing insect of high economic importance. To date, no molecular marker associated with cocoon and shell weights has been identified in this species. In this report, we identified a randomly amplified polymorphic DNA (RAPD) marker and examined its inheritance, and also developed a stable diagnostic sequence-characterized amplified region (SCAR) marker. Silkworms were divided into groups with high (HCSW) and low (LCSW) cocoon and shell weights, and the F2 progeny of a cross between these two groups were obtained. DNA from these silkworms was screened by PCR using 34 random primers and the resulting RAPD fragments were used for cluster analysis and discriminant function analysis (DFA). The clustering pattern in a UPGMA-based dendogram and DFA clearly distinguished the HCSW and LCSW groups. Multiple regression analysis identified five markers associated with cocoon and shell weights. The marker OPW16905 bp showed the most significant association with cocoon and shell weights, and its inheritance was confirmed in F2 progeny. Cloning and sequencing of this 905 bp fragment showed 88% identity between its 134 nucleotides and the Bmc-1/Yamato-like retroposon of A. mylitta. This marker was further converted into a diagnostic SCAR marker (SCOPW 16826 bp). The SCAR marker developed here may be useful in identifying the right parental stock of tasar silk-worms for high cocoon and shell weights in breeding programs designed to enhance the productivity of tasar silk.
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Affiliation(s)
- Suhrid R Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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Ye W. Development of PrimeTime-Real-Time PCR for Species Identification of Soybean Cyst Nematode (Heterodera glycines Ichinohe, 1952) in North Carolina. J Nematol 2012; 44:284-290. [PMID: 23481469 PMCID: PMC3547338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Indexed: 06/01/2023] Open
Abstract
Soybean cyst nematode (SCN) is an obligate, sedentary parasite that is a major pathogen of soybean and accounts for an estimated 1 billion dollars in production losses annually in the United States of America. This paper describes the development of a real-time PCR method for rapid, sensitive, species-specific and accurate identification of SCN alone or on mixed populations with other nematodes in North Carolina. The 83-bp DNA fragment of PrimeTime-real-time PCR was designed based on a 477-bp-SCN-SCAR marker previously proved to be SCN-specific. A total of 44 populations including cyst forming nematodes (Heterodera glycines, H. fici, H. schachtii, H. trifolii, Cactodera weissi, Globodera tabacum, Meloidodera floridensis and other unidentified cyst nematodes) and non-cyst forming nematodes (Ditylenchus dipsaci, Meloidogyne incognita and Xiphinema chambersi) were tested in this study, all SCN populations are tested positive and non-SCN populations negative. This assay for the detection and identification has been successfully applied for testing a single SCN cyst, a 2(nd)-stage-SCN juvenile, a single SCN egg, up to ten SCN cysts, a 10-fold dilution of a single 2(nd)-stage-SCN juvenile and 20-fold dilution of one SCN cyst. The assay is not SCN-race specific. It gave an accurate positive result when SCN is mixed with other cyst species. Also, nematode universal primers/probes for real-time PCR amplification as a nematode endogenous control to detect the presence of 18S ribosomal RNA (rRNA) gene were employed in this assay, so that a SCN-negative sample can be tested to exclude false negative. This method will be very useful for a broad range of research programs as well as the regulatory response and management of SCN in North Carolina and other region of the southeastern U.S.A.
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Affiliation(s)
- Weimin Ye
- Nematologist, Section Chief, Nematode Assay Section, Agronomic Division, North Carolina Department of Agriculture & Consumer Services, Raleigh, NC 27607, USA
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