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Mohammadbagheri L, Nasr-Esfahani M, Abdossi V, Naderi D. Genetic diversity and biochemical analysis of Capsicum annuum (Bell pepper) in response to root and basal rot disease, Phytophthora capsici. PHYTOCHEMISTRY 2021; 190:112884. [PMID: 34388481 DOI: 10.1016/j.phytochem.2021.112884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
This study analyzed the genetic variability and biochemical characteristics of edible and ornamental accessions of pepper, Capsicum annuum, in response to root and basal rot disease (RCR), caused by Phytophthora capsici, using resistance screening and genetic variability via Inter Simple Sequence Repeat marker (ISSR), bio-mass parameters, and enzymatic activity of Peroxidase or peroxide reductases (POX), Superoxide dismutase (SOD), Polyphenol oxidase (PPOs), Catalase (CAT), Phenylalanine ammonia-lyase (PAL), β-1,3-glucanase and phenolic content. The resistance in C. annuum '37ChilPPaleo', '19OrnP-PBI' and '23CherryPOrsh' and susceptibility in '2BP-PBI', '24BP-301' and '26BPRStarlet' accessions were confirmed. Nineteen out of 21 ISSR primers generated 185 polymorphic bands with a mean percentage band of 98.5 %, and an average number of bands of 9.9 per primer. Biomass parameters were significantly higher in resistant genotypes than the susceptible ones and non-inoculated controls. All the seven candidate enzymes were highly up-regulated in the resistant C. annuum accessions '19OrnP-PBI', '37ChillP-Paleo' and '23CherryP-Orsh' inoculated with P. capsici The mean level of enzyme activity varied from 1.5 to 5.6-fold higher in the resistant C. annuum, of which SOD was increased by 5.6 fold, followed by PAL 4.40 and PPO 3.75 fold in comparison to susceptible and non-inoculated controls. Overall, there was no significant correlation between resistance and genetic variability, and also between genetic variability and enzyme activity levels. However, there was a highly significant correlation between the resistance, bio-mass parameters and enzyme activity levels.
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Affiliation(s)
- Leila Mohammadbagheri
- Horticultural Department, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mehdi Nasr-Esfahani
- Plant Protection Research Department, Isfahan Agriculture and Natural Resource Research and Education Center, AREEO, Isfahan, Iran.
| | - Vahid Abdossi
- Horticultural Department, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Davood Naderi
- Horticulture Department, Agricultural Faculty and Young Researcher and Elite Club, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
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Lee J. Development and Evolution of Molecular Markers and Genetic Maps in Capsicum Species. COMPENDIUM OF PLANT GENOMES 2019. [DOI: 10.1007/978-3-319-97217-6_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Mishra R, Rout E, Mohanty JN, Joshi RK. Sequence-tagged site-based diagnostic markers linked to a novel anthracnose resistance gene RCt1 in chili pepper ( Capsicum annuum L.). 3 Biotech 2019; 9:9. [PMID: 30622847 PMCID: PMC6312824 DOI: 10.1007/s13205-018-1552-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 12/21/2018] [Indexed: 01/04/2023] Open
Abstract
Anthracnose, caused by Colletotrichum spp. is the most devastating disease of chili (Capsicum annuum) in the tropical and subtropical regions of the world. The present study aimed at molecular mapping and development of markers linked to a new gene for anthracnose resistance in the chili cultivar 'Punjab Lal'. Phenotypic evaluation of F1, F2, and BC1F1 populations derived from a cross between 'Punjab Lal' and susceptible cultivar 'Arka Lohit' against a virulent isolate of C. truncatum revealed that anthracnose resistance in Punjab Lal is governed by a monogenic-dominant gene designated as RCt1. Forty-four (28 ISSRs and 16 AFLPs) out of 201 markers exhibited parental polymorphism and were used in bulk segregant analysis. Three ISSRs (ISSR411493, ISSR581485, and ISSR1121857) and one AFLP marker (E-ACA/M-CTG516) showed precise polymorphism between resistant and susceptible bulks, and were used for genotyping F2 and BC1 populations. The four putative fragments were converted into sequence-tagged site (STS) markers and southern blotting confirmed their association with the resistance locus. Molecular mapping revealed that the STS markers CtR-431 and CtR-594 were closely linked to the RCt1 locus in coupling at distances of 1.8 and 2.3 cM, respectively. Furthermore, both of these markers showed the presence of resistance-linked allele in seven genotypes including the highly resistant C. chinnese 'PBC932' and C. baccatum 'PBC80' while negatively validated in 32 susceptible genotypes. Therefore, CtR431 and CtR-594 could be recommended as efficient diagnostic markers to facilitate the introgression of RCt1 locus into susceptible chili variants towards the development of high-yielding anthracnose resistance genotypes in C. annuum background.
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Affiliation(s)
- Rukmini Mishra
- Functional Genomics Laboratory, Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha India
| | - Ellojita Rout
- Functional Genomics Laboratory, Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha India
| | - Jatindra Nath Mohanty
- Functional Genomics Laboratory, Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha India
| | - Raj Kumar Joshi
- Functional Genomics Laboratory, Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha India
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
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Kuluev BR, Baymiev AK, Gerashchenkov GA, Chemeris DA, Zubov VV, Kuluev AR, Baymiev AK, Chemeris AV. Random Priming PCR Strategies for Identification of Multilocus DNA Polymorphism in Eukaryotes. RUSS J GENET+ 2018. [DOI: 10.1134/s102279541805006x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fahmi MR, Solihin DD, Shao Z, Pouyaud L, Berrebi P. Population genetic structure of the tropical eelAnguilla bicolorin Indonesian waters based on microsatellite markers. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i2.a1.2015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Melta Rini Fahmi
- Research Station of Ornamental Fish Culture, Jl Perikanan No 13 Pancoran Mas, Depok, Indonesia
| | - Dedy Duryadi Solihin
- Department of Biology, Faculty of Mathematics and Natural Science, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia
| | - Zaojun Shao
- Institut des Sciences de l'Evolution (ISEM) UMR 5554 UMII-CNRS-IRD, Université Montpellier II, CC 065, Place E. Bataillon, 34095 Montpellier Cedex 5, France;,
| | - Laurent Pouyaud
- Institut des Sciences de l'Evolution (ISEM) UMR 5554 UMII-CNRS-IRD, Université Montpellier II, CC 065, Place E. Bataillon, 34095 Montpellier Cedex 5, France;,
| | - Patrick Berrebi
- Institut des Sciences de l'Evolution (ISEM) UMR 5554 UMII-CNRS-IRD, Université Montpellier II, CC 065, Place E. Bataillon, 34095 Montpellier Cedex 5, France;,
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Nybom H, Weising K, Rotter B. DNA fingerprinting in botany: past, present, future. INVESTIGATIVE GENETICS 2014; 5:1. [PMID: 24386986 PMCID: PMC3880010 DOI: 10.1186/2041-2223-5-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/02/2013] [Indexed: 12/20/2022]
Abstract
Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".
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Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University for Agricultural Sciences, Fjälkestadsvägen 459, Kristianstad 29194, Sweden
| | - Kurt Weising
- Plant Molecular Systematics, Institute of Biology, University of Kassel, Kassel 34109, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhöferallee 3, Frankfurt 60438, Germany
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Molecular profiling for genetic variability in Capsicum species based on ISSR and RAPD markers. Mol Biotechnol 2012; 51:137-47. [PMID: 21861246 DOI: 10.1007/s12033-011-9446-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The taxonomic identity of Capsicum species is found to be difficult as it displays variations at morpho-chemical characters. Twenty-two accessions of six Capsicum species, namely, C. annuum, C. baccatum, C. chinense, C. eximium, C. frutescens, and C. luteum were investigated for phenotypic diversity based on flower color and for genetic differences by molecular makers. The genetic cluster analyses of 27 RAPD and eight ISSR primers, respectively, revealed genetic similarities in the ranges of 23-88% and 11-96%. Principal component analysis of the pooled RAPD and ISSR data further supports the genetic similarity and groupings. Different species showed variations in relation to corolla shade of flower. C. annuum accessions formed a single cluster in the molecular analysis as maintaining their flower characteristic. C. chinense accession shared flower features with the accessions of C. frutescens and were found to be closer at genotypic level. C. luteum was found to be rather closer to C. baccatum complex, both phenotypically and genetically. The only accession of C. eximium presenting purple flowers falls apart from the groupings. The floral characteristics and the molecular markers are found to be useful toward the delineation of the species specificity in Capsicum collection and identification of genetic stock.
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Hernández A, Aranda E, Martín A, Benito MJ, Bartolomé T, de Gúa Córdoba M. Efficiency of DNA typing methods for detection of smoked paprika "pimenton de la vera" adulteration used in the elaboration of dry-cured Iberian pork sausages. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:11688-11694. [PMID: 20958044 DOI: 10.1021/jf102414q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The purpose of this work was to develop a PCR method for the identification of smoked paprika "Pimentón de la Vera" adulteration with paprika elaborated from varieties of pepper foreign to the la Vera region, in central western Spain. Three autochthonous varieties of pepper, Jaranda, Jariza, and Bola, and the varieties Papri Queen, Papri King, Sonora, PS9794, and Papri Ace, foreign to the La Vera region, were used in the study. Analyses of the ITS and 5.8S rDNA, RAPD-PCR, SSR, and ISSR were tested. RAPD-PCR, SSR, and ISSR analyses allowed differentiation among the varieties of paprika analyzed. There was no difference in the sequence of ITS1-5.8S rDNA-ITS2. In addition, with the RAPD-PCR primers S13 and S22, two molecular markers were obtained of 641 and 704 bp, respectively, which allowed all of the smoked paprika varieties to be differentiated from paprikas elaborated with the five foreign varieties. These two molecular markers were investigated as a basis for detecting the adulteration of smoked paprika with paprika elaborated from foreign varieties of pepper.
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Affiliation(s)
- Alejandro Hernández
- Nutrición y Bromatología, Escuela de Ingenieńas Agrarias, University ofExtremadura, Ctra. de Cáceres s/n, 06071 Badajoz, Spain
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Forensic botany: Usability of bryophyte material in forensic studies. Forensic Sci Int 2007; 172:161-3. [DOI: 10.1016/j.forsciint.2006.11.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 11/16/2006] [Accepted: 11/19/2006] [Indexed: 11/20/2022]
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Kramer B, Skelton P, Van Der Bank H, Wink M. Allopatric differentiation in theMarcusenius macrolepidotusspecies complex in southern and eastern Africa: the resurrection ofM. pongolensisandM. angolensis, and the description of two new species (Mormyridae, Teleostei). J NAT HIST 2007. [DOI: 10.1080/00222930701250987] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Ward J, Peakall R, Gilmore SR, Robertson J. A molecular identification system for grasses: a novel technology for forensic botany. Forensic Sci Int 2005; 152:121-31. [PMID: 15978338 DOI: 10.1016/j.forsciint.2004.07.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Revised: 07/02/2004] [Accepted: 07/07/2004] [Indexed: 10/26/2022]
Abstract
Our present inability to rapidly, accurately and cost-effectively identify trace botanical evidence remains the major impediment to the routine application of forensic botany. Grasses are amongst the most likely plant species encountered as forensic trace evidence and have the potential to provide links between crime scenes and individuals or other vital crime scene information. We are designing a molecular DNA-based identification system for grasses consisting of several PCR assays that, like a traditional morphological taxonomic key, provide criteria that progressively identify an unknown grass sample to a given taxonomic rank. In a prior study of DNA sequences across 20 phylogenetically representative grass species, we identified a series of potentially informative indels in the grass mitochondrial genome. In this study we designed and tested five PCR assays spanning these indels and assessed the feasibility of these assays to aid identification of unknown grass samples. We confirmed that for our control set of 20 samples, on which the design of the PCR assays was based, the five primer combinations produced the expected results. Using these PCR assays in a 'blind test', we were able to identify 25 unknown grass samples with some restrictions. Species belonging to genera represented in our control set were all correctly identified to genus with one exception. Similarly, genera belonging to tribes in the control set were correctly identified to the tribal level. Finally, for those samples for which neither the tribal or genus specific PCR assays were designed, we could confidently exclude these samples from belonging to certain tribes and genera. The results confirmed the utility of the PCR assays and the feasibility of developing a robust full-scale usable grass identification system for forensic purposes.
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Affiliation(s)
- J Ward
- School of Botany and Zoology, Australian National University, Canberra, ACT 0200, Australia.
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Kim D, Pemberton H, Stratford AL, Buelaert K, Watkinson JC, Lopes V, Franklyn JA, McCabe CJ. Pituitary tumour transforming gene (PTTG) induces genetic instability in thyroid cells. Oncogene 2005; 24:4861-6. [PMID: 15897900 DOI: 10.1038/sj.onc.1208659] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cancer reflects the progressive accumulation of genetic alterations and subsequent genetic instability of cells. Cytogenetic studies have demonstrated the importance of aneuploidy in differentiated thyroid cancer development. The pituitary tumour transforming gene (PTTG), also known as securin, is a mitotic checkpoint protein which inhibits sister chromatid separation during mitosis. PTTG is highly expressed in many cancers and overexpression of PTTG induces aneuploidy in vitro. Using fluorescent intersimple sequence repeat PCR (FISSR-PCR), we investigated the relationship between PTTG expression and the degree of genetic instability in normal and tumorous thyroid samples. The genomic instability index (GI index) was 6.7-72.7% higher in cancers than normal thyroid tissues. Follicular thyroid tumours exhibited greater genetic instability than papillary tumours (27.6% (n=9) versus 14.5% (n=10), P=0.03). We also demonstrated a strong relationship between PTTG expression and the degree of genetic instability in thyroid cancers (R2=0.80, P=0.007). To further investigate PTTG's role in genetic instability, we transfected FTC133 thyroid follicular cells and observed increased genetic instability in cells overexpressing PTTG compared with vector-only-transfected controls (n=3, GI Index VO=29.7+/-5.2 versus PTTG=63.7+/-6.4, P=0.013). Further, we observed a dose response in genetic instability and PTTG expression (GI Index low dose (0.5 microg DNA/ six-well plate) PTTG=15.3%+/-1.7 versus high dose (3 microg DNA) PTTG=50.8%+/-3.3, P=0.006). Overall, we describe the first use of FISSR-PCR in human cancers, and demonstrate that PTTG expression correlates with genetic instability in vivo, and induces genetic instability in vitro. We conclude that PTTG may be an important gene in the mutator phenotype development in thyroid cancer.
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Affiliation(s)
- Dae Kim
- Division of Medical Sciences, 2nd Floor IBR, University of Birmingham, Edgbaston, Birmingham B12 5TT, UK.
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Abstract
Sherlock Holmes said "it has long been an axiom of mine that the little things are infinitely the most important", but never imagined that such a little thing, the DNA molecule, could become perhaps the most powerful single tool in the multifaceted fight against crime. Twenty years after the development of DNA fingerprinting, forensic DNA analysis is key to the conviction or exoneration of suspects and the identification of victims of crimes, accidents and disasters, driving the development of innovative methods in molecular genetics, statistics and the use of massive intelligence databases.
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Affiliation(s)
- Mark A Jobling
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom.
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Kethidi DR, Roden DB, Ladd TR, Krell PJ, Retnakaran A, Feng Q. Development of SCAR markers for the DNA-based detection of the Asian long-horned beetle, Anoplophora glabripennis (Motschulsky). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2003; 52:193-204. [PMID: 12655607 DOI: 10.1002/arch.10082] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
DNA markers were identified for the molecular detection of the Asian long-horned beetle (ALB), Anoplophora glabripennis (Mot.), based on sequence characterized amplified regions (SCARs) derived from random amplified polymorphic DNA (RAPD) fragments. A 2,740-bp DNA fragment that was present only in ALB and not in other Cerambycids was identified after screening 230 random primers in a PCR-based assay system. Three pairs of nested 22-mer oligonucleotide primers were designed on the basis of the sequence of this fragment and were used to perform diagnostic PCR. The first pair of primers (SCAR1) amplified a single 745-bp fragment of ALB DNA, but this did not differentiate ALB from other species. The other two pairs of SCAR primers (SCAR2 and SCAR3) amplified bands of 1,237- and 2,720-bp, respectively, that were capable of differentiating ALB from other closely related non-native and native Cerambycids, such as A. chinensis (Forster), A. malasiaca (Thomson), A. nobilis (Ganglbauer), Monochamus scutellatus (Say), Plectrodera scalator (Fab), Saperda tridentata (Olivier), and Graphisurus fasciatus (Degeer). The latter two SCAR markers could be amplified using DNA extracted from body parts of ALB such as the wing, the leg, and the antennae as well as tissues from all the developmental stages including the egg, larva, pupa, and adult. These markers were also capable of identifying ALB using the DNA extracted from frass. Our results demonstrate that the SCAR markers we have identified can be used for unambiguously identifying ALB from other closely related Cerambycids using a simple PCR procedure.
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Affiliation(s)
- Damodar R Kethidi
- Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
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