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Integration of advanced technologies for plant variety and cultivar identification

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Abstract

Identification of plant variety and cultivar is pivotal in the agricultural sector due to the abundance of plant varieties and cultivars developed in many crop species. However, plant variety and cultivar identification via basic morphological features is problematic and challenging when differentiating closely related species not only due to their limited differences but also due to technical limitations of the process being time-consuming, labour-intensive and costly, and statistically imprecise information being available due to phenotypic plasticity. Therefore, it is imperative to have rapid and highly efficient techniques to mitigate these limitations. This review provides an overview and summarization of the development and application of molecular markers such as Random Amplified Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), Simple Sequence Repeats (SSR), Inter-simple sequence repeats (ISSR), Amplified Fragment Length Polymorphism (AFLP), Single nucleotide polymorphism (SNP) and DNA barcoding, High-resolution melting (HRM) and biosensor technology as potential tools in the identification of plant variety and cultivar.

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References

  • Agarwal M, Shrivastava N and Padh H 2008 Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 27 617–631

    Article  CAS  PubMed  Google Scholar 

  • Aka Kaçar Y, Lezzoni AF and Çetiner S 2005 Sweet cherry cultivar identification by using SSR markers. J. Biol. Sci. 5 616–619

    Article  Google Scholar 

  • Amador DM, Brazeau D, Farmerie B, Blake A, Clark G and Whitten M 2001 Amplified Fragment Length Polymorphisms (AFLP) Workshop (Interdisciplinary Center for Biotechnology Research: University of Florida, Gainsville)

    Google Scholar 

  • Anand D, Prabhu KV and Singh AK 2012 Analysis of molecular diversity and fingerprinting of commercially grown Indian rice hybrids. J. Plant Biochem, Biot. 21 173–179

    Article  CAS  Google Scholar 

  • Annicchiarico P, Nazzicari N, Ananta A, Carelli M, Wei Y and Brummer C 2016 Assessment of cultivar distinctness in Alfalfa: A comparison of genotyping-by-sequencing, simple-sequence repeat marker, and morphophysiological observations. Plant Genome 9 1–12

    Article  CAS  Google Scholar 

  • Archak S, Gaikwad AB, Diksha Gautam Rao EVVB, Swam KM and Karihaloo JL 2003 DNA fingerprinting of Indian cashew (Anacardium occidentale L.) varieties using RAPD and ISSR techniques. Euphytica 230 397–404

    Article  Google Scholar 

  • Babu KN, Rajesh MK, Samsudeen K, Minoo D, Suraby EJ, Anupama K and Ritto P 2014 Randomly amplified polymorphic DNA (RAPD) and derived techniques; in Molecular Plant Taxonomy (ed) Besse P (Totowa: Humana Press) 191–209

    Chapter  Google Scholar 

  • Bakappa S, Talebi E and Subramanya G 2011 Role of molecular markers (RAPD & ISSR) in silkworm conservation. Int. J. Adv. Biol. Res. 1 1–7

    Google Scholar 

  • Besnard G, Breton C, Baradat P, Khadari B and Bervillé A 2001 Cultivar identification in olive based on RAPD markers. J. Am. Soc. Hortic. Sci. 126 668–675

    Article  CAS  Google Scholar 

  • Bhalla N, Jolly P, Formisano N and Estrela P 2016 Introduction to biosensors. Essays Biochem. 60 1–8

    Article  PubMed  PubMed Central  Google Scholar 

  • Cabezas JA, Ibáñez J, Lijavetzky D, Vélez D, Bravo G, Rodríguez V, Carreño I, Jermakow A, et al. 2011 48 SNP set for grapevine cultivar identification. BMC Plant Biol. 11 153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • CBOL Plant Working Group 2009 A DNA Barcode for Land Plants. Proc. Natl. Acad. Sci. USA 106 2794–12797

    Article  Google Scholar 

  • Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink HA, et al. 2008 Development of a set of SNP markers present in expressed genes of the apple. Genomics 92 353–358

    Article  PubMed  CAS  Google Scholar 

  • Chase MW and Fay MF 2009 Barcoding of Plants and Fungi. Science 325 682–683

    Article  CAS  PubMed  Google Scholar 

  • Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N and Savolainen V 2005 Land plants and DNA barcodes: short-term and longterm goals. Philos. Trans. r. Soc. Lond. b. Biol. Sci. 360 1889–1895

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chatterjee SN, Vijayan K, Roy GC and Nair CV 2004 ISSR profiling of genetic variability in the ecotypes of Anthereae mylitta Drury, the tropical tasar silkworm. Russ. J. Genet. 40 152–159

    Article  CAS  Google Scholar 

  • Chen H, Liu L, Wang L, Wang S, Wang ML and Cheng X 2015 Development of SSR markers and assessment of genetic diversity of adzuki bean in the Chinese germplasm collection. Mol. Breed. 35 191

    Article  CAS  Google Scholar 

  • Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, et al. 2010 Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE 5 e8613

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cheon KS, Baek J, Cho YI, Lee Jeong YM. and YY, Oh J and Choi I, 2018 Single nucleotide polymorphism (SNP) discovery and kompetitive allele-specific PCR (KASP) marker development with Korean japonica rice varieties. Plant Breed. Biotech. 6 91–403

    Article  Google Scholar 

  • Clark LC Jr and Lyons C 1962 Electrode systems for continuous monitoring in cardiovascular surgery. Ann. NY. Acad. Sci. 102 29–45

    Article  CAS  PubMed  Google Scholar 

  • Congiu L, Chicca M, Cella R, Rossi R and Bernacchia G 2000 The use of random amplified polymorphic DNA (RAPD) markers to identify strawberry varieties: a forensic application. Mol. Ecol. 9 229–232

    Article  CAS  PubMed  Google Scholar 

  • Cowan RS and Fay MF 2012 Challenges in the DNA barcoding of plant material. Methods Mol. Biol. 862 23–33

    Article  CAS  PubMed  Google Scholar 

  • Crochemore ML, Nunes LM, Andrade GA, Molinari HBC and Vasconcellos ME 2004 Varietal identification of coffee seeds by RAPD technique. Braz. Arch. Biol. Technol. 47 7–11

    Article  Google Scholar 

  • Croxford AE, Rogers T, Caligari PD and Wilkinson MJ 2008 High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar. New Phytol. 180 594–607

    Article  CAS  PubMed  Google Scholar 

  • Dawes J, Lim LC and Cheong L 1999 The dragon fish (Havant: Kingdom Books)

    Google Scholar 

  • Devran Z, Goknur A and Mesci L 2016 Development of molecular markers for the Mi-1Gene in tomato using the KASP genotyping assay. Hortic. Environ. Biotechnol. 57 156–160

    Article  Google Scholar 

  • Diaz S, Pire C, Ferrer J and Bonete MJ 2003 Identification of Phoenix dactylifera L. varieties based on amplified fragment length polymorphism (AFLP) markers. Cell Mol. Biol. Lett. 8 891–900

    CAS  PubMed  Google Scholar 

  • Enan MR and Ahmed A 2016 Cultivar-level phylogeny using chloroplast DNA barcode psbK-psbI spacers for identification of Emirati date palm (Phoenix dactylifera L.) varieties. Genet. Mol. Res. 15 15038470

    Article  Google Scholar 

  • Erali M, Voelkerding KV and Wittwer CT 2008 High resolution melting applications for clinical laboratory medicine. Exp. Mol. Pathol. 85 50–58

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fang J, Twito T, Zhang Z and Chao CT 2005 Genetic relationships among fruiting-mei (Prunus mume Sieb. et Zucc.) cultivars evaluated with AFLP and SNP markers. Genome 49 1256–1264

    Article  Google Scholar 

  • Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC, Percy DM and Hajibabaei M 2008 Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS ONE 3 e2802

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fraga J, Rodriguez J, Fuentes O, Fernandez-Calienes A and Castex M 2005 Optimization of random amplified polymorphic DNA techniques for use in genetic studies of Cuban Triatominae. Rev. Inst. Med. Trop. Sao Paulo 4 295–300

    Article  Google Scholar 

  • Fu XJ, Pei JX, Zheng YT, Guo DD, Yang QH, Jin HX, Zhu DH, Dong D, et al. 2019 DNA Fingerprinting of Vegetable Soybean Cultivar ‘Zhexian No. 9’using 101 New Developed HRM-Based SNP Markers. Legume Res. -an International Journal 43 8–17

    Google Scholar 

  • Ganopoulos I, Argiriou A and Tsaftaris A 2011 Microsatellite high resolution melting (SSR-HRM) analysis for authenticity testing of protected designation of origin (PDO) sweet cherry products. Food Control 22 532–541

    Article  CAS  Google Scholar 

  • Ganopoulos I, Madesis P and Tsaftaris A 2012 Universal ITS2 barcoding DNA region coupled with high-resolution melting (HRM) analysis for seed authentication and adulteration testing in leguminous forage and pasture species. Plant Mol. Biol. Rep. 30 1322–1328

    Article  CAS  Google Scholar 

  • Ganopoulos I, Tsaballa A, Xanthopoulou A, Madesis P and Tsaftaris, 2013 A. Sweet cherry cultivar identification by high-resolution-melting (HRM) analysis using gene-based SNP markers. Plant Mol. Biol. Rep. 31 763–768

    Article  CAS  Google Scholar 

  • Gao L, Jia J and Kong X 2016 A SNP-based molecular barcode for characterization of common wheat. PLoS ONE 11 e0150947

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gogoi B and Bhau BS 2018 DNA barcoding of the genus Nepenthes (Pitcher plant): a preliminary assessment towards its identification. BMC Plant Biol. 18 153

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gomes S, Castro C, Barrias S, Pereira L, Jorge P, Fernandes JR and Martins-Lopes P 2018 Alternative SNP detection platforms, HRM and biosensors, for varietal identification in Vitis vinifera L. using F3H and LDOX genes. Sci. Rep. 8 1–12

    Article  Google Scholar 

  • Goremykin VV, Holland B, Hirsch-Ernst KI and Hellwig FH 2005 Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Mol. Biol. Evol. 22 1813–1822

    Article  CAS  PubMed  Google Scholar 

  • Guo YP, Saukel J, Mittermayr R and Ehrendorfer F 2005 AFLP analyses demonstrate genetic divergence, hybridization, and multiple polyploidization in the evolution of Achillea (Asteraceae-Anthemideae). New Phytologist 166 273–290

    Article  CAS  PubMed  Google Scholar 

  • Gupta PK, Roy JK and Prasad M 2001 Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr. Sci. 80 524–535

    CAS  Google Scholar 

  • Han J, Wang WY, Leng XP, Guo L, Yu ML, Jiang WB and Ma RJ 2014 Efficient identification of ornamental peach cultivars using RAPD markers with a manual cultivar identification diagram strategy. Genet. Mol. Res. 13 32–42

    Article  CAS  PubMed  Google Scholar 

  • Hao DC, Chen SL and Xiao PG 2010 Sequence characteristics and divergent evolution of the chloroplast psbA-trnH noncoding region in gymnosperms. J. Appl. Genet. 51 259–273

    Article  CAS  PubMed  Google Scholar 

  • Hebert PD, Cywinska A, Ball SL and Dewaard JR 2003 Biological identifications through DNA barcodes. Proc. Biol. Sci. 270 313–321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hebert PD and Gregory TR 2005 The promise of DNA barcoding for taxonomy. Syst. Biol. 54 852–859

    Article  PubMed  Google Scholar 

  • Heo S, Kim C and Chung YS 2019 High-resolution melting analysis for identification of apple cultivars using simple sequence repeat markers. Plant Bioteh. Rep. 13 337–344

    Article  Google Scholar 

  • Herrmann MG, Durtschi JD, Bromley LK, Wittwer CT and Voelkerding KV 2006 Amplicon DNA melting analysis for mutation scanning and genotyping: cross-platform comparison of instruments and dyes. Clin. Chem. 52 494–503

    Article  CAS  PubMed  Google Scholar 

  • Hidayat T, Abdullah FI, Kuppusamy C, Samad AA and Wagiran A 2012 Molecular identification of Malaysian pineapple cultivar based on internal transcribed spacer region. APCBEE Procedia 4 146–151

    Article  CAS  Google Scholar 

  • Hou YC, Yan ZH, Wei YM and Zheng YL 2005 Genetic diversity in barley from west China based on RAPD and ISSR analysis. Barley Genet. Newsl. 35 9–22

    Google Scholar 

  • Islam MS, Thyssen GN, Jenkins JN and Fang DD 2015 Detection, validation, and application of Genotypingby-Sequencing based single nucleotide polymorphisms in Upland cotton. Plant Genome 8 1–10

    Article  CAS  Google Scholar 

  • Jaakola L, Suokas M and Häggman H 2010 Novel approaches based on DNA barcoding and high-resolution melting of amplicons for authenticity analyses of berry species. Food Chem. 123 494–500

    Article  CAS  Google Scholar 

  • Jehan T and Lakhanpaul S 2006 Single nucleotide polymorphism (SNP)-methods and applications in plant genetics: a review. Indian J. Biotech. 5 435–439

    CAS  Google Scholar 

  • Joshi SP, Ranjekar PK and Gupta VS 1999 Molecular markers in plant genome analysis. Curr. Sci. 77 230–240

    CAS  Google Scholar 

  • Kahn K and Plaxco KW 2010 Principles of Biomolecular Recognition; in Recognition receptors in biosensors (ed) Zourob M (New York: Springer) 3–46

    Chapter  Google Scholar 

  • Kalia RK, Rai MK, Kalia S, Singh R and Dhawan A 2011 Microsatellite markers: an overview of the recent progress in plants. Euphytica 177 309–334

    Article  CAS  Google Scholar 

  • Kar PK, Vijayan K, Nair CV, Mohandas TP, Saratchandra B and Thangavelu K 2005 Genetic variability and genetic structure of wild and semi-domestic populations of tasar silkworm (Antheraea mylitta) ecorace Daba as revealed through ISSR markers. Genetica 125 173–183

    Article  CAS  PubMed  Google Scholar 

  • Karaagac E, Yilma S, Cuesta-Marcos A and Vales I 2014 Molecular analysis of potatoes from the pacific Northwest Tri-State cultivar development program and selection of markers for practical DNA fingerprinting applications. Am. J. Cardiol. 91 195–203

    CAS  Google Scholar 

  • Karakousis A, Barr AR, Chalmers KJ, Ablett GA, Holton TA, Henry RJ, Lim P and Langridge P 2003 Potential of SSR markers for plant breeding and variety identification in Australian barley germplasm. Aust. J. Agric. Res. 54 1197–1210

    Article  CAS  Google Scholar 

  • Karp A, Kresovich S, Bhat KV, Ayad WG and Hodgkin T 1997 Molecular tools in plant genetic resources conservation: A guide to technologies. IPGRI Technical Bulletin No. 2. Rome: International Plant Genetic Resources Institute

  • Korir NK, Han J, Shangguan L, Wang C, Kayesh E, Zhang Y and Fang J 2012 Plant variety and cultivar identification: advances and prospects. Crit. Rev. Biotechnol. 33 111–125

    Article  PubMed  Google Scholar 

  • Kress WJ and Erickson DL 2008 DNA barcodes: genes, genomics, and bioinformatics. Proc. Natl. Acad. Sci. 105 2761–2762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kress WJ, Erickson DL, Swenson NG, Thompson J, Uriarte M and Zimmer man JK 2010 Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot. PLoS ONE 5 e15409

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kress WJ and Erickson DLA 2007 two-locus global DNA barcode for land plants: the coding rbcL gene complements the noncoding trnH-psbA spacer region. PLoS ONE 2 e508

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA and Janzen DH 2005 Use of DNA barcodes to identify flowering plants. Proc. Natl. Acad. Sci. USA 102 8369–8374

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumari N and Thakur SK 2014 Randomly amplified polymorphic DNA-A brief review. Am. J. Anim. Vet. Sci. 9 6–13

    Article  Google Scholar 

  • Ledesma NA, Matulac JM, Sevilleja JE and Enriquez ML 2020 Detecting strawberry cultivar misidentification in the Philippines using single nucleotide polymorphism markers from the anthocyanin reductase gene. bioRxiv. https://doi.org/10.1101/2020.02.02.922369

  • Lee SC, Wang CH, Yen CE and Chang C 2017 DNA barcode and identification of the varieties and provenances of Taiwan’s domestic and imported made teas using ribosomal internal transcribed spacer 2 sequences. J. Food. Drug. Anal. 125 260–274

    Article  CAS  Google Scholar 

  • Lei Y, Yang F, Tang L, Chen K and Zhang GJ 2015 Identification of Chinese herbs using a sequencing-free nanostructured electrochemical DNA biosensor. Sensors 15 29882–29892

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li F, Feng Y, Dong P, Yang L and Tang B 2011 Gold nanoparticles modified electrode via simple electrografting of in situ generated mercaptophenyl diazonium cations for development of DNA electrochemical biosensor. Biosens. Bioelectron. 26 1947–1952

    Article  CAS  PubMed  Google Scholar 

  • Li JY, Wang J and Zeigler RS 2014 The 3,000 rice genomes project: new opportunities and challenges for future rice research. GigaScience. 3 1–3

    Article  CAS  Google Scholar 

  • Li L, Fang Z, Zhou J, Chen H, Hu Z, Gao L, Chen L, Ren S, et al. 2017 An accurate and efficient method for large-scale SSR genotyping and applications. Nucleic Acids Res. 45 e88

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liew M, Pryor R, Palais R, Meadows C, Erali M, Lyon E and Wittwer C 2004 Genotyping of single-nucleotide polymorphisms by high resolution melting of small amplicons. Clin. Chem. 50 1156–1164

    Article  CAS  PubMed  Google Scholar 

  • Liu G, Ning H, Ayidaerhan N and Aisa HA 2016 Evaluation of DNA barcode candidates for the discrimination of Artemisia L. Mitochondrial DNA A 28 956–964

    Article  CAS  Google Scholar 

  • Lochlainn SÓ, Amoah S, Graham NS, Alamer K, Rios JJ, Kurup S, Stoute A, Hammond JP, et al. 2011 High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes. Plant Methods 7 43

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lombard V, Baril CP, Dubreuil P, Blouet F and Zhang D 2000 Genetic relationships and fingerprinting of rapeseed cultivars by AFLP: consequences for varietal registration. Crop Sci. 40 1417–1425

    Article  CAS  Google Scholar 

  • Lowe AJ, Hanotte O and Guarino L 1996 Standardization of molecular Genetic techniques for the characterization of germplasm collections: The case of Random Amplified Polymorphic DNA (RAPD). Plant Genet. Res. Newslett. 107 50–54.

    Google Scholar 

  • Lowe RS 2008 Overview of Biosensor and Bioarray Technologies; in Handbook of Biosensors and Biochips (eds) RS Marks, CR Lowe, DC Cullen and HH Weetall, I Karube (Weinheim: Wiley)

  • Mackay JF, Wright CD and Bonfiglioli RG 2008 A new approach to varietal identification in plants by microsatellite high resolution melting analysis: application to the verification of grapevine and olive cultivars. Plant Methods 4 8

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mammadov J, Aggarwal R, Buyyarapu R and Kumpatla S 2012 SNP markers and their impact on plant breeding. Int. J. Plant Biol. 2012 728398

    Google Scholar 

  • Merkouropoulos G, Ganopoulos I, Tsaftaris A, Papadopoulos I and Drogoudi P 2016 Combination of high resolution melting (HRM) analysis and SSR molecular markers speeds up plum genotyping: case study genotyping the Greek plum GeneBank collection. Plant Genet. Resour. 15 366–375

    Article  CAS  Google Scholar 

  • Métais I, Aubry C, Hamon B, Jalouzot R and Peltier D 2000 Description and analysis of genetic diversity between commercial bean lines (Phaseolus vulgaris L.). Theor. Appl. Genet. 101 1207–1214

    Article  Google Scholar 

  • Mishra P, Kumar A, Nagireddy A, Mani DN, Shukla AK, Tiwari R and Sundaresan V 2016 DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnol. J. 14 8–21

    Article  CAS  PubMed  Google Scholar 

  • Mochida K, Yamazaki Y and Ogihara Y 2003 Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol. Genet. Genomics. 270 371–377

    Article  CAS  PubMed  Google Scholar 

  • Moe AM and Weiblen GD 2011 Development and characterization of microsatellite loci in dioecious figs (Ficus, Moraceae). Am. J. Bot. 98 e25–e27

    Article  CAS  PubMed  Google Scholar 

  • Mohindra V, Mishra A, Palanichamy M and Ponniah AG 2001 Cross-species amplification of Catla catla microsatellite locus in Labeo rohita. Indian J. Fish 48 103–108

    Google Scholar 

  • Moisan-Thiery M, Marhadour S, Kerlan MC, Dessenne N, Perramant M, Gokelaere T and Le Hingrat Y 2005 Potato cultivar identification using simple sequence repeats markers (SSR). Potato Res. 48 191–200

    Article  Google Scholar 

  • Montgomery JL, Sanford LN and Wittwer CT 2010 High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev. Mol. Diagn. 10 219–240.

    Article  CAS  PubMed  Google Scholar 

  • Muchugi A, Kadu C, Kindt R, Kipruto H, Lemurt S, Olale K, Nyadoi P, Dawson I, et al. 2008 Molecular markers for tropical trees; in A Practical Guide to Principles and Procedures (eds) I Dawson and R Jamnadass (Gigiri: World Agroforestry Centre) pp 37–38

  • Munthali M, Ford-Lloyd BV and Newbury HJ 1992 The random amplification of polymorphic DNA for fingerprinting plants. Genome Res. 1 274–276

    Article  CAS  Google Scholar 

  • Nagaoka T and Ogihara Y 1997 Applicability of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers. Theor. Appl. Genet. 94 597–602

    Article  CAS  Google Scholar 

  • Newmaster SG, Fazekas AJ, Steeves RAD and Janovec J 2008 Testing candidate plant barcode regions in the Myristicaceae. Mol. Ecol. Resour. 8 480–490

    Article  CAS  PubMed  Google Scholar 

  • Osathanunkul M 2018 Bar-HRM for authenticating soursop (Annona muricata) tea. Sci. Rep. 8 1–7

    Article  Google Scholar 

  • Osathanunkul M, Madesis P and De Boer H 2015 Bar-HRM for authentication of plant-based medicines: evaluation of three medicinal products derived from Acanthaceae species. PLoS ONE 10 e0128476

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Osathanunkul M, Suwannapoom C, Khamyong N, Pintakum D, Lamphun SN, Triwitayakorn K, Osanthanunkul K and Madesis P 2016 Hybrid analysis (barcode-high resolution melting) for authentication of Thai herbal products, Andrographis paniculata (Burm. F.) Wall ex Nees. Pharmacogn Mag. 12 S71

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Parks EJ and Moyer JW 2004 Evaluation of AFLP in poinsettia: Polymorphism selection, analysis, and cultivar identification. J. Am. Soc. Hortic. Sci. 129 863–869

    Article  CAS  Google Scholar 

  • Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G and Motto M 1998 Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor. Appl. Genet. 97 1248–1255

    Article  CAS  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S and Rafalski A 1996 The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breed. 2 225–238

    Article  CAS  Google Scholar 

  • Prevost A and Wilkinson MJ 1999 A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor. Appl. Genet. 98 107–112

    Article  CAS  Google Scholar 

  • Provan J, Kumar A, Shepherd L, Powell W and Waugh R 1996 Analysis of intra-specific somatic hybrids of potato (Solanum tuberosum) using simple sequence repeats. Plant Cell Rep. 16 196–199

    Article  CAS  PubMed  Google Scholar 

  • Qian W, Ge S and Hong DY 2001 Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers. Theor. Appl. Genet. 102 440–449

    Article  CAS  Google Scholar 

  • Rafalski JA 2002 Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci. 162 329–333

    Article  CAS  Google Scholar 

  • Rafique B, Iqbal M, Mehmood T and Shaheen MA 2019 Electrochemical DNA biosensors: A review. Sens. Rev. 39 34–50

    Article  Google Scholar 

  • Rahman M, Heng LY, Futra D, Chiang CP, Rashid ZA and Ling TL 2017 A highly sensitive electrochemical DNA biosensor from acrylic-gold nano-composite for the determination of arowana fish gender. Nanoscale. Res. Lett. 12 484

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Reed GH and Wittwer CT 2004 Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin. Chem. 50 1748–1754

    Article  CAS  PubMed  Google Scholar 

  • Reja V, Kwok A, Stone G, Yang L, Missel A, Menzel C and Bassam B 2010 ScreenClust: Advanced statistical software for supervised and unsupervised high resolution melting (HRM) analysis. Methods 50 S10–S14

    Article  CAS  PubMed  Google Scholar 

  • Ririe KM, Rasmussen RP and Wittwer CT 1997 Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem. 245 154–160

    Article  CAS  PubMed  Google Scholar 

  • Rolland M, Dupuy A, Pelleray A and Delavault P 2016 Molecular identification of broomrape species from a single seed by high resolution melting analysis. Front. Plant Sci. 7 1838

    Article  PubMed  PubMed Central  Google Scholar 

  • Rout GR, Bhatacharya D, Nanda RM, Nayak S and Das P 2003 Evaluation of genetic relationships in Dalbergia species using RAPD markers. Biodivers. Conserv. 12 197–206

    Article  Google Scholar 

  • Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W and Waugh R 1997 Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor. Appl. Genet. 95 714–722

    Article  CAS  Google Scholar 

  • Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry ST, Mullikin JC, et al. 2001 A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409 928–933

    Article  CAS  PubMed  Google Scholar 

  • Sass C, Little DP, Stevenson DW and Specht CD 2007 DNA barcoding in the Cycadales: testing the potential of proposed barcoding markers for species identification of cycads. PloS ONE 11 e1154

    Article  CAS  Google Scholar 

  • Saunders JA, Mischke S and Hemeida AA 2001 The use of AFLP techniques for DNA fingerprinting in plants. CEQ 2000XL application information (California: Beckman Coulter, Inc.)

    Google Scholar 

  • Savelkoul PHM, Aarts HJM, De Haas J, Dijkshoorn L, Duim B, Otsen M, Rademaker JL, Schouls S, et al. 1999 Amplified-fragment length polymorphism analysis: the state of an art. J. Clin. Microbiol. 37 3083–3091

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scott D and Fuller J 1976 The reproductive biology of Scleropages formosus (Müller and Schlegel) (Osteoglossomorpha, Osteoglossidae) in Malaya, and the morphology of its pituitary gland. J. Fish Biol. 8 45–53

    Article  Google Scholar 

  • Semagn K, Babu R, Hearne S and Olsen MS 2014 Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): Over view of the technology and its application in crop improvement. Mol. Breed. 33 1–14

    Article  CAS  Google Scholar 

  • Shangguan LF, Wang YZ, Li XY, Wang YJ, Song CN and Fang JG 2012 Identification of selected apricot cultivars using RAPD and EST-SSR markers. Caryologia 65 130–139

    Article  Google Scholar 

  • Shaw J, Lickey EB, Schilling EE and Small RL 2007 Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am. J. Bot. 94 275–288

    Article  CAS  PubMed  Google Scholar 

  • Shruthi GS, Amitha CV and Mathew BB 2014 Biosensors: a modern day achievement. J. Instrument Technol. 2 26–39

    Google Scholar 

  • Simko I 2016 High-resolution DNA melting analysis in plant research. Trends Plant Sci. 21 528–537

    Article  CAS  PubMed  Google Scholar 

  • Singh BD and Singh AK 2015 Marker-assisted plant breeding: principles and practices (New Delhi: Springer)

    Book  Google Scholar 

  • Soliman MSA, Shedeed ZA and Soliman MM 2018 Morphological, biochemical and DNA barcoding characteristics for some Lantana L. cultivars growing in Egypt. Trop. Plant Res. 5 207–216

    Article  Google Scholar 

  • Song M, Li J, Xiong C, Liu H and Liang J 2016 Applying high-resolution melting (HRM) technology to identify five commonly used Artemisia species. Sci. Rep. 6 34133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Starr JR, Naczi RF and Chouinard BN 2009 Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae). Mol. Ecol. Resour. 9 151–163

    Article  CAS  PubMed  Google Scholar 

  • Steele KA, Quinton-Tulloch MJ, Amgai RB, Dhakal R, Khatiwada SP, Vyas D, Heine M and Witcombe JR 2018 Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing of indica rice. Mol. Breed. 38 38

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Stoeckle MY and Thaler DS 2014 DNA barcoding works in practice but not in (neutral) theory. PloS ONE 9 e100755

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Štorchová H and Olson MS 2007 The architecture of the chloroplast psbA-trnH non-coding region in angiosperms. Plant Syst. Evol. 268 235–256

    Article  CAS  Google Scholar 

  • Suesatpanit T, Osathanunkul K, Madesis P and Osathanunkul M 2017 Should DNA sequence be incorporated with other taxonomical data for routine identifying of plant species? BMC Complement Altern. Med. 17 437

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sun X, Mu Q, Jiang D, Wang C, Wang XC and Fang JG 2012 A new strategy employed for identification of sweet orange cultivars with RAPD markers. Genet. Mol. Res. 11 2071–2080

    Article  CAS  PubMed  Google Scholar 

  • Taheri S, Abdullah TL, Jain SM, Sahebi M and Azizi P 2017 TILLING, high-resolution melting (HRM), and next-generation sequencing (NGS) techniques in plant mutation breeding. Mol. Breed. 37 40

    Article  CAS  Google Scholar 

  • Tanyolac B 2003 Inter-simple sequence repeat (ISSR) and RAPD variation among wild barley (Hordeum vulgare subsp. spontaneum) populations from west Turkey. Genet. Resour. Crop Evo. 50 611–614

    Article  CAS  Google Scholar 

  • Tautz D and Renz M 1984 Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res. 12 4127–4138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tian H, Wang F, Zhao J, Yi H, Wang L, Wang R, Yang Y and Song W 2015 Development of maize SNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties. Mol. Breed. 35 136–146

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tillault AS and Yevtushenko DP 2019 Simple sequence repeat analysis of new potato varieties developed in Alberta, Canada. Plant Direct 3 e00140

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tingey SV, Rafalski JA and Williams SJK 1992 Genetic analysis with RAPD markers; in Proceedings of the Symposium Application of RAPD Technology to Plant Breeding (Minneapolis: Crop Science Society of America, Minneapolis) pp 3–8

  • Tsumura Y, Ohba K and Strauss SH 1996 Diversity and inheritance of inter-simple sequence repeat polymorphisms in Douglasfir (Pseudotsuga menziesii) and sugi (Cryptomeria japonica). Theor. Appl. Genet. 92 40–45

    Article  CAS  PubMed  Google Scholar 

  • Velasco-Garcia MN and Mottram T 2003 Biosensor technology addressing agricultural problems. Biosyst. Eng. 84 1–12

    Article  Google Scholar 

  • Vignal A, Milan D, SanCristobal M and Eggen A 2002 A review on SNP and other types of molecular markers and their use in animal genetics. Genet. Selection Evolution. 34 275–305

    Article  CAS  Google Scholar 

  • Villano C, Miraglia V, Iorizz M, Aversano A and Carputo D 2016 Combined use of molecular markers and high-resolution melting (HRM) to assess chromosome dosage in potato hybrids. J. Hered. 107 187–192

    Article  CAS  PubMed  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, Van der Lee T, Hornes M, Friters A, Po J, et al. 1995 AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 3 4407–4414

    Article  Google Scholar 

  • Vos P and Kuiper M 1997 AFLP analysis; in DNA Markers. Protocols, Applications, and Overviews (ed) G Caetano-Anolles and PM Gresshoff (New York: Wiley-VCH) pp 115–131

  • Vossen RH, Aten E, Roos A and den Dunnen JT 2009 High-Resolution Melting Analysis (HRMA): more than just sequence variant screening. Hum. Mutat. 30 860–866

    Article  CAS  PubMed  Google Scholar 

  • Wang F, Yang Y, Yi H, Zhao J, Ren J, Wang L, Ge J and Jiang B 2017 Construction of an SSR-based standard fingerprint database for corn variety authorized in China. Sci. Agric. Sin. 50 1–14

    Google Scholar 

  • Wang HL, Yang J, Boykin LM, Zhao QY, Wang YJ, Liu SS and Wang XW 2014 Developing conversed microsatellite markers and their implications in evolutionary analysis of the Bemisia tabaci complex. Sci. Rep. 4 6351

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Welsh J and McClelland M 1990 Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18 7213–7218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Williams GK, Kubelik AR, Livak KL, Rafalski JA and Tingey SV 1990 DNA polymorphisms amplified by arbitraray primers are useful as genetic markers. Nucleic Acids Res. 18 6531–6535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wittwer CT, Reed GH, Gundry CN, Vandersteen JG and Pryor RJ 2003 High-resolution genotyping by amplicon melting analysis using LCGreen. Clin. Chem. 49 853–860

    Article  CAS  PubMed  Google Scholar 

  • Wolf T, Eimert K and Ries R 1999 Reliable identification of grapevine rootstock varieties using RAPD PCR on woody samples. Aust. J. Grape Wine Res. 5 34–38

    Article  CAS  Google Scholar 

  • Wu Q, Zhang Y, Yang Q, Yuan N and Zhang W 2019 Review of electrochemical DNA biosensors for detecting food borne pathogens. Sensors 19 4916

    Article  CAS  PubMed Central  Google Scholar 

  • Wu SB, Tavassolian I, Rabiei G, Hunt P, Wirthensohn M, Gibson JP, Ford CM and Sedgley M 2009 Mapping SNP-anchored genes using high-resolution melting analysis in almond. Mol. Genet. Genomics 282 273–281

    Article  CAS  PubMed  Google Scholar 

  • Wu SB, Wirthensohn MG, Hunt P, Gibson JP and Sedgley M 2018 High resolution melting analysis of almond SNPs derived from ESTs. Theor. Appl. Genet. 118 1–4

    Article  CAS  Google Scholar 

  • Wünsch A and Hormaza JI 2002 Molecular characterization of sweet cherry (Prunus avium L) genotypes using peach (Prunus persica (L) Batsch) SSR sequences. Heredity 89 56–63

    Article  PubMed  CAS  Google Scholar 

  • Xanthopoulou A, Ganopoulos I, Koubouris G, Tsaftaris A, Sergendani C, Kalivas A and Madesis P 2013 Microsatellite high-resolution melting (SSR-HRM) analysis for genotyping and molecular characterization of an Olea europaea germplasm collection. Plant Genet. Res. 12 273–277

    Article  Google Scholar 

  • Xanthopoulou A, Ganopoulos I, Tsaballa A, Nianiou-Obeidat I, Kalivas A, Tsaftaris A and Madesis P 2014 Summer squash identification by High-Resolution-Melting (HRM) analysis using gene-based EST–SSR molecular markers. Plant Mol. Biol. Rep. 32 395–405

    Article  CAS  Google Scholar 

  • Xie Q, Zhang H, Yan F, Yan C, Wei S, Lai J, Wang Y and Zhang B 2019 Morphology and molecular identification of twelve commercial varieties of kiwifruit. Molecules 24 888

    Article  PubMed Central  CAS  Google Scholar 

  • Yang DU, Kim MK, Mohanan P, Mathiyalagan R, Seo KH, Kwon WS and Yang DC 2017 Development of a single-nucleotide-polymorphism marker for specific authentication of Korean ginseng (Panax ginseng Meyer) new cultivar “G-1.” J. Ginseng Res. 41 31–35

    Article  PubMed  Google Scholar 

  • Yang F, Ding F, Chen H, He M, Zhu S, Ma X, Jiang L and Li H 2018 DNA barcoding for the identification and authentication of animal species in traditional medicine. Evid. Based Complementary Altern. Med. 2018 5160254

    Article  Google Scholar 

  • Yang J, Zhang J, Han R, Zhang F, Mao A, Luo J, Dong B, Liu H, et al. 2019 Target SSR-seq: a novel SSR genotyping technology associate with perfect SSRs in genetic analysis of cucumber varieties. Front. Plant Sci. 10 531

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang S, Fresnedoramírez J, Wang M, Cote L, Schweitzer P, Barba P, Takacs EM, Clark M, et al. 2016 A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. Hortic. Res. 3 16002

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yao H, Song J, Liu C, Luo K, Han J, Li Y, Pang X, Xu H, et al. 2010 Use of ITS2 region as the universal DNA barcode for plants and animals. PloS ONE 5 e13102

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yonemoto Y, Chowdhury AK, Kato H and Macha MM 2006 Cultivars identification and their genetic relationships in Dimocarpus longan subspecies based on RAPD markers. Sci. Hortic. 109 147–152

    Article  CAS  Google Scholar 

  • Yu K, Van Deynze A and Pauls KP 1993 Random amplified polymorphic DNA (RAPD) analysis; in Methods in Plant Molecular and Biotechnology (eds) Glick BR and Thompson JE (Boca Raton: CRC Press) 287–301

    Google Scholar 

  • Yu Y, Saghai Maroof M, Buss G, Maughan P and Tolin S 1994 RFLP and microsatellite mapping of a gene for soybean mosaic virus resistance. Phytopathology 1 60–64

    Article  Google Scholar 

  • Yuan J, Wen Z, Gu C and Wang D 2014 Introduction of high throughput and cost effective SNP genotyping platforms in soybean. Plant Genet. Genom. Biotechnol. 2 90–94

    Article  Google Scholar 

  • Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCrown B, Harbut R, et al. 2012 Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am. J. Bot. 99 193–208

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Yang J, Zhang L, Luo J, Zhao H, Zhang J and Wen C 2020a A new Snp genotyping technology target Snp-seq and its application in genetic analysis of cucumber varieties. Sci. Rep. 10 5623

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang S, Li B, Chen Y, Shaibu AS, Heng H and Sun J 2020b Molecular-Assisted Distinctness and Uniformity Testing Using SLAF-Sequencing Approach in Soybean. Genes 11 175

    Article  CAS  PubMed Central  Google Scholar 

  • Zhang YP, Tan HH, Cao SY, Wang XC, Yang G and Fan JG 2012 A novel strategy for identification of 47 pomegranate (Punica granatum) cultivars using RAPD markers. Genet. Mol. Res. 11 3032–3041

    Article  CAS  PubMed  Google Scholar 

  • Zhu Y, Wang Q, Hu J, Zhu L, Wang J, Zhu S and Guan Y 2013 High resolution melting curve analysis: an efficient method for fingerprinting of hybrid rice cultivars and their parental lines. Aust J. Crop Sci. 7 2048–2053

    Google Scholar 

  • Zietkiewicz E, Rafalski A and Labuda D 1994 Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20 176–183

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We would like to thank to the Malaysian Agricultural Research and Development Institute (MARDI) for the research funding, PRB 405, MARDI Development Grant. Schematic representations were generated in Adobe Illustrator with the support of Biorender (©BioRender - biorender.com).

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Correspondence to Han Yih Lau.

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Corresponding editor: Manchikatla Venkat Rajam

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Azizi, M.M.F., Lau, H.Y. & Abu-Bakar, N. Integration of advanced technologies for plant variety and cultivar identification. J Biosci 46, 91 (2021). https://doi.org/10.1007/s12038-021-00214-x

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