Decoding Plant Diversity: Modern Molecular Tools in Biodiversity Research | InformativeBD

Shahid Ali Chand, Muhammad Zohaib Hassan, Umair Rasool Azmi,  Muhammad Ilyas,  Iqra Kanwal, Ghulam Mujtaba Atif,  Aqdas Hameed, Atif Haroon, Tayyaba Yasin, Muhammad Huzaifa Mahmood,  Muhammad Yousof Zahoor, and Muhammad Nabeel Aslam, from the  different institute of Pakistan, wrote a Review article about, Decoding Plant Diversity: Modern Molecular Tools in Biodiversity Research. Entitled, Review on use of recent molecular techniques to access biodiversity in plants. This research paper published by the Journal of Biodiversity and Environmental Sciences | JBES. an open access scholarly research journal on Biodiversity. under the affiliation of the International Network For Natural Sciences| INNSpub. an open access multidisciplinary research journal publisher.

Abstract

Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species. DNA barcoding uses particular regions of DNA making helping in categorization and recognize unknown species. Researchers now interested to generate DNA barcodes designed for all living organisms and to build up data accessible to public to help in understanding of natural biodiversity of world. Cyclotides are peptides derived from plants with particular head to tail cyclic backbone that have three disulphide bonds by forming a cystine knot. Recent information about DNA barcoding can be used for detection of unidentified biological specimens to a taxonomic group, accurate detection of phytomedicinals, and in the biodiversity of living organisms.

Read more : Cleaning Leachate Naturally: Constructed Wetlands for Iligan City’s Landfill | InformativeBD

Introduction

Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity. DNA barcoding is especially used to determine the data base that identifies different species. Random Amplified Polymorphic DNA (RAPD) technique is PCR based procedure which is uses the random primers which bind to the nonspecific positions on the DNA and amplification of DNA and some molecular markers are also utilizes PCR primers comprising of nonspecific sequences in different length and size of nucleotides. Microsatellites and single nucleotide polymorphisms (SNP) Assortment arises through reproduction slippage, inadequate crossing over, modifications enhancement or disturbing the sequences of replications, although single nucleotide polymorphisms SNPs originate through point mutations. Simple series replications are tandem repeats of small as 10 base pairs and DNA sequences that are useful markers for genomic mapping and Loss of heterozygosity of well-defined chromosomal loci. Single nucleotide polymorphisms SNPs is type of genetic variations of different plant population in biodiversity. The nucleotides are associated at specific position but in SNPs the substitution of a single nucleotide to another nucleotide that distinguish the diversity of plants on genetic bases (Altschul et al., 1990).

The conservation and sustainable use of plant genetic resources require accurate identification of their accession. The emergence of DNA-based markers has changed the practice of species identification techniques(Ahmad et al., 2019).The dramatic advances in molecular genetics over the last few years have provided workers involved in the conservation of plant genetic resources with a range of new techniques for easy and reliable identification of plant species(Armstrong et al., 2005). Many of these techniques have been successfully used to study the extent and distribution of variation in species genepools and to answer typical evolutionary and taxonomic questions.

Many of these techniques have been successfully used to study the extent and distribution of variation in species gene-pools and to answer typical evolutionary and taxonomic questions. DNA barcoding is a practice with the purpose to discover the varieties based on species specific differences in short sequences of their DNA (Hebert et al., 2003). DNA barcoding utilizes principles of biochemistry, microbiology and biotechnology to recognize plant species in most efficiently detection method that is faster and accurate as compared to other traditional methods. This skill is now adopted in morphological characteristics, physiological conditions and allows species discovery without individual taxonomic information (Erickson et al., 2014). This has enabled research scientists especially in field of molecular biology to put efforts on DNA barcoding technique to estimate the herbal plant and related biological products accuracy (Hebert et al., 2003).

Sequencing based molecular techniques provide better resolution at intra-genus and above level, while frequency data from markers such as random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and microsatellites provide the means to classify individuals into nominal genotypic categories and are mostly suitable for intra-species genotypic variation study. This distinction is important to grasp for population studies, particularly when the diversity data are used as a basis for making decisions about conservation of plant resources. For instance, a recent study on Napier grass has showed that AFLP is incompatible with RAPD and morphological data; reregistration of all accessions of Napier grass based on DNA barcoding is suggested as a means to resolve the lingering problems regarding the identity of accessions. The main objective of this review is to provide a basic understanding of the recently developed molecular tools and their potential application in the conservation of plant resources (Olsvik et al.,1993).

The aims of the research are to access the biodiversity of different plants using molecular techniques and for the identification of different organisms. Molecular techniques such as Amplified Fragment Length Polymorphism (AFLP), Random Amplified Polymorphic DNA (RAPD), DNA barcoding, Microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. To access the different verities of plants and microorganisms these techniques evaluate the biodiversity between them. As in case of diseased plant to access the pathogen attack on susceptible plant and change in growth pattern of normal plant.These techniques are most necessity part of research on biodiversity and genetics that distinguish the next verities in future. Resistant verities of different plants having R gene that have high potential to resist the pathogen attack. These techniques play a significant role in RNA, DNA and Protein synthesis etc.

Reference

Ahmad I, Khan S, Naeem M, Hayat M, Azmi UR, Ahmed S, Murtaza G, Irfan M. 2019. Molecular Identification of Ten Palm Species using DNA Fingerprinting, Int. J. Pure App. Biosci 7(1), 46-51.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol 215, 403-410.

Armstrong KF, Ball SL. 2005. DNA barcodes for biosecurity: invasive species identification. Philos Trans R Soc B BiolSci 360,1813-1823.

Baldwin BG.1992. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: An example from the Compositae. Mol. Phylogenet. Evol 1, 3-16.

Coissac E, Hollingsworth PM, Lavergne S, Taberlet P. 2016. From barcodes to genomes: extending the concept of DNA barcoding. Molecular Ecology 25, 1423-1428.

Costion CM, Kress WJ, Crayn DM. 2016. DNA barcodes confirm the taxonomic and conservation status of a species of tree on the brink of extinction in the Pacific. PLOS ONE 11, e0155118.

Craik DJ. 2015. Plant cyclotides. Advances in Botanical Research, Volume 76, London: Academic Press.

Erickson DL, Jones FA, Swenson NG, Pei N, Bourg N, Chen W, Davies SJ, Ge X, Hao Z, Howe RW, Huang CL, Larson A, Lum S, Lutz JA, Ma K, Meegaskumbura M, Mi X, Parker JD, Fang Sun I, Wright J, Wolf AT, Ye W, Xing D, Zimmerman JK, Kress WJ. 2014. Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: A megaphy logeny approach. Frontiers in Genetics 5, 358.

Hamilton JP, Buell CR. 2012. Advances in plant genome sequencing. Plant J, 70, 177-190.

Hebert PD, Cywinska A, Ball SL, de Waard JR. 2003. Biological identifications through DNA barcodes. Proc Bio lSci, 270, 313-321.

Kress WJ, Erickson DL, Jones FA, Swenson NG, Perez R, Sanjur O, Bermingham E. 2009. Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proceedings of the National Academy of Sciences USA 106, 1862-18626.

Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. 2005. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences USA 102, 8369-8374.

Kress WJ. 2011. DNA barcoding and systematic monographs. In: T Stuessy, W Lack eds. Monographic plant systematics: Fundamental assessment of plant biodiversity. Berlin: Regnum Vegetabile 153. A.R. G. Gantner Verlag K.G. 49-71.

Lahaye R, Bank M, Bogarin D. 2008. DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci USA, 105, 2923-2928.

Liu YJ, Newmaster SG, Wu XJ, Liu Y, Ragupathy S, Motley T, Long CL. 2013. Pinelliahunanensis (Araceae), a new species supported by morphometric analysis and DNA barcoding. Phytotaxa 130, 1-13.

Newmaster SG, Fazekas AJ, Steeves RAD, Janovec J. 2008. Testing candidate plant barcode regions in the Myristicaceae.Molecular Ecology Resources 8, 480-490.

Newmaster SG, Grguric M, Shanmughanandhan D, Ramalingam S, Ragupathy S. 2013. DNA barcoding detects contamination and substitution in North American herbal products. BMC Medicine 11, 222.

Nicole S, Negrisolo E, Eccher G, Mantovani R, Patarnello T, Erickson DL, Kress WJ, Barcaccia G. 2012. DNA barcoding as a reliable method for the authentication of commercial seafood products. Food Technology and Biotechnology 50, 387-398.

Olsvik O, Wahlberg J, Petterson B, Uhlén M, Popovic T, Wachsmuth IK, Fields PI. 1993. Use of automated sequencing of polymerase chain reaction-generated amplicons to identify three types of cholera toxin subunit B in Vibrio cholerae O1 strains. J. Clin. Microbiol. 31, 22-25.

Schuster SC. 2008. Next-generation sequencing transforms today’s biology. Nat. Methods 5,16-18.

Shafiq S, Adeel M, Raza H, Iqbal R, Ahmad Z, Naeem M, Sheraz M, Ahmed U, Azmi UR. 2019. Effects of Foliar Application of Selenium in Maize (Zea Mays L.) under Cadmium Toxicity. Biological Forum-An International Journal 11(2), 27-3.

Swenson NG. 2012. Phylogenetic analyses of ecological communities using DNA barcode data. In: WJ Kress, DL Erickson eds. DNA barcodes: Methods and protocols. New York: Humana Press, Springer Science+Publishing Media, LLC. 409-419.

Swenson NG. 2013. The assembly of tropical tree communities the advances and shortcomings of phylogenetic and functional trait analyses. Ecography 36, 264-276.

Techen N, Parveen I, Pan Z, Khan IA. 2014. DNA barcoding of medicinal plant material for identification. Curr Opin Biotechnol 25, 103-110.

Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. 1995. AFLP: A new technique for DNA fingerprinting. Nucl. Acids Res 23, 4407-4414.

Webb CO, Donoghue MJ. 2005. Phylomatic: Tree assembly for applied phylogenetics. Molecular Ecology Notes 5, 181-183.

Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl. Acids Res. 18, 6531-6535.

Article source : Review on use of recent molecular techniques to access biodiversity in plants