A Brief Review of Molecular Techniques to Assess Plant Diversity

Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. 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. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species.

[1]  Pål Nyrén,et al.  The history of pyrosequencing. , 2007, Methods in molecular biology.

[2]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[3]  J. H. van den Berg,et al.  Species relationships in Lactuca s.l. (Lactuceae, Asteraceae) inferred from AFLP fingerprints. , 2001, American journal of botany.

[4]  C. Anfinsen The Molecular Basis of Evolution , 1959, The Yale Journal of Biology and Medicine.

[5]  M. Nei Molecular Evolutionary Genetics , 1987 .

[6]  N C Dracopoli,et al.  Progress in high throughput SNP genotyping methods , 2002, The Pharmacogenomics Journal.

[7]  High RAPD but no cpDNA sequence variation in the endemic and endangered plant, Heptacodium miconioides Rehd. (Caprifoliaceae) , 2006, Genetica.

[8]  R. Koebner,et al.  DNA profiling and plant variety registration. III: The statistical assessment of distinctness in wheat using amplified fragment length polymorphisms , 1998, Euphytica.

[9]  M. Uhlén,et al.  Direct solid phase sequencing of genomic and plasmid DNA using magnetic beads as solid support. , 1989, Nucleic acids research.

[10]  S. Nadler Advantages and disadvantages of molecular phylogenetics: a case study of ascaridoid nematodes. , 1995, Journal of nematology.

[11]  A. Hipp,et al.  Phylogeny and biogeography of Croton alabamensis (Euphorbiaceae), a rare shrub from Texas and Alabama, using DNA sequence and AFLP data , 2006, Molecular ecology.

[12]  M. Marra,et al.  Applications of next-generation sequencing technologies in functional genomics. , 2008, Genomics.

[13]  C. Colombo,et al.  Genetic divergence among gerbera accessions evaluated by RAPD. , 2009 .

[14]  S. Quake,et al.  Sequence information can be obtained from single DNA molecules , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[15]  T. Popović,et al.  Use of automated sequencing of polymerase chain reaction-generated amplicons to identify three types of cholera toxin subunit B in Vibrio cholerae O1 strains , 1993, Journal of clinical microbiology.

[16]  R. Fleischer,et al.  Prospects for the use of Next-Generation Sequencing Methods in Ornithology , 2010 .

[17]  A. Kilian,et al.  Diversity arrays: a solid state technology for sequence information independent genotyping. , 2001, Nucleic acids research.

[18]  Han Xia,et al.  Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.) , 2010, BMC Plant Biology.

[19]  O. Rognli,et al.  Genetic diversity in a germplasm collection of roseroot (Rhodiola rosea) in Norway studied by AFLP , 2008 .

[20]  Y. Mitsui,et al.  Development and characterization of microsatellite loci in the endangered Tricyrtis ishiiana (Convallariaceae), a local endemic plant in Japan , 2009, Conservation Genetics.

[21]  Agnes P Chan,et al.  Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis) , 2010, BMC Plant Biology.

[22]  P. Taberlet,et al.  Using AFLP to resolve phylogenetic relationships in a morphologically diversified plant species complex when nuclear and chloroplast sequences fail to reveal variability. , 2003, Molecular phylogenetics and evolution.

[23]  S. Schuster Next-generation sequencing transforms today's biology , 2008, Nature Methods.

[24]  W. Guo,et al.  Ecological risk assessment using RAPD and distribution pattern of a rare and endangered species. , 2007, Chemosphere.

[25]  O. Seberg,et al.  Molecular Techniques in the Assessment of Botanical Diversity , 1996 .

[26]  Hui-Chun Li,et al.  Genetic variation and its relationship to root weight in the sweet potato as revealed by RAPD analysis , 2009 .

[27]  D. Soltis,et al.  Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next‐generation sequencing and Sequenom iPLEX MassARRAY genotyping , 2010, Molecular ecology.

[28]  S. An,et al.  Genetic structure of the endangered plant Neolitsea sericea (Lauraceae) from the Zhoushan archipelago using RAPD markers. , 2005, Annals of botany.

[29]  J. Doyle,et al.  Infrageneric phylogeny of the genus Gentiana (Gentianaceae) inferred from nucleotide sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA , 1996 .

[30]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[31]  J. Tohme,et al.  Use of AFLP markers in surveys of plant diversity. , 2005, Methods in enzymology.

[32]  J. Landers,et al.  Using high-throughput SNP technologies to study cancer , 2006, Oncogene.

[33]  Tom Coenye,et al.  Taxonomy and Identification of the Burkholderia cepacia Complex , 2001, Journal of Clinical Microbiology.

[34]  L. Mucina,et al.  AFLPs are incompatible with RAPD and morphological data in Pennisetum purpureum (Napier grass) , 2009 .

[35]  A. Shasany,et al.  Phenotypic and RAPD diversity among 80 germplasm accessions of the medicinal plant isabgol (Plantago ovata, Plantaginaceae). , 2009, Genetics and molecular research : GMR.

[36]  W. John Kress,et al.  A DNA barcode for land plants , 2009, Proceedings of the National Academy of Sciences.

[37]  D. Soltis,et al.  Molecular systematics of Saxifragaceae sensu stricto , 1993 .

[38]  R. Hogers,et al.  SNPWave: a flexible multiplexed SNP genotyping technology. , 2004, Nucleic acids research.

[39]  J. M. Prober,et al.  A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. , 1987, Science.

[40]  K. Dixon,et al.  Conservation genetics of the rare and endangered Leucopogon obtectus (Ericaceae) , 2001, Molecular ecology.

[41]  R. Varshney,et al.  AFLP-based molecular characterization of an elite germplasm collection of Jatropha curcas L., a biofuel plant. , 2009, Plant science : an international journal of experimental plant biology.

[42]  Gabriel O. Romero,et al.  Genetic fingerprinting: Advancing the frontiers of crop biology research , 2009 .

[43]  Ralph Rapley,et al.  Molecular analysis and genome discovery , 2004 .

[44]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[45]  H. Bayley,et al.  Continuous base identification for single-molecule nanopore DNA sequencing. , 2009, Nature nanotechnology.

[46]  Angel Carracedo,et al.  SNPs in forensic genetics: a review on SNP typing methodologies. , 2005, Forensic science international.

[47]  Virander S. Chauhan,et al.  Novel genetic mapping tools in plants , 2002 .

[48]  Rolando Perez,et al.  Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama , 2009, Proceedings of the National Academy of Sciences.

[49]  J. Rafalski Novel genetic mapping tools in plants: SNPs and LD-based approaches , 2002 .

[50]  P. Taberlet,et al.  A phylogeny of the European gentians inferred from chloroplast trnL (UAA) intron sequences , 1996 .

[51]  B. Hyman,et al.  Genotyping of Apolipoprotein E: Comparative Evaluation of Different Protocols , 2003, Current protocols in human genetics.

[52]  P. Jarne,et al.  Microsatellites, from molecules to populations and back. , 1996, Trends in ecology & evolution.

[53]  H. Comes,et al.  Phylogeny and quaternary history of the European montane/alpine endemic Soldanella (Primulaceae) based on ITS and AFLP variation. , 2001, American journal of botany.

[54]  Nathan Blow,et al.  DNA sequencing: generation next-next , 2008, Nature Methods.

[55]  M. Smale,et al.  Molecular tools in plant genetic resources conservation: a guide to the technologies. , 1997 .

[56]  D. Spencer,et al.  Generation and analysis of expressed sequence tags from the medicinal plant Salvia miltiorrhiza , 2010, Science China Life Sciences.

[57]  Detlef Weigel,et al.  Next Generation Molecular Ecology , 2010, Molecular ecology.

[58]  S. Krauss Complete exclusion of nonsires in an analysis of paternity in a natural plant population using amplified fragment length polymorphism (AFLP) , 1999 .

[59]  B. G. Baldwin Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the compositae. , 1992, Molecular phylogenetics and evolution.

[60]  S. Tingey,et al.  Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. , 1993, Trends in genetics : TIG.

[61]  M. Sun,et al.  Comparative analysis of phylogenetic relationships of grain amaranths and their wild relatives (Amaranthus; Amaranthaceae) using internal transcribed spacer, amplified fragment length polymorphism, and double-primer fluorescent intersimple sequence repeat markers. , 2001, Molecular phylogenetics and evolution.

[62]  R. Henry,et al.  Single-nucleotide polymorphism detection in plants using a single-stranded pyrosequencing protocol with a universal biotinylated primer. , 2003, Analytical biochemistry.

[63]  S. Christensen,et al.  Development and use of an expressed sequenced tag library in quinoa (Chenopodium quinoa Willd.) for the discovery of single nucleotide polymorphisms , 2005 .

[64]  James F. Smith Phylogenetics of seed plants : An analysis of nucleotide sequences from the plastid gene rbcL , 1993 .

[65]  K. Livak,et al.  DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. , 1990, Nucleic acids research.

[66]  M. Uhlén,et al.  Variations in the cytomegalovirus major immediate-early gene found by direct genomic sequencing , 1992, Journal of clinical microbiology.

[67]  D. Janzen,et al.  Use of DNA barcodes to identify flowering plants. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[68]  M. Esqueda,et al.  Genetic variability of wild Agave angustifolia populations based on AFLP: A basic study for conservation , 2009 .

[69]  P. F. Kauff Group , 2000, Elegant Design.

[70]  A. Moore,et al.  Transgenic chickpeas (Cicer arietinum L.) expressing a sequence-modified cry2Aa gene. , 2010 .

[71]  P. Patel,et al.  The GAA triplet-repeat expansion in Friedreich ataxia interferes with transcription and may be associated with an unusual DNA structure. , 1998, American journal of human genetics.

[72]  Jeffrey G. Reifenberger,et al.  Direct RNA sequencing , 2009, Nature.

[73]  D. Nickerson,et al.  The utility of single nucleotide polymorphisms in inferences of population history , 2003 .

[74]  D. Botstein,et al.  Construction of a genetic linkage map in man using restriction fragment length polymorphisms. , 1980, American journal of human genetics.

[75]  M. Ronaghi,et al.  Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.

[76]  Jianquan Liu,et al.  Genetic variation in the endangered Anisodus tanguticus (Solanaceae), an alpine perennial endemic to the Qinghai-Tibetan Plateau , 2007, Genetica.

[77]  P. Vos,et al.  AFLP: a new technique for DNA fingerprinting. , 1995, Nucleic acids research.

[78]  Yong Wang,et al.  Genome Sequencing in Open Microfabricated High Density Picoliter Reactors , 2005 .

[79]  Y. Mitsui,et al.  Isolation and characterisation of microsatellite loci in Calystegia soldanella (Convolvulaceae), an endangered coastal plant isolated in Lake Biwa, Japan , 2009, Conservation Genetics.

[80]  R. Varshney,et al.  Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys , 2007 .

[81]  Qi Zhou,et al.  Genetic diversity analysis and conservation of the endangered Chinese endemic herb Dendrobium officinale Kimura et Migo (Orchidaceae) based on AFLP , 2008, Genetica.

[82]  S. Hokanson,et al.  Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus×domestica borkh. core subset collection , 1998, Theoretical and Applied Genetics.

[83]  J. Strassmann,et al.  Microsatellites and kinship. , 1993, Trends in ecology & evolution.

[84]  P. Ranjekar,et al.  MOLECULAR MARKERS IN PLANT GENOME ANALYSIS , 1999 .

[85]  J. Maloof,et al.  Sequence diversity in three tomato species: SNPs, markers, and molecular evolution , 2009, BMC Plant Biology.

[86]  M. Ronikier The use of AFLP markers in conservation genetics--a case study on Pulsatilla vernalis in the Polish lowlands. , 2002, Cellular & molecular biology letters.

[87]  E. M. Gillet,et al.  Which DNA marker for which purpose , 2000 .

[88]  B. Ford-Lloyd,et al.  The random amplification of polymorphic DNA for fingerprinting plants. , 1992, PCR methods and applications.

[89]  S. Koren,et al.  Assembly algorithms for next-generation sequencing data. , 2010, Genomics.

[90]  R. Fani,et al.  Application of multiplex single nucleotide primer extension (mSNuPE) to the identification of bacteria: the Burkholderia cepacia complex case. , 2010, Journal of microbiological methods.

[91]  E. Bitocchi,et al.  Adaptation and diversity along an altitudinal gradient in Ethiopian barley (Hordeum vulgare L.) landraces revealed by molecular analysis , 2010, BMC Plant Biology.