Evaluation of pyrosequencing for large-scale identificationof plant species (grasses as a model)

Grasses (Poaceae) are among the most important and widely cultivated plants. Identification of grass species using morphological characters is a difficult task for nonspecialists, and it is not always an accurate method. DNA-based molecular markers have been widely used as an alternative towards more accurate identification of plant species. The molecular method that can be effective for large-scale identification of grass species, however, must satisfy requirements for specific amplification of DNA and reveal enough variability to distinguish species. The goal of this study was to evaluate the ability of pyrosequencing to detect SNP polymorphisms for an optimal discrimination of grass species. PCR amplifications and the sequencing of 19 fragments of chloroplast genes were performed using a pooled DNA template of 32 British native grass species to be identified and chloroplast DNA-specific universal primers. Based on amplicon size and sequence variance, the 6 most variable loci (psbE&F, rbcL.1, ndhF.1, ndhF.2, ndhF.3, and clpP&rps12) were selected to be targeted for pyrosequencing of the species analyzed. The pyrosequenced regions contained sufficient polymorphisms to allow the complete diagnosis of all species analyzed, except for Elymus caninus and Elytrigia repens, which had identical sequences unique from the remaining species. When targeted loci were pyrosequenced in representative species of the 2 economically important grass genera Festuca L. (8 species) and Poa L. (11 species), all species in each genus could be separated. Should the SNP markers developed here proved to be species-specific, they can provide a valuable tool for reliable diagnosis of grasses and applications (e.g., forensic botany) moving forward.

Anahtar Kelimeler:

Grasses, identification, pyrosequencing, species-specific markers

Evaluation of pyrosequencing for large-scale identificationof plant species (grasses as a model)

Keywords:

Grasses, identification, pyrosequencing, species-specific markers,

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Ahmadian A, Ehn M, Hober S (2006). Pyrosequencing: history, biochemistry and future. Clin Chim Acta 363: 83–94.
Aiken SG, Consaul LL, Dallwitz MJ (1996). Grasses of the Canadian Arctic Archipelago: a DELTA database for interactive identification and illustrated information retrieval. Can J Bot 74: 1812–1825.
Alexander AM, Pecoraro C, Styche A, Rudert WA, Benos PV, Ringquist S, Trucco M (2005). SOP3: A web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by pyrosequencing. Biotechniques 38: 87–94.
Andréasson H, Asp A, Alderborn A, Gyllensten U, Allen M (2002). Mitochondrial sequence analysis for forensic identification using pyrosequencing technology. Biotechniques 32: 124–126, 128, 130–133.
Armonienė R, Stukonis V, Paplauskienė V, Brazauskas G (2010). The genetic diversity of fine-leaved fescue (Festuca L.) species in Lithuania. In: Huyghe C, editor. Sustainable Use of Genetic Diversity in Forage and Turf Breeding. Amsterdam, the Netherlands: Springer, pp. 41–45.
Beard JB (1973). Turfgrass: Science and Culture. Englewood Cliffs, NJ, USA: Prentice Hall.
Bor NL (1952). The genus Poa L. in India. Part I. J Bombay Nat Hist Soc 50: 787–783.
Chandra A, Dubey A (2010). Identification of species-specific RAPD markers in genus Cenchrus. J Environ Biol 31: 403–407.
Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002). SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3: 19.
Constable G (1985). Grasslands and Tundra: Planet Earth. New York, NY, USA: Time Life Books.
Fakruddin MD, Chowdhury A (2012). Pyrosequencing - an alternative to traditional Sanger sequencing. Am J Biochem Biotechnol 8: 14–20.
Fermanian TW, Michalski RS (1989). Weeder - an advisory system for the identification of grasses in turf. Agronomy J 81: 312– 316.
Ferri G, Alù M, Corradini B, Beduschi G (2009). Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach. Int J Legal Med 123: 395–401.
Ford CS, Ayres KL, Toomey N, Haider N, Stahl JVA, Kelly L, Wilstöm N, Hollingsworth P, Duff RJ, Hoot SB et al. (2009). Selection of candidate coding DNA barcoding regions for use on land plants. Bot J Linn Soc 159: 1–11.
Galli Z, Penksza K, Kiss E, Sági L, Heszky LE (2006). Low variability of internal transcribed spacer rDNA and trnL (UAA) intron sequences of several taxa in the Festuca ovina aggregate (Poaceae). Acta Biol Hung 57: 57–69.
Gealy DR, Tai TH, Sneller CH (2002). Identification of red rice, rice, and hybrid populations using microsatellite markers. Weed Sci 50: 333–339.
Gharizadeh B, Ghaderi M, Donnelly D, Amini B, Wallin KL, Nyrén P (2003). Multiple-primer DNA sequencing method. Electrophoresis 24: 1145–1151.
Gillespie LJ, Boles R (2001). Phylogenetic relationships and infraspecific variation in Canadian Arctic Poa based on chloroplast DNA restriction site data. Can J Bot 79: 679–701.
Gillespie LJ, Soreng RJ (2005). A phylogenetic analysis of the bluegrass genus Poa based on cpDNA restriction site data. Syst Bot 30: 84–105.
Gulsen O, Shearman RC, Vogel KP, Lee DJ, Heng-Moss T (2005). Organelle DNA diversity among buffalo grasses from the Great Plains of North America determined by cpDNA and mtDNA RFLPs. Crop Sci 45: 186–192.
Haider N (2003). Development and use of universal primers in plants. PhD, University of Reading, Reading, UK.
Haider N (2012). Evidence for the origin of the B genome of bread wheat based on chloroplast DNA. Turk J Agric For 36: 13–25.
Haider N, Nabulsi I (2008). Identification of Aegilops L. species and Triticum aestivum L. based on chloroplast DNA. Genet Resour Crop Evol 55: 537–549.
Haider N, Nabulsi I, Kamary Y (2010a). Identification of Orchidaceae species of northern west of Syria based on chloroplast DNA. Russ J Genet 46: 1067–1078.
Haider N, Nabulsi I, MirAli N (2010b). Comparison of the efficiency of A-PAGE and SDS-PAGE, ISSRs and RAPDs in resolving genetic relationships among Triticum and Aegilops species. Genet Resour Crop Evol 57: 1023–1039.
Haider N, Nabulsi I, MirAli N (2012). Identification of species of Vicia subgenus Vicia (Fabaceae) using chloroplast DNA data. Turk J Agric For 36: 297–308.
Haider N, Wilkinson MJ (2011). A set of plastid DNA-specific universal primers for flowering plants. Russ J Genet 47: 1204– 1215.
Han S, Kim S, Yang CH, Seo J (2005). Genetical identification of Akebia and Aristolochia species by using Pyrosequencing. J Biotechnol 120: 360–363.
Hastings PAS (2004). Mitochondrial DNA analysis by pyrosequencing. MSc, University of Central Florida, Orlando, FL, USA.
Kellogg EA (1985). A biosystematic study of the Poa secunda complex. J Arnold Arboretum 66: 201–242.
Kindiger BK, Conley T (2009). Utilizing single primers as molecular markers in Poa spp. Jap Soc Grassland Sci 55: 206–215.
Krishnan S, Samson NP, Ravichandran P, Narasimhan D, Dayanandan P (2000). Phytoliths of Indian grasses and their potential use in identification. Bot J Linn Soc 132: 241–252.
Kumar J, Verma V, Goyal A, Shahi AK, Sparoo R, Sangwan RS, Qazi GN (2009). Genetic diversity analysis in Cymbopogon species using DNA markers. Plant Omics J 2: 20–29.
Langaee T, Ronaghi M (2005). Genetic variation analyses by pyrosequencing. Mutat Res 573: 96–102.
Leem K, Kim SC, Yang CH, Seo J (2005). Genetic identification of Panax ginseng and Panax quinquefolius by pyrosequencing methods. Biosci Biotechnol Biochem 69: 1771–1773.
Li A, Ge S (2001). Genetic variation and clonal diversity of Psammochloa villosa (Poaceae) detected by ISSR markers. Ann Bot 87: 585–590.
Li D, Rothballer M, Engel M, Hoser J, Schmidt T, Kuttler C, Schmid M, Schloter M, Hartmann A (2012). Phenotypic variation in Acidovorax radicis N35 influences plant growth promotion. FEMS Microbiol Ecol 79: 751–762.
Liu Q, Li L, Zhang N, Liu JIE, Shi Y (2010). Development and characterization of chloroplast microsatellite markers in Pseudoroegneria and Leymus (Poaceae: Triticeae). J Genet 89: e11–e22.
Marsh S (2007). Pyrosequencing applications. Methods Mol Biol 373: 15–24.
Mason-Gamer RJ (2004). Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass. Syst Biol 53: 25–37.
Nilsson RH, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E (2009). The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiol Lett 296: 97–101.
Novais RC, Thorstenson YR (2011). The evolution of Pyrosequencing® for microbiology: from genes to genomes. J Microbiol Methods 86: 1–7.
Paäakinskiene I, Griffiths CM, Bettany AJE, Paplauskiene V, Humphreys MW (2000). Anchored simple-sequence repeats as primers to generate species-specific DNA markers in Lolium and Festuca grasses. Theor Appl Genet 100: 384–390.
Parani M, Rajesh K, Lakshmi M, Parducci L, Szmidt AE, Parida A (2001). Species identification in seven small millet species using polymerase chain reaction-restriction fragment length polymorphism of trnS-psbC gene region. Genome 44: 495–499.
Patterson JT, Larson SR, Johnson PG (2005). Genome relationships in polyploid Poa pratensis and other Poa species inferred from phylogenetic analysis of nuclear and chloroplast DNA sequences. Genome 48: 76–87.
Ridgway KP, Duck JM, Young JPW (2003). Identification of roots from grass swards using PCR-RFLP and FFLP of the plastid trnL (UAA) intron. BMC Ecol 3: 8.
Ringquist S, Pecoraro C, Gilchrist CMS, Styche A, Rudert WA, Benos PV, Trucco M (2005). SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms. Nucleic Acids Res 33: W548–W552.
Ronaghi M, Elahi E (2002). Discovery of single nucleotide polymorphisms and mutations by pyrosequencing. Comp Funct Genomics 3: 51–56.
Ronaghi M, Shokralla S, Gharizadeh B (2007). Pyrosequencing for discovery and analysis of DNA sequence variations. Pharmacogenomics 8: 1437–1441.
Ronaghi M, Uhlen M, Nyren P (1998). A sequencing method based on real-time pyrophosphate. Science 281: 365–363.
Salk JJ, Sanchez JA, Pierce KE, Rice JE, Soares KC, Wangh LJ (2006). Direct amplification of single-stranded DNA for pyrosequencing using linear-after-the-exponential (LATE)- PCR. Anal Biochem 353: 124–132.
Scheef EA, Casler MD, Jung G (2003). Development of species- specific SCAR markers in bentgrass. Crop Sci 43: 345–349.
Silvar C, Perovic D, Casas AM, Igartua E, Ordon F (2011). Development of a cost-effective pyrosequencing approach for SNP genotyping in barley. Plant Breeding 130: 394–397.
Siqueira JF Jr, Fouad AF, Rôças IN (2012). Pyrosequencing as a tool for better understanding of human microbiomes. J Oral Microbiol 4: 10743.
Soininen EM, Valentini A, Coissac E, Miquel C, Gielly L, Brochmann C, Brysting AK, Sİnstebİ JH, Ims RA, Yoccoz NG et al. (2009). Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Front Zool 6: 16.
Soreng RJ (1990). Chloroplast-DNA phylogenetics and biogeography in a reticulating group: Study in Poa (Poaceae). Am J Bot 77: 1383–1400.
Soreng RJ, Bull RD, Gillespie LJ (2010). Phylogeny and reticulation in Poa based on plastid trnTLF and nrITS sequences with attention to diploids. In: Seberg O, Peterson G, Barfod A, Davis JI, editors. Diversity, Phylogeny, and Evolution in the Monocotyledons. Aarhus, Denmark: Aarhus University Press, pp. 619–643.
Stace CA, Al-Bermani AKKA, Wilkinson MJ (1992). The distinction between the Festuca ovina L. and Festuca rubra L. aggregates in the British Isles. Watsonia 19: 107–112.
Stace CA (1997). New Flora of the British Isles. 2nd ed. Cambridge, UK: Cambridge University Press.
Stebbins GL (1956). Cytogenetics and evolution of the grass family. Am J Bot 43: 890–905.
Steven B, McCann S, Ward NL (2012). Pyrosequencing of plastid 23S rRNA genes reveals diverse and dynamic cyanobacterial and algal populations in two eutrophic lakes. FEMS Microbiol Ecol 82: 607–615.
Studer B, Widmer F, Enkerli J, Kölliker R (2006). Development of novel microsatellite markers for the grassland species Lolium multiflorum, L. perenne and Festuca pratensis. Mol Ecol Notes 6: 1108–1110.
Taberlet P, Gielly L, Pautou G, Bouvet J (1991). Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biology 17: 1105–1109.
Tzvelev NN (1989). The system of grasses (Poaceae) and their evolution. Bot Rev 55: 141–203.
Wallinger C, Juen A, Staudacher K, Schallhart N, Mitterrutzner E, Steiner EM, Thalinger B, Traugott M (2012). Rapid plant identification using species- and group-specific primers targeting chloroplast DNA. PLoS One 7: e29473.
Wang L, Luhm R, Lei M (2007). SNP and mutation analysis. Adv Exp Med Biol 593: 105–116.
Ward J, Gilmore SR, Robertson J, Peakall R (2009). A grass molecular identification system for forensic botany: a critical evaluation of the strengths and limitations. J Forensic Sci 54: 1254–1260.
Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB (2007). Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144: 32–42.
Wheeler DJB, Jacobs SWL, Norton BE (1990). Grasses of New South Wales. 2nd ed. Armidale, Australia: University of New England Monographs.
Zapiola ML, Cronn RC, Mallory-Smith CA (2010). Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera. Mol Ecol Resour 10: 738–740.