Simple sequence repeat markers that identify Claviceps species and strains
Tóm tắt
Claviceps purpurea is a pathogen that infects most members of Pooideae, a subfamily of Poaceae, and causes ergot, a floral disease in which the ovary is replaced with a sclerotium. When the ergot body is accidently consumed by either man or animal in high enough quantities, there is extreme pain, limb loss and sometimes death. This study was initiated to develop simple sequence repeat (SSRs) markers for rapid identification of C. purpurea. SSRs were designed from sequence data stored at the National Center for Biotechnology Information database. The study consisted of 74 ergot isolates, from four different host species, Lolium perenne, Poa pratensis, Bromus inermis, and Secale cereale plus three additional Claviceps species, C. pusilla, C. paspali and C.
fusiformis. Samples were collected from six different counties in Oregon and Washington over a 5-year period. Thirty-four SSR markers were selected, which enabled the differentiation of each isolate from one another based solely on their molecular fingerprints. Discriminant analysis of principle components was used to identify four isolate groups, CA Group 1, 2, 3, and 4, for subsequent cluster and molecular variance analyses. CA Group 1 consisting of eight isolates from the host species P. pratensis, was separated on the cluster analysis plot from the remaining three groups and this group was later identified as C. humidiphila. The other three groups were distinct from one another, but closely related. These three groups contained samples from all four of the host species. These SSRs are simple to use, reliable and allowed clear differentiation of C. humidiphila from C. purpurea. Isolates from the three separate species, C. pusilla, C. paspali and C.
fusiformis, also amplified with these markers. The SSR markers developed in this study will be helpful in defining the population structure and genetics of Claviceps strains. They will also provide valuable tools for plant breeders needing to identify resistance in crops or for researchers examining fungal movements across environments.
Tài liệu tham khảo
Oregon Seed Association. http://www.oregonseed.org/ (2014). Accessed 25 Sept 2015.
Young W. Crop and soil science, Oregon State University. http://cropandsoil.oregonstate.edu/content/oregon-grass-and-legume-seed-production (2014). Accessed 25 Sept 2015.
Alderman S, Coats D, Crowe F. Impact of Ergot on Kentucky bluegrass grown for seed in Northeastern Oregon. Plant Dis. 1996;80:853–5.
Pažoutová S. Evolutionary strategy of Claviceps. In: White JF, Bacon CW, Hywel-Jones NL, Spatafora JW, editors. Clavicipitalean Fungi: evolutionary biology, chemistry, biocontrol and cultural impacts. New York: Marcel Dekker; 2003. p. 329–54.
Schumann GL. Ergot. Plant Health Inst. 2000. doi:10.1094/PHI-I-2000-1016-01.
Miedaner T, Geiger H. Biology, Genetics, and Management of ergot (Claviceps spp.) in rye, sorghum, and pearl millet. Toxins. 2015;7:659–78. doi:10.3390/toxins7030659.
Randhawa H, Asif M, Pozniak C, Clarke J, Graf R, Fox S, Humphreys G, Knox R, DePauw R, Singh A, Cuthbert R, Hucl P, Spaner D. Application of molecular markers to wheat breeding in Canada. Review. Plant Breeding. 2013;132:458–71.
Parh D, Jordan D, Aitken E, McIntyre L, Godwin I. Sorghum ergot: revealing the genetic architecture of resistance. Proceedings of the 4th International Crop Sciences Congress (1–4). 2004.
Jungehülsing U, Tudzynski P. Analysis of genetic diversity in Claviceps purpurea by RAPD markers. Mycol Res. 1997;101(1):1–6.
Pažoutová S, Cagaš B, Kolínská R, Honzátko A. Host Specialization of different populations of ergot fungus (Claviceps purpurea). Czech J. Genet. Plant Breeding. 2002;38(2):75–81.
Pažoutová S, Olšovská J, Linka M, Kolínská R, Flieger M. Chemoraces and habitat specialization of Claviceps purpurea populations. Appl Environ Microbiol. 2000;66(12):5419–25.
Pažoutová S, Raybould A, Honzátko A, Kolínská R. Specialized population of Claviceps purpurea from salt marshes. Mycol Res. 2002;106(2):210–4.
Negård M, Uhlig S, Kauserud H, Andersen T, Høiland K, Vrålstad T. Links between Genetic Groups, Indole alkaloid profiles and ecology within the grass-parasitic Claviceps purpurea species complex. Toxins. 2015;7(5):1431–56.
Pažoutová S, Pešicová K, Chudíčková M, Šrůtka P, Kolařík M. Delimitation of cryptic species inside Claviceps purpurea. Fungal Biol. 2015;2015(119):7–26. doi:10.1016/j.funbio.2014.10.003.
Fisher AJ, Gordon TR, Ditomaso JM. Geographic distribution and diversity in Claviceps purpurea from salt marsh habitats and characterization of Pacific coast populations. Mycol Res. 2005;109:439–46.
Douhan G, Smith M, Huyrn K, Westbrook A, Beerli P, Fisher A. Multigene analysis suggests ecological speciation in fungal pathogen Claviceps purpurea. Mol Ecol. 2008;17(9):2276–86.
Oeser B, Beaussart F, Haarmann T, Lorenz N, Nathues E, Rolke Y, Scheffer J, Weiner J, Tudzynski P. Expressed sequence tags from the flower pathogen Claviceps purpurea. Mol Plant Path. 2009;10(5):665–84.
Schardl CL, Young C, Hesse U, Amyotte S, Andreeva K, Calie P, Fleetwood D, Haws D, Moore N, Oeser B, Panaccione D, Schweri K, Voisey C, Farman M, Jaromczyk J, Roe B, O’Sullivan D, Scott B, Tudzynski P, An Z, Arnaoudova E, Bullock C, Charlton N, Chen L, Cox M, Dinkins R, Florea S, Glenn A, Gordon A, Güldener U, Harris D, Hollin W, Jaromczyk J, Johnson R, Khan A, Leistner E, Leuchtmann A, Li C, Liu J, Liu M, Mace W, Machado C, Nagabhyru P, Pan J, Schmid J, Sugawara K, Steiner U, Takach J, Tanaka E, Webb J, Wilson E, Wiseman J, Yoshida R, Zeng Z. Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genet. 2013;9(2):e1003323. doi:10.1371/journal.pgen.1003323.
Powell W, Machray G, Provan J. Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1996;1:215–22.
Scott J, Kaur N, Alderman S, Walenta D, Hamm P, Frost K, Dung J. Molecular differentiation of Claviceps isolates from Kentucky bluegrass and perennial ryegrass in Oregon and Washington. Poster session presented at: epidemiology-population biology genetics. APS Annual Meeting, Pasadena, CA; 2015.
National Center for Biotechnology Information. NCBI BioSample number: SAMEA2272775. http://www.ncbi.nlm.nih.gov/bioproject/PRJEA76493/ (2015). Accessed 25 Sept 2015.
Dutech C, Eknjalbert J, Fournier E, Delmotte F, Barrès B, Carlier J, Tharreau D, Giraud T. Challenges of microsatellite isolation in fungi. Fungal Genet Biol. 2007;44:933–49.
Gilmore B, Hummer K, Bassil N. DNA extraction protocols from dormant buds of twelve woody plant genera. J. Amer. Pomol. Soc. 2011;65:201–7.
Faircloth BC. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Mol Ecol Resources. 2015;2008(8):92–4. doi:10.1111/j.1471-8286.2007.01884.x.
Rozen S, Skaletsky HJ. Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S, editors. Bioinformatics Methods and Protocols: Methods in Mol Bio. Totowa: Humana Press; 2000.
Koressaar T, Remm M. Enhancements and modifications of primer design program Primer3. Bioinformatics. 2007;23(10):1289–91.
Untergrasser A, Cutcutache T, Koressaar T, Ye J, Faircloth B, Remm M, Rozen S. Primer3—new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115.
Schuelke M. An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol. 2000;18:233–4.
Brownstein MJ, Carpten JD, Smith JR. Modulation of non-templated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping. Biotechniques. 1996;20(6):1004–6 (1008–10).
Jombart T. Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 2015;2008(24):1403–5. doi:10.1093/bioinformatics/btn129.
Jombart T, Devillard S, Balloux F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics. 2010;11:94. doi:10.1186/1471-2156-11-94.
Jombart T, Ahmed I. Adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. 2011;27(21):3070–1. doi: 10.1093/bioinformatics/btr521.
R Development Core Team, R version 3.2.1 “World-Famous Astronaut.” R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing. http://www.R-project.org/ (2015). Accessed 25 Sept 2015.
Kamvar ZN, Tabima JF, Grünwald NJ. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ. 2014;2:e281. doi:10.7717/peerj.281.
Bruvo R, Michiels NK, D’Souza TG, Schulenburg H. A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level. Mol Ecol. 2004;13(7):2101–6.
Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–9.
Liu K, Muse S. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 2005;21:2128–9.
Spellerberg I, Fedor P. A tribute to Claude Shannon (1916–2001) and a plea for more rigorous use of species richness, species diversity and the ‘Shannon-Wiener’ index. Glob Ecol Biogeogr. 2003;12:177–9.