DArT-based characterisation of genetic diversity in a Miscanthus collection from Poland

Atienza S, Satovic Z, Petersen K, Dolstra O, Martin A (2002) Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers. Theor Appl Genet 105:946–952 Castillo A, Ramírez MC, Martín AC, Kilian A, Martín A, Atienza SG (2013) High-throughput genotyping of wheat-barley amphiploids utilising diversity array technology (DArT). BMC Plant Biol 13:87 Chiang YC, Chou CH, Lee PR, Chiang TY (2001) Detection of leaf-associated fungi based on PCR and nucleotide sequence of the ribosomal internal transcribed spacer (ITS) in Miscanthus. Bot Bull Acad Sinica 42:39–44 Chouvarine P, Cooksey AM, McCarthy FM, Ray DA, Baldwin BS, Burgess SC, Peterson DG (2012) Transcriptome-based differentiation of closely-related Miscanthus lines (transcriptome-based differentiation of Miscanthus). PLoS One 7:e29850 Clifton-Brown JC, Lewandowski I, Andersson B, Basch G, Christian DG, Kjeldsen JB, Jorgensen U, Mortensen JV, Riche AB, Schwarz KU, Tayebi K, Teixeira F (2001) Performance of 15 Miscanthus genotypes at five sites in Europe. Agron J 93:1013–1019 Dice LR (1945) Measures of the amount of ecologic association between species. Ecology 26:297–302 Dominguez-Garcia MC, Belaj A, De la Rosa R, Satovic Z, Heller-Uszynska K, Kilian A, Martin A, Atienza SG (2012) Development of DArT markers in olive (Olea europaea L.) and usefulness in variability studies and genome mapping. Sci Hortic 136:50–60 Earl DA (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361 Głowacka K, Clark LV, Adhikari S, Peng J, Ryan Stewart J, Nishiwaki A, Yamada T, Jørgensen U, Hodkinson TR, Gifford J (2015) Genetic variation in Miscanthus × giganteus and the importance of estimating genetic distance thresholds for differentiating clones. GCB Bioenergy 7:386–404 Greef J, Deuter M (1993) Syntaxonomy of Miscanthus × giganteus Greef et Deu. Angew Bot 67:87–90 Greef J, Deuter M, Jung C, Schondelmaier J (1997) Genetic diversity of European Miscanthus species revealed by AFLP fingerprinting. Genet Resour Crop Ev 44:185–195 Grzebelus D, Iorizzo M, Senalik D, Ellison S, Cavagnaro P, Macko-Podgorni A, Heller-Uszynska K, Kilian A, Nothnagel T, Allender C (2014) Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers. Mol Breeding 33:625–637 Hauser LA, Crovello TJ (1982) Numerical analysis of generic relationships in Thelypodieae (Brassicaceae). Syst Bot 7:249–268 Heaton EA, Dohleman FG, Long SP (2008a) Meeting US biofuel goals with less land: the potential of Miscanthus. Glob Change Biol 14:2000–2014 Heaton EA, Flavell RB, Mascia PN, Thomas SR, Dohleman FG, Long SP (2008b) Herbaceous energy crop development: recent progress and future prospects. Curr Opin Biotech 19:202–209 Heller-Uszynska K, Uszynski G, Huttner E, Evers M, Carlig J, Caig V, Aitken K, Jackson P, Piperidis G, Cox M, Gilmour R, D’Hont A, Butterfield M, Glaszmann JC, Kilian A (2011) Diversity Arrays Technology effectively reveals DNA polymorphism in a large and complex genome of sugarcane. Mol Breed 28:37–55 Hernández P, Dorado G, Laurie D, Martin A, Snape J (2001) Microsatellites and RFLP probes from maize are efficient sources of molecular markers for the biomass energy crop Miscanthus. Theor Appl Genet 102:616–622 Hodkinson TR, Chase MW, Lledó DM, Salamin N, Renvoize SA (2002) Phylogenetics of Miscanthus, Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers. J Plant Res 115:381–392 Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:e25–e25 James KE, Schneider H, Ansell SW, Evers M, Robba L, Uszynski G, Pedersen N, Newton AE, Russell SJ, Vogel JC (2008) Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms. PLoS One 3:e1682 Jeżowski S (2008) Yield traits of six clones of Miscanthus in the first 3 years following planting in Poland. Ind Crops Prod 27:65–68 Jeżowski S, Glowacka K, Kaczmarek Z (2009) Wstępna ocena głównych parametrów wymiany gazowej związanych z fotosyntezą w odniesieniu do plonowania traw energetycznych z rodzaju Miscanthus w pierwszym roku uprawy. Acta Agrophysica 14:73–81 Jeżowski S, Głowacka K, Kaczmarek Z (2011) Variation on biomass yield and morphological traits of energy grasses from the genus Miscanthus during the first years of crop establishment. Biomass Bioenergy 35:814–821 Jones MB, Finnan J, Hodkinson TR (2015) Morphological and physiological traits for higher biomass production in perennial rhizomatous grasses grown on marginal land. GCB Bioenergy 7:375–385 Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, Caig V, Heller-Uszynska K, Jaccoud D, Hopper C, Aschenbrenner-Kilian M, Evers M, Peng K, Cayla C, Hok P, Uszynski G (2012) Diversity Arrays Technology: a generic genome profiling technology on open platforms. In: Pompanon F, Bonin A (eds) Data production and analysis in population genomics. Humana Press, New York, pp 67–89 Lee NY (1964a) Taxonomic studies on the genus Miscanthus: anatomical patterns of leaves. Bot Mag Tokyo 77:122–130 Lee NY (1964b) Taxonomic studies on the genus Miscanthus: relationships among the section, subsection and species, part 1. J Jpn Bot 39:196–205 Lee NY (1964c) Taxonomic studies on the genus Miscanthus: relationships among the section, subsection and species, part 2. J Jpn Bot 39:257–268 Lee NY (1964d) Taxonomic studies on the genus Miscanthus: relationships among the section, subsection and species, part 3. J Jpn Bot 39:289–298 Lewandowski I, Clifton-Brown JC, Andersson B, Basch G, Christian DG, Jorgensen U, Jones MB, Riche AB, Schwarz KU, Tayebi K, Teixeira F (2003) Environment and harvest time affects the combustion qualities of Miscanthus genotypes. Agron J 95:1274–1280 Mace ES, Xia L, Jordan DR, Halloran K, Parh DK, Huttner E, Wenzl P, Kilian A (2008) DArT markers: diversity analyses and mapping in Sorghum bicolor. BMC Genom 9:26 Matlaga DP, Davis AS (2013) Minimizing invasive potential of Miscanthus × giganteus grown for bioenergy: identifying demographic thresholds for population growth and spread. J App Ecol 50:479–487 Mos M, Banks SW, Nowakowski DJ, Robson PRH, Bridgwater AV, Donnison IS (2013) Impact of Miscanthus × giganteus senescence times on fast pyrolysis bio-oil quality. Bioresour Technol 129:335–342 Oliver R, Jellen E, Ladizinsky G, Korol A, Kilian A, Beard J, Dumlupinar Z, Wisniewski-Morehead N, Svedin E, Coon M (2011) New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L. Theor Appl Genet 123:1159–1171 Ovesná J, Kučera L, Vaculová K, Milotová J, Snape J, Wenzl P, Huttner E, Kilian A, Martelli G, Milella L (2013) Analysis of the genetic structure of a barley collection using DNA Diversity Array Technology (DArT). Plant Mol Biol Rep 31:280–288 Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295 Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959 Quinn LD, Allen DJ, Stewart JR (2010) Invasiveness potential of Miscanthus sinensis: implications for bioenergy production in the United States. GCB Bioenergy 2:310–320 Raman H, Stodart B, Cavanagh C, Mackay M, Morell M, Milgate A, Martin P (2010) Molecular diversity and genetic structure of modern and traditional landrace cultivars of wheat (Triticum aestivum L.). Crop Pasture Sci 61:222–229 Rohlf F (1997) NTSYS-pc 2.1. Numerical taxonomy and multivariate analysis system Exeter Software. Exeter publishing Setauket, NY Sang T, Zhu W (2011) China’s bioenergy potential. GCB Bioenergy 3:79–90 Sharma M, Nagavardhini A, Thudi M, Ghosh R, Pande S, Varshney RK (2014) Development of DArT markers and assessment of diversity in Fusarium oxysporum f. sp. ciceris, wilt pathogen of chickpea (Cicer arietinum L.). BMC Genom 15:454 Simko I, Eujayl I, van Hintum TJ (2012) Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations. Plant Sci 184:54–62 Von Mark VC, Kilian A, Dierig DA (2013) Development of DArT marker platforms and genetic diversity assessment of the US collection of the new oilseed crop Lesquerella and related species. PLoS One 8:e64062 Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (2004) Diversity arrays technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101:9915–9920 Xia L, Peng K, Yang S, Wenzl P, De Vicente MC, Fregene M, Kilian A (2005) DArT for high-throughput genotyping of cassava (Manihot esculenta) and its wild relatives. Theor Appl Genet 110:1092–1098 Zhao H, Yu JY, You FM, Luo MC, Peng JH (2011) Transferability of microsatellite markers from Brachypodium distachyon to Miscanthus sinensis, a potential biomass crop. J Integr Plant Biol 53:232–245