Abstract
In this study, we developed single nucleotide polymorphism (SNP) markers to identify cultivars of the polyploid Rosa hybrida using genotyping-by-sequencing (GBS). Sequences obtained from GBS libraries of the genomes of 79 rose cultivars were aligned to contigs created by de novo assembly, and these contigs ranged from 200 to 2,591 bp, with an average of 305 bp per contig. We selected 1,778 SNPs from 13,488 putative SNPs. SNP markers that were present in more than 70% of the 79 cultivars were selected and evaluated, both on the basis of polymorphism information content values and level of heterozygosity, and 20 SNP markers were ultimately selected for high- throughput analysis. From these 20 SNP markers, 4 were successfully converted to markers for DNA chip assays. High resolution melting analysis was carried out to further distinguish rose genotypes. Using a set of seven SNP markers, we identified 70.9% of the 79 rose cultivars, and 87.5% of the 16 new cultivars developed in Goyang City. This paper is the first to report the development of a SNP marker set to identify Rosa hybrida cultivars by GBS.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Literature Cited
Australian Government (2009) The biology and ecology of Rosa x hybrida (rose). Department of health and ageing office of the gene technology regulator. Ver 2, pp.11
Bang SW, Song K, Sim SC, Chung SM (2016) Marker-assisted selection for monoecy in chamoe (Cucumis melo L.). Korean J Hortic Sci Technol 34:134–141
Beissinger TM, Hirsch CN, Sekhon RS, Foerster JM, Johnson JM, Muttoni G, Vaillancourt B, Buell CR, Kaeppler SM et al. (2013) Marker density and read depth for genotyping populations using genotyping-by-sequencing. Genetics 193:1073–1081
Byers RL, Harker D, Yourstone SM, Maughan PJ, Udall JA (2012) Development and mapping of SNP assays in allotetraploid cotton. Theor Appl Genet 124:1201–1214
Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510
Debener T, Gudin S (2000) Rose: genetics and breeding. Plant Breed Rev 17:59–189
Debener T, Linde M (2009) Exploring complex ornamental genomes: the rose as a model plant. Crit Rev Plant Sci 28:267–280
Doyle JJ and Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, v.19, pp 11–15
Esselink GD, Smulders MJ, Vosman B (2003) Identification of cut rose (Rosa hybrida) and rootstock varieties using robust sequence tagged microsatellite site markers. Theor Appl Genet 106:277–286
Gar O, Sargent DJ, Tsai CJ, Pleban T, Shalev G, Byrne DH, Zamir D (2011) An autotetraploid linkage map of rose (Rosa hybrida) validated using the strawberry (Fragaria vesca) genome sequence. PLoS ONE 6:e20463
Gudin S (2003). Breeding. In: Roberts AV, Debener T, Gudin S, editors. eds. Encyclopedia of rose science. Oxford: Academic Press, pp 25–30
He J, Zhao X, Laroche A, Lu ZX, H, Li Z (2014) Genotyping-bysequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 5: 484
Hirakawa H, Shirasawa K, Kosugi S, Tashiro K, Nakayama S, Yamada M, Kohara M, Watanabe A, Kishida Y et al. (2014) Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. DNA res 21:169–181
Kim J, Kim DS, Park S, Lee HE, Ahn YK, Kim JH, Yang HB, Kang BC (2016) Development of a high-throughput SNP marker set by transcriptome sequencing to accelerate genetic background selection in Brassica rapa. Hortic Environ Biotechnol 57:280–290
Kimura T, Nishitani C, Iketani H, Ban Y, Yamamoto T (2006) Development of microsatellite markers in rose. Mol Ecol Notes 6:810–812
Koning-Boucoiran CF, Gitonga VW, Yan Z, Dolstra O, van der Linden CG, van der Schoot J, Uenk GE, Verlinden K, Smulders MJ et al. (2012) The mode of inheritance in tetraploid cut roses. Theor Appl Genet 125:591–607
Longhi S, Giongo L, Buti M, Surbanovski N, Viola R, Velasco R, Ward JA, Sargent DJ (2014) Molecular genetics and genomics of the Rosoideae: state of the art and future perspectives. Hortic Res 1 doi:10.1038/hortres.2014.1
Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248
van Orsouw NJ, Hogers RCJ, Janssen A, Yalcin F, Snoeijers S, Verstege E, Schneiders H, van der Poel H, van Oeveren J et al. (2007) Complexity reduction of polymorphic sequences (CRoPS): A novel approach for large-scale polymorphism discovery in complex genomes. PLoS ONE 2:e1172
Park YH, Ahn SG, Choi YM, Oh HJ, Ahn DC, Kim JG, Kang JS, Choi YW, Jeong BR (2010) Rose (Rosa hybrida L.) EST-derived microsatellite markers and their transferability to strawberry (Fragaria spp.). Sci Hortic 125:733–739
Perrier X, Flori A, Bonnot F (2003) Methods for data analysis. In: Hamon P, Seguin M, Perrier X, Glazmann JC (eds) Genetic diversity of cultivated tropical plants. Science Publishers, Inc and Cirad, Montpellier, pp 31–63
Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by sequencing approach. PLoS ONE 7: e32253
Scariot V, Akkak A, Botta R (2006) Characterization and genetic relationships of wild species and old garden roses based on microsatellite analysis. J Am Soc Hortic Sci 131:66–73
Simon WB, Davey JW, Johnston JS, Shelton AM, Heckel DG, Jiggins CD, Blazter ML (2011) Lingkage mapping comparative genomics using next generation RAD sequencing of a non model organism. PLoS ONE 6: e19315
Sparinska A, Zarina R, Rostoks N (2009) Diversity in Rosa rugosa × Rosa hybrida interspecific cultivars. Acta Hortic 836:111–116
Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcger AL, Jaiswal P, Mockaitis K, Liston A et al. (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43:109–116
Thomson MJ (2014) High-throughput SNP genotyping to accelerate crop improvement. Plant Breed Biotechnol 2:195–212
Vartia S, Villanueva-Canas JL, Finarelli J, Farrell ED, Collins PC, Hughes GM, Carlsson JE, Gauthier DT, McGinnity P et al (2016) A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding. R Soc Open Sci 3:150565
Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnahar SK, Troggio M et al. (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 42:833–839
Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J et al. (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494
Yan Z, Denneboom C, Hattendorf A, Dolstra O, Debener T, Stam P, Visser PB (2005) Construction of an integrated map of rose with AFLP, SSR, PK, RGA, SCAR and morphological markers. Theor Appl Genet 110:766–777
Yang H, Li C, Lam HM, Clements J, Yan G, Zhao S (2015) Sequencing consolidates molecular markers with plant breeding practice. Theor Appl Genet 128:779–795
Zhang L (2003) Genetic linkage mapping in tetraploid and diploid rose. Dissertation, Clemson University.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
13580_2017_268_MOESM1_ESM.xlsx
Supplementary Table 1. Results of genotyping of rose cultivars using DNA chip assay and high-resolution melting (HRM) analysis
Rights and permissions
About this article
Cite this article
Heo, MS., Han, K., Kwon, JK. et al. Development of SNP markers using genotyping-by-sequencing for cultivar identification in rose (Rosa hybrida). Hortic. Environ. Biotechnol. 58, 292–302 (2017). https://doi.org/10.1007/s13580-017-0268-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13580-017-0268-0