In barley, breeding using good genetic characteristics can improve the quality or quantity of crop characters from one generation to the next generation. The development of effective molecular markers in barley is crucial for understanding and analyzing the diversity of useful alleles. In this study, we conducted genetic relationship analysis using expressed sequence tag-simple sequence repeat (EST-SSR) markers for barley identification and assessment of barley cultivar similarity. Seeds from 82 cultivars, including 31 each of naked and hulled barley from the Korea Seed and Variety Service and 20 of malting barley from the RDA-Genebank Information Center, were analyzed in this study. A cDNA library of the cultivar Gwanbori was constructed for use in analysis of genetic relationships, and 58 EST-SSR markers were developed and characterized. In total, 47 SSR markers were employed to analyze polymorphisms. A relationship dendrogram based on the polymorphism data was constructed to compare genetic diversity. We found that the polymorphism information content among the examined cultivars was 0.519, which indicates that there is low genetic diversity among Korean barley cultivars. The results obtained in this study may be useful in preventing redundant investment in new cultivars and in resolving disputes over seed patents. Our approach can be used by companies and government groups to develop different cultivars with distinguishable markers. In addition, the developed markers can be used for quantitative trait locus analysis to improve both the quantity and the quality of cultivated barley.
This is a preview of subscription content, log in to check access.
Buy single article
Instant access to the full article PDF.
Price includes VAT for USA
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
This is the net price. Taxes to be calculated in checkout.
Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 114:359–372
Bernet GP, Bramardi S, Calvache O, Carbonell EA, Asins MJ (2003) Applicability of molecular markers in the context of protection of new varieties of cucumber. Plant Breed 122:146–152
Bungartz A, Klaus M, Mathew B, Léon J, Naz AA (2016) Development of new SNP derived cleaved amplified polymorphic sequence marker set and its successful utilization in the genetic analysis of seed color variation in barley. Genomics 107:100–107
Fiust A, Rapacz M, Wójcik-Jagła M, Tyrka M (2015) Development of DArT-based PCR markers for selecting drought-tolerant spring barley. J Appl Genet 56:299–309
Gailing O, Bodénès C, Finkeldey R, Kremer A, Plomion C (2013) Genetic mapping of EST-derived simple sequence repeats (EST-SSRs) to identify QTL for leaf morphological characters in a Quercus robur full-sib family. Tree Genet Genomes 9:1361–1367
Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Herrmann RG (1991) Construction of an RFLP map of barley. Theor Appl Genet 83:250–256
Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185
Jia Q, Zhu J, Wang J, Yang J, Zhang G (2016) Genetic mapping and molecular marker development for the gene Pre2 controlling purple grains in barley. Euphytica 208:215–223
Karsai I, Szűcs P, Mészáros K, Puskás K, Bedő Z, Veisz O (2007) Barley (Hordeum vulgare L.) marker linkage map: a case study of various marker types and of mapping population structure. Cereal Res Commun 35:1551–1562
Kleinhofs A, Kilian A, Maroof MS, Biyashev RM, Hayes P, Chen FQ, Lapitan N, Fenwick A, Blake TK, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu B, Sorrells M, Heun M, Franckowiak JD, Hoffman D, Skadsen R, Steffenson BJ (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705–712
Kwon YS, Hong JH, Choi KJ (2011) Genetic diversity of Korean barley (Hordeum vulgare L.) varieties using microsatellite markers. Korean J Breed Sci 43:243–250
Li JZ, Sjakste TG, Röder MS, Ganal MW (2003) Development and genetic mapping of 127 new microsatellite markers in barley. Theor Appl Genet 107:1021–1027
Macaulay M, Ramsay L, Powell W, Waugh R (2001) A representative, highly informative’ genotyping set’ of barley SSRs. Theor Appl Genet 102:801–809
Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam KhN, Latif MA (2013) A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. Int J Mol Sci 14:22499–22528
Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200
Nandha PS, Singh J (2014) Comparative assessment of genetic diversity between wild and cultivated barley using gSSR and EST-SSR markers. Plant Breed 133:28–35
Pedersen C, Linde-Laursen I (1995) The relationship between physical and genetic distances at the Hor1 and Hor2 loci of barley estimated by two-colour fluorescent in situ hybridization. Theor Appl Genet 91:941–946
Pillen K, Binder A, Kreuzkam B, Ramsay L, Waugh R, Förster J, Léon J (2000) Mapping new EMBL-derived barley microsatellites and their use in differentiating German barley cultivars. Theor Appl Genet 101:652–660
Ponyared P, Ponsawat J, Tongsima S, Seresangtakul P, Akkasaeng C, Tantisuwichwong N (2016) ESAP plus: a web-based server for EST-SSR marker development. BMC Genomics 17(Suppl 13):1035
Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 96:1360–1385
Ramsay L, Macaulay M, Degli Ivanissevich S, MacLean K, Cardle L, Fuller J, Edwards KJ, Tuvesson S, Morgante M, Massari A, Maestri E, Marmiroli N, Sjakste T, Ganal M, Powell W, Waugh R (2000) A simple sequence repeat-based linkage map of barley. Genet 156:1997–2005
Ramsay L, Russell J, Macaulay M, Booth A, Thomas WTB, Waugh R (2004) Variation shown by molecular markers in barley: genomic and genetic constraints. Aspects Appl Biol 72:147–154
Rohlf FJ (2000) NTSYSpc. Numerical Taxonomy and Multivariate Analysis System-Version 2.l0b. Applied Biostatistics Inc., New York
Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci 8:321–329
Shan X, Blake TK, Talbert LE (1999) Conversion of AFLP markers to sequence-specific PCR markers in barley and wheat. Theor Appl Genet 98:1072–1078
Shariflou MR, Hassani ME, Sharp PJ (2001) A PCR-based DNA marker for detection of mutant and normal alleles of the Wx-D1 gene of wheat. Plant Breed 120:121–124
Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Michell SE, Kresovick S, Ziegle J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L): comparison with data from RFLPs and pedigree. Theor Appl Genet 95:163–173
Sneath PHA, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. Freeman WH, San Francisco
So EH, Choi SJ, Ko EB, Song IH, Lee JH (2004) Hordein fingerprinting for cultivar discrimination in national list of barley. Korean J Crop Sci 49:256–260
Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422
Varshney RK, Marcel TC, Ramsay L, Russell J, Röder MS, Stein N, Waugh R, Langridge P, Niks RE, Graner A (2007) A high density barley microsatellite consensus map with 775 SSR loci. Theor Appl Genet 114:1091–1103
Wright JM, Bentzen P (1995) Microsatellites: genetic markers for the future. Molecular genetics in fisheries. Springer, Netherlands, pp 117–121
Zhang M, Mao W, Zhang G, Wu F (2014) Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley. PLoS One 9(4):e94881
Zhou G, Zhang Q, Tan C, Zhang X, Li C (2015) Development of genome-wide InDel markers and their integration with SSR, DArT and SNP markers in single barley map. BMC Genomics 16:804
This work was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET) through the Agri-Bio Industry Technology Development Program, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA) (313043-03-3-HD050).
Conflict of interest
The authors declare that they have no conflict of interest.
About this article
Cite this article
Jo, W., Kim, H. & Kim, K. Development and characterization of polymorphic EST based SSR markers in barley (Hordeum vulgare). 3 Biotech 7, 265 (2017). https://doi.org/10.1007/s13205-017-0899-y
- EST-SSR marker
- Genetic similarity