Using SSR markers for assessment genetic diversity and detection drought escape candidate genes in barley lines (Hordeum vulgare L.)
Abstract
Assessment of genetic diversity using molecular markers is one of the primary and important steps in breeding programs. In this study, genetic diversity of 52 barley lines evaluated using 68 SSR primer pairs and 47 primer pairs produced clear and polymorphic banding pattern. In general, 153 polymorphic alleles de-tected. The number of observed polymorphic alleles varied from 2 to 9, with an average of 3.26 alleles per locus. Polymorphic Information Content (PIC) ranged from 0.07 to 0.81, with an average of 0.45. In this research, SSR markers differentiated the studied lines efficiently. Using cluster analysis, studied barley lines divided into two groups. Genetic diversity was relatively corresponding with geographical origins, because the lines related to a country somewhat diverged from each other. Two-rowed Iranian and Chinese barleys classified in one subgroup. Also, most six-rowed barleys classified in one subgroup. Association mapping analysis was used to identify candidate genes for drought escape in barley lines and 16 informative markers were identified after which confirmation in other tests could be suitable for marker assisted breeding drought escape.
Keywords
Association analysis; barley; genetic diversity; Microsatellite markers (SSR); drought escape
References
Agrama, H.A.; Eizenga, G.C.; Yan, W. Association mapping of yield and its components in rice cultivars. Molecular Breeding, v.19, p.341–356, 2007.
Bassam, B.J.; Caetano-Anolles, G.; Gresshoff, P. M. Fast and sensitive silver staining of DNA in polyacryla-mide gels. Analytical Biochemistry, v.19, p.680–683, 1991.
Doulis, A.; Harfouche, A.; Aravanopoulos, F. Rapid, high quality DNA isolation from cypress (Cupressus sempervirens L.) needles and optimization of the RAPD marker technique. Plant Molecular Biology Reporter, v.17, p. 411-412, 1999.
El-Awady, A.M.M; El-Tarras, A.E.A. Genetic diversity of some Saudi barley (Hordeum vulgare L.) landraces based on microsatellite markers. African journal of biotechnology, v.11 (21), p. 4826 4832, 2012.
Excoffier, L.; Laval, G.; Schneider, S. Arlequin Version 3.0. An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, v.1, p. 47–50, 2005.
FAO. FAO statistical database. http://faostat.fao.org/faostat/collections?subset=agriculture. 2010.
Feng, Z.Y.; Zhang, Y.Z.; Zhang, L.L.; Ling, H. Q. Genetic diversity and geographical differentiation of Hor-deum vulgar ssp. spontaneum in Tibet using microsatellite markers. High Technology Letters, v.13, p.46-53, 2003.
Hamza, S.; Ben Hamida, W.; Rebaï, A.; Harrabi, M. SSR-based genetic diversity assessment among Tunisian winter barley and relationship with morphological traits. Biological Science. Euphytica, v.135, p. 107-118, 2004.
Kannan, B.; Senapathy, S.; Raj, A.G.B.; Chandra, S.; Muthiah, A.; Dhanapal, A.P.; Hash, C.T. Association Analysis of SSR Markers with Phenology ,Grain, and Stover-Yield Related Traits in Pearl Millet (Pennisetum glaucum (L.) R. Br.). The scientific world journal, p.1-15, 2014.
Kraakman, A.T.; Niks, R.E.; van den Berg, P.M.; Stam, P.; van Eeuwijk, F.A. Linkage disequilibrium map-ping of yield and yield stability in modern spring barley cultivars. Genetics, v.168, p.435 446, 2004.
Liu, J. PowerMarker V3.25 Manual. http://www.powermarker.net. 2004.
Liu, Z.W.; Biyashev, R.M.; Saghaie Maroof, M.A. Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theoretical and Applied Genetics, v.93(5), p.869-876, 1996.
Matsuoka, Y.; Mitchell, S.E.; Kresovich, S.; Goodman, M.; Doebley, J. Microsatellite in Zea variability, patterns of mutations and use for evolutionary studies. Theoretical and Applied Genetics, v.104, p.436-450, 2002.
Meszaros, K.; Karsai, I.; Kuti, C.; Banyai, J.; Lang, L.; Bedo, Z. Efficiency of different marker systems for genotype fingerprinting and for genetic diversity studies in barley (Hordeum vulgare L.). South African Journal of Botany, p.43-48, 2007.
Nandha, P.S.; Singh, J. Comparative assessment of genetic diversity between wild and cultivated barley using SSR and EST-SSR markers. Plant Breeding, v.133 (1), p. 28–35, 2014.
Oweis, T.; Hachum, A. Supplemental Irrigation for Improved Rainfed Agriculture in WANA Region. In: S.P. Wani et al. (Ed.). Rainfed Agriculture: unlocking the potential. CAB International, London, UK, 2009. p.182-196.
Peakall, R.; Smouse, P.E. GENALEX 6: Genetic analysis in excel. Population genetic software for teaching and research. Molecular Ecology Notes, v.6, p.288-295, 2006.
Pirseyedi, S.M.; Mardi, M.; Naghavi, M.R.; Poor Iran Doost, H.; Sadeghzadeh, D.; Mohammadi, S.A.; Ghare-yazie, B. Evalution of genetic diversity and identification of informative markers for morphological characters in Sardari derivated wheat lines. Pakistan Journal of Biological Sciences, v.9(13), p.2411-2418, 2006.
Russell, J.; Fuller, J.D.; Macaulay, M.; Hatz, B.G.; Jahoor, A.; Powell, W.; Waugh, R. Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theoretical and Applied Genetics, v.95(4), p. 714-722, 1997.
Saghai Maroof, M.A.; Biyashev, R.; Yang, G.P.; Zhang, Q.; Allard, R.W. Extraordinarily polymorphic mi-crosatellite DNA in barley: species diversity, chromosomal locations and population dynamics. Proceed-ings of the National Academy of Sciences, v.91(12), p.5466-5470, 1994.
Samarah, N.H. Effects of drought stress on growth and yield of barley. Agronomy for Sustainable Develop-ment, p.145–149, 2005.
Senior, M.L.; Murphy, J.P.; Goodman, M.M.; Stuber, C.W. Utility of SSRs for determining genetic similari-ties and relationships in maize using an agarose gel system. Crop Science, v.38, p.1088–1098, 1998.
Struss, D.; Plieske, J. Use of microsatellite markers for detection of genetic diversity in barley populations. Theoretical and Applied Genetics, v.97, p.308- 315. 1998.
Tamura, k.; Peterson, D.; Peterson, N.; Stecher, G.; Nei, M.; Kumar, S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, v.28(10), p.2731–2739, 2011.
Varshney, R.K.; Marcel, T.C.; Ramsay, L.; Russell, J.; Röder, M.S.; Stein, N.; Waugh, R.; Langridge, P.; Niks, R.E.; Graner, A. A high density barley microsatellite consensus map with 775 SSR loci. Theoreti-cal and Applied Genetics, v.114(6), p. 1091-1103, 2007.
Wei, Y.M.; Hou, Y.C.; Yan, Z.H.; Wu, W.; Zhang, Z.Q.; Liu, D.C.; Zheng, Y.L. Microsatellite DNA poly-morphism divergence in Chinese wheat (Triticum aestivum L.) landraces highly resistant to Fusarium head blight. Journal of Applied Genetics, v.46, p. 3-9, 2005.
Wilson, L.M.; Whitt, S.R.; Ibanez, A.M.; Rocheford, T.R.; Goodman, M.M.; Buckler, I.V. Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell, v.16, p. 2719–2733, 2004.
Zhang, D.; Bowden, R.L; Yu, J.; Carver, B.F.; Bai, G. Association Analysis of Stem Rust Resistance in U.S. Winter Wheat. The Scientific World Journal. PLoS One, v.9 (7): e103747, 2014.
Zhang, X.Y.; Li, C.W.; Wang, L.F.; Wang, H.M.; You, G.X.; Dong, Y.S. An estimation of the minimum number of SSR alleles needed to reveal genetic relationships in wheat varieties. Information from large-scale planted varieties and cornerstone breeding parents in Chinese wheat improvement and production. Theoretical and Applied Genetics, v.106(1), p.112-117, 2002.
Department of Agricultural Biotechnology, Faculty of Agriculture, Payame Noor University, Karaj, Alborz, Iran Iran, Islamic Republic of
Genomics Department; Agricultural Biotechnology Institute Northwest and West (Tabriz), Agricultural Biotechnology Research Institute of Iran (ABRII), Assistant Professor, Dept .of Agronomy & Plant Breeding, Faculty of Agricultural Sciences, University of Mohaghegh Ardabili, Ardabil, Iran Iran, Islamic Republic of
Department of Agricultural Biotechnology, Payame Noor University, Tehran, Iran. Iran, Islamic Republic of
Dryland Agricultural Research Insti. (DARI), Maragheh, Iran. Iran, Islamic Republic of
Department of Agronomy & Plant Breeding, Faculty of Agriculture, University of Tabriz, Iran. Iran, Islamic Republic of
All articles published in electronic form under CC BY-SA 4.0, in open access, the full content of the licence is available at: https://creativecommons.org/licenses/by-sa/4.0/legalcode.pl .
