Transferability of wheat SSR markers for determination of genetic diversity and relationships of barley varieties

Document Type : Research Paper

Authors

1 Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran.

2 Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.

3 ِDepartment of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.

4 Dryland Agriculture Research Institute of Iran, Maragheh, Iran.

10.22034/jppb.2020.13277

Abstract

Simple sequence repeat (SSR) markers are simple PCR-based co-dominant markers, which are highly polymorphic and informative due to the number and frequency of alleles, and thus they are most utilized among the molecular markers. However, the development of SSR markers is costly and time-consuming. Cross-species transferability of SSRs allows the SSRs isolated from one species to apply on a closely related species, which increases the utility of previously isolated SSRs. This study demonstrated the cross-species transferability of 196 SSR primer pairs of wheat in genetic diversity analysis of 40 varieties of barley (Hordeum vulgare L.). Of the 196 SSR primer pairs assayed, 59 (30.1%) showed transferability. Of the 59 primer pairs, 21 pairs were polymorphic with the polymorphism information content ranging from 0.19 to 0.70. The number of alleles detected at each locus ranged from one to seven with an average of 3.57. Cluster analysis using the Minimum Evolution algorithm and the coefficient of Number of Differences assigned the genotypes into five groups.

Keywords


Article Title [فارسی]

انتقال پذیری نشانگر های SSR گندم برای بررسی تنوع و روابط ژنتیکی ارقام جو

Authors [فارسی]

  • هما زلقی 1
  • سید ابوالقاسم محمدی 2
  • محمد مقدم 3
  • بهزاد صادق زاده 4
1 گروه به نژادی و بیوتکنولوژی گیاهی، دانشگاه تبریز، تبریز.
2 گروه به نژادی و بیوتکنولوژی گیاهی دانشگاه تبریز، تبریز.
3 گروه به نژادی و بیوتکنولوژی گیاهی دانشگاه تبریز، تبریز.
4 موسسه تحقیقات کشاورزی دیم کشور، مراغه.
Abstract [فارسی]

نشانگرهای SSR نشانگرهای هم بارز مبتنی بر  PCR هستند که به دلیل ماهیت چندآللی و فراوانی بالای آللی، دارای چندشکلی بالا و حاوی اطلاعات زیادی می­ باشند و بنابراین کاربرد فروانی در میان نشانگرهای مولکولی دارند. در عین حال، توسعه نشانگرهای SSR بسیار پرهزینه و زمان­ بر می­ باشد. انتقال پذیری بین گونه­ ای نشانگرهای  SSRامکان استفاده از نشانگرهای SSR طراحی شده برای یک گونه را در گونه­ های نزدیک فراهم می­ کند و بنابراین فراوانی استفاده از نشانگرهایی را که قبلا طراحی شده ­اند، افزایش می­ دهد. در این مطالعه انتقال­ پذیری و چندشکلی 169 نشانگر SSR که برای گندم (Triticum aestivum L.) طراحی شده بودند، در 40 ژنوتیپ جو (Hordeum vulgare L.)  بررسی شد. از 169 نشانگر، 59 (30.1%) آغازگر انتقال­ پذیری نشان دادند که از این 59 جفت آغازگر، 21 جفت چندشکل بودند (با متوسط ارزش PIC 0.19 تا 0.68). تعداد الل مشاهده شده در هر جایگاه بین 1 تا 7 الل و با متوسط 3.57 متغیر بود. تجزیه خوشه ­ای با استفاده از الگوریتم Minimum Evaluation و ضریب فاصله Number of Difference ژنوتیپ­ ها را در 5 گروه مجزا قرار داد.

Keywords [فارسی]

  • انتقال پذیری
  • جو
  • گندم
  • SSR
Basudeba K, Kumar JR and Sanghamitra N, 2013. Cross-amplification polymorphism of rice        microsatellites in Zingiberaceae. Research Journal of Biotechnology 8(3): 76-83.
Castillo A, Budak H, Varshney RK, Dorado G, Graner A and Hernandez P, 2008. Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis. BMC Plant Biology 8: 97. doi.org/10.1186/1471-2229-8-97.
Chen SHY, Lin TY, Lin CHW, Chen WY, Yang CHH and Ku HM, 2010. Transferability of rice SSR markers to bamboo. Euphytica 175: 23-33.
Erayman M, Elhan E, Guzel Y and Eren AH, 2014. Transferability of SSR markers from distantly related legumes to Glycyrrhiza species. Turkish Journal of Agriculture and Forestry 38: 32-38.
Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N and Balyan HS, 2003. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Molecular Genetics and Genomics 270: 315-323.
Khodayari H, Saeidi H, Akhavan Roofigar A, Rahiminejad MR, Purkheirandish M and Komatsuda T, 2012. Genetic diversity of cultivated barley landraces in Iran measured using microsatellites. International Journal of Bioscience, Biochemistry and Bioinformatics 4: 287-290.
Kuleung C, Baenziger PS and Dweikat I, 2004. Transferability of SSR markers among wheat, rye and triticale. Theoretical and Applied Genetics 108: 1147-1150.
Liu K and Muse SV, 2005. PowerMarker: an integrated analysis environment for genetic marker data. Bioinformatics 21: 2128-2129.
Lio YC, Lio S, Lio D, Wei YX, Lio C, Yang YM, Tao CG and Lio WS, 2014. Exploiting EST databases for the development and characterization of EST-SSR marker in blueberry (Vaccinium) and their crop species transferability in Vaccinium spp. Scientia Horticulturae 176: 319-329.
Magurran AE, 2004. Measuring Biological Diversity. Blackwell, pp. 215.
Mohammadvand Latifi M, Jamali SH, Mobasser S, Sadeghi L and Sadeghian SY, 2012. Identification and distinctness of barley varieties using SSR markers. Journal of Plant Physiology and Breeding 1(2): 73.
Naceur, A.B., Chaabane, R., El-Faleh, M., Ramla, C.A.D., Nada, A., Sakr, M. and Naceur, M.B. 2012. Genetic diversity analysis of North Africa’s barley using SSR markers. Journal of Genetic Engineering and Biotechnology, 10: 13-21.
Nie, M. 1973. Analysis of gene diversity in subdivided populations. Proceeding of National Academy of Sciences of the United States of America, 70: 3321-3323.
Peakall, R., Gilmore, S., Keys, W., Morgante, M. and Rafalski, A. 1998. Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Molecular Biology and Evolution, 15(10): 1275-1287.
Peakall, R.O.D. and Smouse, P.E. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 1: 288-295.
Powell, W., Machray, G.C. and Provan, J. 1996. Polymorphism revealed by simple sequence repeats. Trends in Plant Science, 1: 215-222.
Saghai-Maroof, M.A., Biyashev, R.M., Yang, G.P., Zhang, Q. and Allard. R.W. 1994. Extra ordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. Proceeding of the National Academy of Sciences of the United States of America, 91: 5466-5470.
Sing, R., Narzary, D., Bhardwaj, J., Sing, A.K., Kumar, S. and Kumar, A. 2014. Molecular diversity and SSR transferability studies in Vetiver grass (Vetiveria Zizanioides L. Nash). Industrial Crops and Products, 53: 187-198.
Singh, R.K., Singh, R.B., Singh, S.P. and Sharma, M.L. 2011. Identification of sugarcane microsatellites associated to sugar content in sugarcane and transferability to other cereal genomes. Euphytica, 182: 335-354.
Tamura, K., Dudley, J., Nei, M. and Kumar, S. 2011. MEGA 5: Molecular evolutionary genetics analysis (MEGA) software, version 5.0. Molecular Biology and Evolution, 24: 1596-1599.
Tang, J., Gao, L., Cao, Y. and Jia, J. 2006. Homologous analysis of SSR-ESTs and transferability of wheat SSR-EST markers across barley, rice, and maize. Euphytica, 151: 87-93.
Varshney, R.K. 2004. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye, and rice. Plant Science, 168: 195-202.
Wang, M.L., Barkley, N.A., Yu, J.-K., Dean, R.E., Newman, M.L., Sorrells, M.E. and Pederson, G.A. 2004. Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation. Plant Genetic Resources, 3(1): 45-57.
Yildiz, M., Cuevas, H.E., Sensoy, S., Erdinc, C. and Baloch, F.S. 2015. Transferability of Cucurbita SSR markers for genetic diversity assessment of Turkish bottle gourd (Lagenaria siceraria) genetic resources. Biochemical Systematics and Ecology, 59: 45-53.
Zaloglu, S., Kafkas, S., Dogan, Y. and Gunery, M. 2015. Development and characterization of SSR Markers from pistachio (Pistacia vera L.) and their transferability to eight pistacia species. Scientia Horticulturae, 189: 94-103.
Zeid, M., Yu, J.K., Goldowitz, I., Denton, M.E., Costich, D.E., Jayasuriya, C.T., Saha, M., Elshire, R., Benscher, D., Breseghello, F., Munkvold, J., Varshney, R.K., Belay, G. and Sorrells, M.E. 2010. Cross-amplification of EST-derived markers among 16 grass species. Field Crops Research, 118: 28-35.
Zhang, L.Y., Bernard, M., Leroy, P., Feuillet, C. and Sourdille, P. 2005.  High transferability of bread wheat EST-derived SSRs to other cereals. Theoretical and Applied Genetics, 111: 677-687.