TRANSFERABILITY AND POLYMORPHISM OF BARLEY MICROSATELLITE MARKERS ACROSS H-GENOME CONTAINING SPECIES IN THE GENUS HORDEUM (H. VULGARE AND H. BULBOSUM)

Document Type : Research Paper

Authors

1 PhD Student / Department of Biology, University of Isfahan, Isfahan, Iran

2 Assistant Professor / Department of Biology, University of Isfahan, Isfahan, Iran

3 Professor / Department of Biology, University of Isfahan, Isfahan, Iran

4 Professor / Crop Genome Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

Abstract

Limited numbers of microsatellite markers are available for genetic characterization of Hordeum bulbosum which comprises the secondary genepool of cultivated barely. The objective of this study was to evaluate the transferability of microsatellite markers from H. vulgare to H. bulbosum and a preliminary evaluation of their polymorphism. From ninety-three pairs barley SSR primer tested for transferability, all of them  amplified DNA segments in H. vulgare (11 accessions) and48 pairs (51.61%) were transferable to the H. bulbosum (5 accessions) with high level of polymorphism. Twenty-two (23.65%) SSR markers showed transferability to H. murinum used as outgroup. A total of 546 alleles were detected by 48 transferred primer pairs in all accessions. The number of alleles per locus ranged from 3 to 13 with an average of 11.375 alleles per locus. The PICvalues were ranged from 0.161 to 0.621 with an average of 0.477. The value of PIC in H. vulgare (average PIC = 0.639) was significantly higher than H. bulbosum (average PIC = 0.316). In dendrogram generated based on SSR data accessions were divided into groups related to their taxonomic classifications, indicating the efficiency of barley SSRs for phylogenetic analyses in H genome containing species in the genus Hordeum. Based on the results of this study, it can be suggested that the cross species transferable barley SSRs are valuable molecular tools, for genetic diversity analyses in the H. bulbosum for which limited number of microsatellite markers are available. This study provided a set of efficient SSR markers from publicly available barley microsatellite markers for the genetic characterization of H. bulbosum.

Keywords

Article Title [Persian]

قابلیت انتقال و تنوع ریزماهوارک‌های جو زراعی به گونه‌های واجد ژنوم H در جنس جو (Hordeum vulgare, H. bulbosum)

Authors [Persian]

  • حامد خدایاری 1
  • حجت‌الله سعیدی 2
  • محمدرضا رحیمی‌نژاد 3
  • تاکائو کوماتسودا 4
1 دانشجوی دکتری / گروه زیست‌شناسی دانشگاه اصفهان
2 استادیار / گروه زیست‌شناسی دانشگاه اصفهان
3 استاد / گروه زیست‌شناسی دانشگاه اصفهان
4 استاد / مرکز تحقیقات ژنومی گیاهان زراعی، موسسه علوم زیستی کشاورزی (NIAS)، سوکوبا، ژاپن
Abstract [Persian]

تعداد محدودی مارکرهای ریزماهوارک مناسب برای بررسی تنوع وراثتی گونه‌ی H. bulbosumوجود دارد. در این مطالعه قابلیت انتقال ریزماهوارک‌های جو زراعی به گونه‌ی H. bulbosumو تنوع پذیری آنها مورد بررسی قرار گرفته است. از 93 زوج پرایمر SSR آزمایش شده همگی در گونه‌ی H. vulgare(11 نمونه بذر) قطعاتی از DNA را تکثیر نمودند ولی تنها 46 زوج از آنها (61/51%) قابلیت انتقال به گونه H. bulbosum (5 نمونه بذر) با سطح قابل ملاحظه‌ای از تنوع را نشان دادند. در گونه‌ی  H. murinum که به عنوان برون گروه استفاده شده بود 22 زوج پرایمر SSR (65/23%) قابلیت انتقال نشان دادند. در PCR انجام شده با استفاده از 48 مارکر SSR تعداد 546 آلل در کل جمعیت‌ها تشخیص داده شد. تعداد آلل‌ها در هر جایگاه وراثتی SSR بین 3 تا 13 با میانگین 375/11 آلل بود. مقدار PIC محاسبه شده برای هر مارکر بین 161/0 تا 621/0 با میانگین 477/. بود. مقدار PIC در گونه‌ی H. vulgare (با میانگین 639/0) به طور معنی داری بالاتر از H. bulbosum(با میانگین 316/0) بود. در دندروگرام حاصل جمعیت‌ها بر اساس گروه های تاکسونومیک از هم جدا شدند که نشان‌دهنده‌ی کارآیی این مارکرها برای مطالعه فیلوژنی درون این گروه است. نتایج این مطالعه نشان می‌دهد که مایکروساتلایت‌های جو زراعی برای بررسی تنوع وراثتی گونه‌ی H. bulbosumمناسب هستند.
 

Keywords [Persian]

  • Microsatellites
  • Genetic diversity
  • Breeding
  • Transferability
  • H genome
  • Barley
  • germplasm

References

Alves Rafael M., Sebbenn A. M., Artero A. S. & Figueira A. 2006: Microsatellite loci transferability from Theobroma cacao to Theobroma grandiflorum.  -Molecular Ecology Notes. 6: 1219–1221.
Anderson J. A., Churchill G. A., Autrique J. E., Tanksley S. D. & Sorrells M. E. 1992: Optimizing parental selection for genetic linkage maps. -Genome 36: 181-186.
Asfaw Z. & Bothmer R.  1990: Hybridization between landrace varieties of Ethiopian barley (Hordeum vulgare ssp. vulgare) and the progenitor of barley (H. vulgare ssp. spontaneum). -Hereditas 112: 57–64.
Bothmer R., Jacobson N., Baden C, Jorgensen R. B. & Linde-Laursen I. 1995:  An ecographical study of the genus Hordeum. 2nd Ed. -International Plant Genetic Resources Institute, Rome, Italy. pp 1-124.
Bravo J. P., Akemi H. A., Lara C. M., Angelici C. D., Lopes C. R. & Gimenes M. A. 2006: Transferability and use of microsatellite markers for the genetic analysis of the germplasm of some Arachis section species of the genus Arachis. -Genet Mol Biol 29(3): 516-524. 
Brown  A. D. H., Burdon J. J., Grace J. P. 1990: Genetic structure of Glycine canescens, a perennial relative of soybean. -Theoretical and Applied Genetics 79: 729-736.
Castillo A., Budak H., Martin A. C., Dorado G., Borner A., Roder M. & Hernandez P. 2010: Interspecies and intergenus transferability of barley and wheat D-genome microsatellite markers. -Annales of Applied Biology 156: 347–356.
Castillo A., Budak H., Varshney R. K., Dorado G., Graner A. & HernandezP. 2008: Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense. -BMC Plant Biology 8:97 doi:10.1186/1471-2229-8-97.
Dice L. R. 1945: Measures of the amount of ecologic association between species. -Ecology 26: 297-302.
Ellis, J. R. & Burke J. M. 2007: EST-SSRs as a resource for population genetic analysis. -Heredity 99: 125-132.
Fahima T., Roder S., Grama A., Nevo E. 1998: Microsatellite DNA polymorphism divergence in Triticum dicoccoides accessions highly resistant to yellow rust. -Theor Appl Genet 96: 187-195.
Gimenes Marcos A., Hoshino A. A., Barbosa A. V. G., Palmieri D. A. & Lopes C. R. 2007: Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogaea). -BMC Plant Biol 7:9 doi:10.1186/1471-2229-7-9.
Gupta P. K., Rustgi S., Sharma S., Singh R., Kumar N. & Balyan H. S. 2003: Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. -Mol Genet Genomics 270(4): 315-323.
Hernández P., Laurie D. A., Martín A. &  Snape J. W. 2002: Utility of barley and wheat simple sequence repeat (SSR) markers for genetic analysis of Hordeum chilense and tritordeum. -Theoretical and Applied Genetics 104:735–739.
Jenabi T., Saeidi H. & Rahiminejad M. R. 2011: Biodiversity of Secale strictum in Iran measured using microsatellites. -Gentics Resource Crop Evolution 58 (4): 497-505.
Kakeda K., Taketa S. & Komatsuda T. 2009: Molecular phylogeny of the genus Hordeum using thioredoxin-like gene sequences. -Breeding Science 59: 595-601.
Kasha K. J., Pickering R. A., William H. M., Hill A., Oro R., Reader S. & Snape  J.W.1996: GISH and RFLP facilitated identification of a barley chromosome carrying powdery mildew resistance from Hordeum bulbosum.  -Proc. 7th Intl. Barley Genet. Symposium. University Extension Press, University of Saskatchewan 1:.338-340.
Komatsuda T., Nakamura I., Takaiwa F. & Oka S. 1998: Development of STS markers closely linked to the vrs1 locus in barley, Hordeum vulgare. -Genome 41: 680–685.
Liu Z. W., Biashev R. M. & Saghai Maroof M. A. 1996: Development of simple sequence reapeat DNA marker and their integration into a barley linkage map. -Theoretical and Apllied Genetics 93: 869-876.
Martin A., Martin L. M., Cabrera A., Ramirez M. C., Gimenez M. J., Rubiales D., Hernandez P. & Ballesteros J. 1998: The potential of Hordeum chilense in breeding Triticeae species. In: Jaradat AA, Enfield NH (eds) Triticeae III. -Science Publishers, pp. 377–386.
Pickering R. A. 1992: Monosomic and double monosomic substitutions of Hordeum bulbosum L. chromosomes into H. vulgare L. -Theoretical and Apllied Genetics 84: 466-472.
Pickering R. A., Malyshev S., Künzel G., Johnston P. A., Korzun V., Menke M. & Schubert I. 2000: Locating introgressions of Hordeum bulbosum chromatin within the H. vulgare genome. -Theoretical and Apllied Genetics 100: 27-31.
Ramsay L., Macaulay M., Degli Ivanissevich S., Maclean K., Fuller J., Edwards K. J., 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. -Genetics 156: 1997-2005.
Rolf  F. J. 2000: NTSYS-PC: Numerical Taxonomy and Multivariate Analysis System. Ver. 2.1., Exter Software, Setauket, New York, ISBN: 0925031-30-5, pp: 1-38.
Ruge B., Michel M. & Pickering R. A., Proeseler G. & Wehling P. 2000: Gene introgressions from H. bulbosum into cultivated barley cause resistance to different pathogens. -Plant and Animal Genome Conference VIII, 09-12.01.2000. San Diego, CA, USA.
Sharifi Tehrani M., Mardi M., Saeidi H., Gharehyazi B. & Assadi M. 2008:Transferability of  genomic and EST-Microsatellites  from Festuca arundinacea Scherb. to Lolium persicum Boiss. and Hohen. ex Boiss. -International Journal Botany 4 (4): 476-480.
Taketa S., Ando H., Takeda K. & von Bothmer R. 1999: Detection of Hordeum marinum genome in three polyploid Hordeum species and cytotypes by genomic in situ hybridization. -Hereditas 130: 185–188.
Taketa S., Ando H., Takeda K. & von Bothmer R. 2001: Physical locations of 5S and 18S–25S rDNA in Asian and American diploid Hordeum species with the I genome. -Heredity 86: 522–530.
The Iranian Journal of Botany
Volume 17, Issue 2 - Serial Number 2
December 2011
Pages 200-211

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History

  • Receive Date: 27 April 2011
  • Revise Date: 10 October 2011
  • Accept Date: 16 November 2011

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