|
|
|
|
|
| The power of microsatellite markers and AFLPs in revealing the genetic diversity of Hashemi aromatic rice from Iran |
| Alireza Tarang, Anahita Bakhshizadeh Gashti |
| Gilan Branch, Agricultural Biotechnology Research Institute of Iran/Agricultural Research, Education and Extension Organization (AREO), Rasht 8883-418895, Iran |
|
|
|
|
Abstract Hashemi, a popular aromatic rice among Iranians, is famous for its fragrance and taste. Such features are major reasons for its higher price compared to non-aromatic varieties available in Iran. Therefore, the knowledge of genetic diversity of this profitable crop is a fundamental ineterst for plant breeders in future breeding programs. In the present research, genetic diversity among 35 genotypes of Hashemi aromatic rice (Oryza sativa L.) from Guilan and Mazandaran provinces of Iran was estimated using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. Out of 21 SSR and 12 EcoRI-MseI AFLP marker combinations, only 16 SSRs and 10 AFLPs exhibited polymorphic patterns while others were monomorphic. The 10 AFLP primer combinations produced a total of 142 of bands and 20 were polymorphic (14.08%). Moreover, 40 out of 47 bands amplified with 16 SSR markers showed polymorphism (85.1%). The average number of alleles identified by SSR primers was 2.56 alleles per locus with a range of 2 to 4. The average value of polymorphic information content (PIC) was 0.393 and 0.468 for AFLP and SSR markers, respectively. However, the genetic similarity values ranged from 0.26 to 1 for SSRs and 0.21 to 1 for AFLPs. Later, a unweighted pair group method with arithmetic mean (UPGMA) dendrogram was generated and genotypes were clustered into four groups with SSRs at similarity coefficient of 0.55 while AFLPs clustered them into six groups at similarity coefficient of 0.41. Cluster analysis revealed a narrow genetic diversity and low correlation between geographical differentiation and genetic distance within cultivars.
|
|
Received: 22 May 2015
Accepted:
|
| Fund: This research was supported by the Purification of Hashemi Native Rice Varieties in North Regions of Iran, ABRII, Rasht (04-04-91126). |
|
Corresponding Authors:
Alireza Tarang, Tel: +98-93-09021598,
E-mail: a_tarang@hotmail.com
|
Cite this article:
Alireza Tarang, Anahita Bakhshizadeh Gashti.
2016.
The power of microsatellite markers and AFLPs in revealing the genetic diversity of Hashemi aromatic rice from Iran. Journal of Integrative Agriculture, 15(06): 1186-1197.
|
| Aggarwal R, Shenoy V, Ramadevi J, Rajkumar R, Singh L. 2002. Molecular characterization of some Indian Basmati and other elite rice genotypes using fluorescent-AFLP. Theoretical and Applied Genetics, 105, 680–690.Ashfaq M, Khan A. 2012. Genetic diversity in basmati rice (Oryza sativa L.) germplasm as revealed by microsatellite (SSR) markers. Russian Journal of Genetics, 48, 53–62.Bligh H F. 2000. Detection of adulteration of Basmati rice with non-premium long-grain rice. Interntional Journal of Food Science and Technology, 35, 257–265.Brondani C, Borba T C O, Rangel P H N, Brondani R P V. 2006. Determination of genetic variability of traditional varieties of Brazilian rice using microsatellite markers. Genetics and Molecular Biology, 29, 676–684.Faivre-Rampant O, Bruschi G, Abbruscato P, Cavigiolo S, Picco A M, Borgo L, Lupotto E, Piffanelli P. 2011. Assessment of genetic diversity in Italian rice germplasm related to agronomic traits and blast resistance (Magnaporthe oryzae). Molecular Breeding, 27, 233–246.FAO (Food and Agriculture Organization). 2014. faostat3. [2014-9-23]. http://faostat.fao.org/site/339/default.aspxGao J M, Zhang S G, Qi L Y, Zhang Y, Wang C G, Song W Q. 2006. ISSR and AFLP identification and genetic relationships of Chinese elite accessions from the genus Populus. Annals of Forest Science, 63, 499–506.Garris A J, Tai T H, Coburn J, Kresovich S, McCouch S. 2005. Genetic structure and diversity in Oryza sativa L. Genetics, 169, 1631–1638.Germano J, Klein A. 1999. Species-specific nuclear and chloroplast single nucleotide polymorphisms to distinguish Picea glauca, P. mariana and P. rubens. Theoretical and Applied Genetics, 99, 37–49.Jain S, Jain R K, McCouch S R. 2004. Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theoretical and Applied Genetics, 109, 965–977.Kibria K, Nur F, Begum S, Islam M, Paul S, Rahman K, Azam S. 2009. Molecular marker based genetic diversity analysis in aromatic rice genotypes using SSR and RAPD markers. International Journal of Sustainable Crop Production, 4, 23–34.Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio B, Shomura A, Shimizu T, Lin S. 1994. A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nature Genetics, 8, 365–372.Liu C, Musial J, Thomas B. 1999. Genetic relationships among Stylosanthes species revealed by RFLP and STS analyses. Theoretical and Applied Genetics, 99, 1179–1186.Liu K, Muse S V. 2005. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics, 21, 2128–2129.Luan L, Wang X, Long W B, Liu Y H, Tu S B, Zhao Z P, Kong F L, Yu M Q. 2008. Microsatellite analysis of genetic variation and population genetic differentiation in autotetraploid and diploid rice. Biochemical Genetics, 46, 248–266.Ma H, Yin Y, Guo Z F, Cheng L, Zhang L, Zhong M, Shao G J. 2011. Establishment of DNA fingerprinting of Liaojing series of japonica rice. Middle-East Journal of Scientific Research, 8, 384–392.McCouch S, Kochert G, Yu Z, Wang Z, Khush G, Coffman W, Tanksley S. 1988. Molecular mapping of rice chromosomes. Theoretical and Applied Genetics, 76, 815–829.McCouch S R, Chen X, Panaud O, Temnykh S, Xu Y, Cho Y G, Huang N, Ishii T, Blair M. 1997. Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Molecular Biology, 35, 89–99.McGregor C, Lambert C, Greyling M, Louw J, Warnich L. 2000. A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica, 113, 135–144.Moumeni A, Samadi B Y, Wu J, Leung H. 2003. Genetic diversity and relatedness of selected Iranian rice cultivars and disease resistance donors assayed by simple sequence repeats and candidate defense gene markers. Euphytica, 131, 275–284.Nagaraju J, Kathirvel M, Kumar R R, Siddiq E, Hasnain S. 2002. Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers. Proceedings of the National Academy of Sciences the United States of America, 99, 5836–5841.Nandakumar N, Singh A, Sharma, K Mohapara R K, Prabhu T K V, Zaman F U. 2004. Molecular fingerprinting of hybrids and assessment of genetic purityof hybrid seeds in rice using microsatellite markers. Euphytica, 136, 257–264.Neeraja C, Malathi S, Siddiq E. 2006. Subspecies-specific microsatellite markers for rice (Oryza sativa L). Journal of Plant Biochemistry and Biotechnology, 15, 39–41.Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89, 583–590.Ni J, Colowit P M , Mackill D J. 2002. Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Science, 42, 601–607.Prashanth S R, Parani M, Mohanty B P, Talame R, Tuberosa R, Parida A. 2002. Genetic diversity in cultivars and landraces of Oryza sativa subsp. Indica as revealed by AFLP markers. Genome, 45, 451–459.Rodriguez J, Berke T, Engle L, Nienhuis J. 1999. Variation among and within Capsicum species revealed by RAPD markers. Theoretical and Applied Genetics, 99, 147–156.Rogers S O, Bendich A J. 1994. Extraction of total cellular DNA from plants, algae and fungi. In: Plant Molecular Biology Manual. Springer, the Netherlands. pp. 183–190.Rohlf F J. 1992. NTSYS-pc: Numerical taxonomy and multivariate analysis system. In: Applied Biostatistics. Setauket, New York.Russell J, Fuller J, Macaulay M, Hatz B, Jahoor A, Powell W, Waugh R. 1997. Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theoretical and Applied Genetics, 95, 714–722.Sharma A, Sharma R, Machii H. 2000. Assessment of genetic diversity in a Morus germplasm collection using fluorescence-based AFLP markers. Theoretical and Applied Genetics, 101, 1049–1055.Singh N, Choudhury D R, Singh A K, Kumar S, Srinivasan K, Tyagi R, Singh N, Singh R. 2013. Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties. PLOS ONE, 8, e84136.Siwach P, Jain S, Saini N, Chowdhury V K, Jain R K. 2004. Allelic diversity among Basmati and non-Basmati long-grain indica rice varieties using microsatellite markers. Journal of Plant Biochemistry and Biotechnology, 13, 25–32.Spada A, Mantegazza R, Biloni M, Caporali E, Sala F. 2004. Italian rice varieties: Historical data, molecular markers and pedigrees to reveal their genetic relationships. Plant Breeding, 123, 105–111.Tingey S V, del Tufo J P. 1993. Genetic analysis with random amplified polymorphic DNA markers. Plant Physiology, 101, 349.Tu M, Lu B R, Zhu Y, Wang Y. 2007. Abundant within-varietal genetic diversity in rice germplasm from Yunnan Province of China revealed by SSR fingerprints. Biochemical Genetics, 45, 789–801.Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M. 1995. AFLP: A new technique for DNA fingerprinting. Nucleic Acids Research, 23, 4407–4414.Wang Z, Liao L, Yuan X, Guo H, Guo A, Liu J. 2013. Genetic diversity analysis of Cynodon dactylon (bermudagrass) accessions and cultivars from different countries based on ISSR and SSR markers. Biochemical Systematics and Ecology, 46, 108–115.Yu S, Xu W, Vijayakumar C, Ali J, Fu B, Xu J, Jiang Y, Marghirang R, Domingo J, Aquino C. 2003. Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program. Theoretical and Applied Genetics, 108, 131–140.Zhang P, Li J, Li X, Liu X, Zhao X, Lu Y. 2011. Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers. PLoS ONE, 6, e27565.Zhao W, Chung J W, Ma K H, Kim T S, Kim S M, Shin D I, Kim C H, Koo H M, Park Y J. 2009. Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers. Genes and Genomics, 31, 283–292. |
| No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
