농업과학연구 (Korean Journal of Agricultural Science)

  • 제48권2호
  • /
  • Pages.283-297
  • /
  • 2021
  • /
  • 2466-2402(pISSN)
  • /
  • 2466-2410(eISSN)
충남대학교 농업과학연구소 (Institute of Agricultural Science, CNU)
권호 표지
DOI QR코드

DOI QR Code

Genetic diversity analysis of high yielding rice (Oryza sativa) varieties cultivated in Bangladesh

  • Epe, Isma Akter (Department of Genetics and Plant Breeding, Patuakhali Science and Technology University) ;
  • Bir, Md. Shahidul Haque (Department of Crop Science, Chungnam National University) ;
  • Choudhury, Abul Kashem (Department of Genetics and Plant Breeding, Patuakhali Science and Technology University) ;
  • Khatun, Asma (Department of Genetics and Plant Breeding, Patuakhali Science and Technology University) ;
  • Aktar, Most Mohshina (Department of Fisheries Management, Bangladesh Agricultural University) ;
  • Arefin, Md. Shamsul (Department of Soil Science, Bangladesh Agricultural University) ;
  • Islam, Mohammed Aminul (Department of Agriculture Chemistry, Bangladesh Agricultural University) ;
  • Park, Kee Woong (Department of Crop Science, Chungnam National University)
  • 투고 : 2020.09.01
  • 심사 : 2021.05.13
  • 발행 : 2021.06.01
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

Investigation of genetic diversity and molecular characterization in high yielding rice varieties is important for their identification. The experiment was conducted during 2016 - 2017 to analyse the genetic diversity of fifteen high yielding rice varieties in Bangladesh by using random amplification of polymorphic DNA (RAPD) markers. Polymorphism was revealed in 12 RAPD primers out of 30, whereas no other reaction was detected on the remaining 18 primers. The 40 out of 45 bands (88.89%) polymorphics were produced by the primers and ranged from 50 to 100%. The maximum number of polymorphic bands was produced by the primer OPB-18 whereas the lowest number of polymorphic bands belonged to OPC-12. The genetic similarity coefficients were determined with the RAPD data, which ranged from 0.47 to 0.94. The unweighted paired group of arithmetic means (UPGMA) dendrogram presented the studied rice varieties into two major clusters. Moreover, the value of Nei's genetic diversity is 0.26 and the Shanon information index is 0.41. The study produced distinct positions, suggesting that the genotypes were different from each other. The results indicated that these markers could be efficient for comparing the genetic relationships, patterns of variation, and measurement of genetic distance among rice varieties. Considering all of these results, RAPD analysis is found to be an effective tool for estimating the genetic diversity of different rice varieties. The outcomes of this research may contribute to the germplasm data of rice accessions and a future breeding program of rice genotypes.

키워드

참고문헌

  1. Akagi H, Yokozeki Y, Inagaki A, Fujimura T. 1997. Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theoretical and Applied Genetics 94:61-67. https://doi.org/10.1007/s001220050382
  2. Alam SMM, Siddika S, Haque ME, Islam MA, Mukherjee A, Sikar B. 2016. Genetic diversity of some upland and lowland rice cultivars in Bangladesh using RAPD, ISSR and SSR markers. The Nucleus 59:15-23. https://doi.org/10.1007/s13237-015-0148-x
  3. Cao D, Oard JH. 1997. Pedigree and RAPD- based DNA analysis of commercial U.S. rice cultivars. Crop Science 37:1630- 1635. https://doi.org/10.2135/cropsci1997.0011183X003700050037x
  4. Chakravarthi BK, Naravaneni R. 2006. SSR marker based DNA fingerprinting and diversity study in rice (Oryza sativa. L). African Journal of Biotechnology 5:684-688.
  5. Cirillo A, Del Gaudio S, Di Bernardo G, Galderisi U, Cascino A, Cipollaro M. 2009. Molecular characterization of Italian rice cultivars. European Food Research and Technology 228:875-881. https://doi.org/10.1007/s00217-008-1000-1
  6. Clark AG, Lanigan CMS. 1993. Prospects for estimating nucleotide divergence with RAPDs. Molecular Biology and Evolution 10:1069-1111.
  7. Davierwala AP, Chowdari KV, Kumar S, Reddy APK, Ranjekar PK, Guota VS, Doyle JJ, Doyle JL. 1990. Isolation of plant DNA from fresh tissue. Focus 12:13-15.
  8. Fukuoka S, Hosaka K, Kamijima O. 1992. Use of random amplified polymorphic DNAs (RAPDs) for identification of rice accessions. The Japanese Journal of Genetics 67:243-252. https://doi.org/10.1266/jjg.67.243
  9. Halder T, Hoque ME, Islam MM, Ali L, Chowdhury AK. 2016. Morphomolecular characterization of local boro rice (Oryza Sativa L.) germplasm. Bangladesh Journal of Plant Breeding and Genetics 29:01-09. https://doi.org/10.3329/bjpbg.v29i2.33941
  10. Islam SN, Islam MM, Ullah MA, Alam MS. 2015. Molecular characterization of selected landraces of rice for salt tolerance using SSR markers. International Journal of Innovation and Scientific Research 17:206-218.
  11. Jaccard P. 1908. Nouvellesrecherchessur la distribution florale. Bulletin de la SocieteVaudoise des Sciences Naturelles 44:223-270.
  12. Jena M, Panda RS, Sahu RK, Mukherjee AK, Dhua U. 2015. Evaluation of rice genotypes for rice brown plant hopper resistance through phenotypic reaction and genotypic analysis. Crop Protection 78:119-126. https://doi.org/10.1016/j.cropro.2015.08.020
  13. Koizumi N, Morioka S, Mori A, Vongvichith B, Shibukawa K, Nishida K, Watabe K, Takemura T. 2013. Development of nineteen novel polymorphic microsatellite loci of Clupeichthys aesarnensis. Conservation Genetics Resources 5:707-709. https://doi.org/10.1007/s12686-013-9887-7
  14. Kresovich S, McFerson JR. 1992. Assessment and management of plant genetic diversity: Consideration of intra- and interspecific variation. Field Crops Research 29:185-204. https://doi.org/10.1016/0378-4290(92)90025-5
  15. Mani P, Bastin J, Arunkumar R, Ahmed ABA. 2010. RAPD-analysis of genetic variation of four important rice varieties using two OPR primers. ARPN Journal of Agricultural and Biological Science 5:25-31. https://doi.org/10.3844/ajabssp.2010.25.31
  16. Mukherjee M, Padhy B, Srinivasan B, Mahadani P, Baksh SY, Donde R, Singh ON, Behera L, Swain P, Dash SK. 2018. Revealing genetic relationship and prospecting of novel donors among upland rice genotypes using qDTY-linked SSR markers. Rice Science 25:308-319. https://doi.org/10.1016/j.rsci.2018.10.001
  17. Nei M. 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America 70:3321-3323.
  18. Pervaiz ZH, Rabbani MA, Shinwari ZK, Masood MS, Malik SA. 2010. Assessment of genetic variability in rice (Oryza sativa L.) germplasm from Pakistan using RAPD markers. Pakistan Journal of Botany 42:3369-3376.
  19. Rabbani MA, Pervaiz ZH, Masood MS. 2008. Genetic diversity analysis of traditional and improved cultivars of Pakistani rice (Oryza sativa L.) using RAPD markers. Electronic Journal of Biotechnology 11:52-61.
  20. Rashid M. 2007. Detection of polymorphism in rice germplasm using rapd marker. Pakistan Journal of Botany 39:2483-2493.
  21. Ravi M, Geethanjali S, Sameeyafarheen F, Maheswaran M. 2003. Molecular marker based genetic diversity analysis in rice (Oryza sativa L.) using RAPD and SSR markers. Euphytica 133:243-252. https://doi.org/10.1023/A:1025513111279
  22. Saker MM, Youssef SS, Abdallah NA, Bashandy HS, el-Sharkawy AM, Singh A, Kumar Y, Matta NK. 2018. Electrophoretic variation in seed proteins and interrelationships of species in the genus Oryza. Genetic Resources and Crop Evolution 65:1915-1936. https://doi.org/10.1007/s10722-018-0665-y
  23. Skaria R, Sen S, Muneer PMA. 2011. Analysis of genetic variability in rice varieties (Oryza sativa L) of Kerala using RAPD markers. Genetic. Engineering and Biotechnology Journal 24:1-9.
  24. Virk PS, Fond BVL, Jackson MT, Pooni HS, Clemeno TP, Newbury HJ. 1996. Predicting quantitative variation within rice germplasm using molecular markers. Heredity 76:296-304. https://doi.org/10.1038/hdy.1996.43
  25. Virk PS, Newbury HJ, Jackson MT, Ford BVL. 1995. The identification of duplication accessions within a rice germplasm collection using RAPD analysis. Theoretical and Applied Genetics 90:1049-1055. https://doi.org/10.1007/bf00222920
  26. Weising K, Atkinson G, Gardner C. 1995. Genomic fingerprinting by microsatellite-primed PCR: A critical evaluation. PCR Methods Applications 4:249-255. https://doi.org/10.1101/gr.4.5.249
  27. Williams JGK, Kubeik AE, Levak K, Rafalski JA, Tingey SC. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 28:6531-6535.
  28. Won OJ, Eom MY, Kim YT, Bir MSH, Park TS, Uddin MR, Oh TK, Shinogi Y, Park KW. 2017. Growth response of rice and paddy weeds under elevated temperatures. Journal of the Faculty of Agriculture, Kyushu University 62:63-67. https://doi.org/10.5109/1799303
  29. Zhang LN, Cao GL, Han LZ. 2013. Genetic diversity of rice landraces from lowland and upland accessions of China. Rice Science 20:259-266. https://doi.org/10.1016/S1672-6308(13)60139-0