Assessment of molecular genetic diversity of ecuadorian rice cultivars using simple sequence repeat markers

Authors

  • Iris Pérez-Almeida Facultad de Ciencias Agrarias, Universidad de Guayaquil. Guayaquil EC090302 Ecuador
  • Roberto Celi-Herán Instituto Nacional de Investigaciones Agropecuarias, Estación Experimental Litoral Sur, Rice Program, Guayaquil EC092406 Ecuador
  • Fernando Sánchez-Mora Facultad de Ingeniería Agronómica, Campo Experimental La Teodomira, Universidad Técnica de Manabí. Lodana, EC 13132, Ecuador
  • Lenin Paz-Carrasco Instituto Nacional de Investigaciones Agropecuarias, Estación Experimental Litoral Sur, Rice Program, Guayaquil EC092406 Ecuador
  • Belén Ramos-Viteri Instituto Nacional de Investigaciones Agropecuarias, Estación Experimental Litoral Sur, Rice Program, Guayaquil EC092406 Ecuador

Keywords:

cluster análisis, molecular marker, Oryza sativa, rice breeding, variability

Abstract

Molecular markers are useful tools for evaluating genetic diversity and determining cultivar identity.  Thirty simple-sequence-repeat (SSR) markers were selected in order to evaluate the genetic diversity within 76 cultivars of the Ecuadorian Rice Program for breeding. One-hundred-ninety-four alleles were detected in 22 SSR polymorphic markers, number of alleles per marker ranging from 2 to 24, with an average of 9 alleles per locus.  The sizes of the alleles varied between 62 to 280 bp, with an average polymorphism information content value of 0.624, ranging from 0.202 (RM125) to 0.943 (RM413), indicating significant genetic diversity among and within the rice accessions. The average observed heterozygosity (Ho) was 0.086, while average expected genetic diversity (He) was 0.667. A set of eight of the polymorphic SSR markers produced seventeen unique alleles for the genotypes studied and could distinguish released cultivars from the rest of accessions.  A dendrogram constructed using the unweighted pair-group method with arithmetic means (UPGMA) grouped the 76 rice materials in four well differentiated major clusters whereas the Structure program without any a priori information provided support for the existence of three genetically distinct clusters (K = 3).

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References

1. Aguirre, C., R. Alvarado and P. Hinrichsen. 2005. Identificación de cultivares y líneas de mejoramiento de arroz de Chile mediante amplificación de fragmentos polimórficos (AFLP). Agricultura Técnica 65(4): 356-369.
2. Berrio, L.E, E.A Torres, J. Barona and J.B. Cuasquer. 2016. Diversidad genética de las variedades de arroz FLAR liberadas entre 2003-2014. Agrononomia Mesoamericana 27(2): 217-231.
3. Cuevas-Pérez, F., E.P. Guimaraes, L.E. Berrio and D. Gonzales. 1992. Genetic base of the irrigated rice in Latin America and the Caribbean. Crop Science 32(4): 1054-1059.
4. Day-Rubenstein, K.A., P. Heisey, R.A. Shoemaker, J. Sullivan and G. Frisvold. 2005. Crop genetic resources: An economic appraisal. Washington: USDA Economic Information Bulletin http://ageconsearch.umn.edu/record/59388/files/eib2.pdf (retrieved on Jul 30, 2018).
5. Earl D.A. and B.M. von Holdt. 2012. Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conservation Genetics Resources 4(2): 359-361.
6. FAOSTAT (Statistics Division Food and Agriculture Organization of the United Nations). 2018. http://www.fao.org/faostat/ en/#data (retrieved on May 5, 2018).
7. Ferreira M.E and D. Grattapaglia. 1998. Introduction to the use of molecular markers in the genetic analysis. EMBRAPA, Brasil, 220 p.
8. Fuentes, J., F. Escobar, A. Alvarez, G. Gallego, M.C. Duque, M. Ferrer, J. Deus and J. Tohme. 1999. Analyses of genetic diversity in Cuban rice varieties using isozyme, RAPD and AFLP markers. Euphytica 109(2): 107-115.
9. Garris, A.J., T.H. Tai, J. Coburn, S. Kresovich and S.R. McCouch. 2005. Genetic structure and diversity in Oryza sativa L. Genetics 169(3): 1631-1638.
10. Ghneim, T., D. Posso, I. Pérez-Almeida, G. Torrealba, A. Pieters, C. Martinez and J. Tohme. 2008. Assessment of genetic diversity in Venezuelan rice cultivars using simple sequence repeats markers. Electronic Journal of Biotechnology 11(5): 3-4.
11. Giarrocco L.E., M.A. Marassi and G.L. Salerno. 2007. Assessment of genetic diversity in Argentine rice cultivars with SSR markers. Crop Science 47(2): 853-860.
12. Guimaraes E.P., J. Borrero and Y. Ospina-Rey. 1996. Genetic diversity of upland rice germplasm distributed in Latin America. Pesquisa Agropecuaria Brasileira 31(3): 187-194.
13. Keneni, G., E. Bekele, M. Imtiaz and K. Dagne. 2012. Genetic vulnerability of modern crop cultivars: causes, mechanism and remedies. International Journal of Plant Research 2(3): 69-79.
14. MAG (Ministerio de Agricultura y Ganadería). 2015. Boletín situacional de arroz. Coordinación General del Sistema de Información Nacional. Quito. 6 p.
15. Montalvan, R., D. Destro, E.F. Silva and J.C. Montano. 1998. Genetic base of Brazilian upland rice cultivars. Journal of Genetics & Breeding 52(1): 203-209.
16. Orjuela, J., A. Garavito, M. Bonioul, J. Arbelaez, L. Moreno, J. Kimball, G. Wilson, J. Rami, J. Tohme, S. McCouch and M. Lorieux. 2010. A universal core genetic map for rice. Theoretical and Applied Genetics 120(3): 563-572.
17. Parikh, M., K. Motiramani, N. Rastogi and B. Sharma. 2012. Agro-morphological characterization and assessment of variability in aromatic rice germplasm. Bangladesh Journal of Agricultural Research 37(1): 1-8.
18. Peakall, R. and P.E. Smouse. 2006. Genalex 6: Genetic Analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6(1): 288-295.
19. Pérez-Almeida, I., E. Torres, L. Angulo and M. Acevedo. 2011. Genetic diversity among Venezuelan rice cultivars based on parentage coefficient estimation and analysis using microsatellite molecular markers (SSR). Interciencia 36(7): 545-551.
20. Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155(2): 945-959.
21. Rangel, P.H., E.P. Guimaraes and P.C. Neves. 1996. The genetic base of Brazilian irrigated rice (Oryza sativa L.) cultivars. Pesquisa Agropecuaria Brasileira 31(2): 349-357.
22. Roy, S., A. Banerjee, B. Mawkhlieng, A.K. Misra, A. Pattanayak, G.D. Harish et al. 2015. Genetic diversity and population structure in aromatic and quality rice (Oryza sativa L.) landraces from North Eastern India. PLoS ONE 10(6): e0129607.
23. Sneath, P.H. and R.R. Sokal. 1973. Numerical taxonomy: The principles and practice of numerical classification. W.H. Freeman. San Francisco, USA. 573 p.
24. Temnykh, S., W. Park, N. Ayres, S. Cartinhour, N. Hauck, L. Lipovich and S.R. McCouch. 2002. Mapping and genome organization of microsatellites sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics 100(5): 697-712.
25. Travis, A., G. Norton, S. Datta, R. Sarma, T. Dasgupta, F. Savio, M. Macaulay, P. Hedley, K. McNally, M. Sumon, M. Islam and A. Price. 2015. Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal. Rice 8(1): 35.
26. Wei, X., X. Yuan, H. Yu, Y. Wang, Q. Xu and S. Tang. 2009. Temporal changes in SSR allelic diversity of major rice cultivars in China. Journal of Genetics & Genomics 36(6): 363-370.
27. Xu, Q., X. Yuan, Li, X., Wang, S., Feng, Y., Yu, H., Wang, Y., Y. Yang and X. Wei. 2016. The genetic diversity and structure of Indica rice in China as detected by single nucleotide polymorphism analysis. BMC Genetics 17: 53.
28. Yanchuk, A.D. 2001. A quantitative framework for breeding and conservation of forest tree genetic resources in British Columbia. Canadian Journal of Forest Research 31(4): 566-576.
29. Yu, J., S. Hu, J. Wang, G. Wong, S. Li, B. Liu, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296 (5565): 79-92.

Published

2020-03-28

How to Cite

Pérez-Almeida, I., Celi-Herán, R., Sánchez-Mora, F., Paz-Carrasco, L., & Ramos-Viteri, B. (2020). Assessment of molecular genetic diversity of ecuadorian rice cultivars using simple sequence repeat markers. Bioagro, 31(1), 3-12. Retrieved from https://revistas.uclave.org/index.php/bioagro/article/view/2607

Issue

Vol. 31 No. 1 (2019): Bioagro 31)(1)

Section

Artículos

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