Allelic diversity and association analysis for grain quality traits in exotic rice genotypes

Document Type: Research Paper


Gonbad Kavous University, Iran


The present research aims to study the association and allelic diversity of linked microsatellite markers to grain quality QTLs of 84 exotic rice genotypes. To this end, 9 microsatellite markers (RM540, RM539, RM587, RM527, RM216, RM467, RM3188, RM246, RM5461) were used in which a total of 61 alleles were identified with a mean of 6 alleles per locus. The polymorphism information content (PIC) varied from 0.542 (RM540) to 0.812 (RM3188) for SSR markers. Cluster analysis was performed using UPGMA method and genotypes were divided into five groups. Furthermore, based on regression analysis, for rice grain quality properties in flooding conditions as long as drought stresses, 10 alleles were identified. Of these, four alleles with gelatinization temperature, an allele with protein content under flooding conditions, and three alleles with protein content and three alleles with gelatinization temperature were related under drought stress. It should be noted that the RM216-C and RM5461-D alleles were commonly identified in several traits. The presence of common markers for traits is probably due to the consistency of chromosomal locus controlling these traits or pleiotropy. The results of this study may imply that the important identified alleles for example RM216-A for gelatinization temperature (R2=30.1 %) can be used in rice quality improvement programs.


[1]     Allahgholipour, M., Mohammad-Salehi, M. and Ebadi, A.A. 2005. Genetic variation and classification of cultivated rice. J. Agric. Sci, 35(4): 973-981.

[2]     Bagheri, A., Darbandi, A. and Malboobi, M, A. 2002. Practical applications of Plant Molecular Biology. Ferdowsi Mashhad University Press, Mashhad.

[3]     Bartha, R. and Pramer, D. 1965. Features of a flask and methods of measuring the persistence and biological effects of pesticides in soil. Soil. Sci, 100: 68-70.

[4]     Bassam, B.J., Caetano-Anolles, G. and Gresshoff, P. M. 1991. Fast and sensitive silver standing of DNA in polyacrilamid gels. Analytical Biochem, 196: 80-83

[5]     Chamani Mohasses, F., Sami’zadeh, H., Rabi’ei, B. and Sohani, M. 2012. Evaluating the genetic diversity of 9 rice lines using the ISSR molecular markers. 12th Iranian Congress, 6: 1-12.

[6]     Deshmukh, V.V. 2012. Genome-wide association mapping of drought resistance traits in rice (Oryza sativa L.). MSc thesis, Tamil Nadu Agricultural University, Tamil, The India.

[7]     He, P., Li, S.G., Qian, Q., Ma, Y.Q. and Li, J.Z. 1999. Genetic analysis of rice grain quality. Theor. Apel. Genet, 98: 502-508.

[8]     Juliano, B.O. 1979. Amylose analysis in rice-A review. In: Proc. Workshop on Chemical Aspects of Rice Grain Quality. IRRI: Los Bafnos, Laguna, Philippines.

[9]     Lau WCP, Rafii MY, Ismail MR, Puteh A, Latif MA and Ramli A. 2015. Review of functional markers for improving cooking, eating, and the nutritional qualities of rice. Front. Plant Sci. 6:832-842.

[10]  Liu K., Muse SV. 2005. Power Marker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 21(9):2128-9

[11]  Little, R.R., Hilder, G.B. and Dawson, E.H. 1958. Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem, 35: 111-126.

[12]  Momeni, A. S. 1995. Investigating the combining ability of gene type of activity and study of correlation for important agronomic traits in different rice varieties. Master's Thesis, University of Tehran, Tehran, Iran.

[13]  Mondini, L., Noorani, A. and Mario, A. 2009. Assessing plant genetic diversity by molecular tools. Divers, 1: 19-35.

[14]  Musyoki, M.A., Kioko, W.F., Mathew, N.P., Daniel, A., Muriira, K.G., Wavinya, N.D., Felix, M., Chemutai, L.R., Mwenda, N.S., Kiambi, M.J. and Ngithi, N. L. 2015. Genetic diversity studies on selected rice (Oryza sativa L.) genotypes basedon amylose content and gelatinization temperature. Advances in Crop Sci. and Technol, 3(5): 1-6.

[15]  Nevo, E. 1978. Genetic variation in natural populations. Patterns and theory. Theor. Popul. Biol, 13: 121-127.

[16]  Nikzadeh Talebi, S., Alaami, A., Esfahani, M. and Ebadi, A.S. 2016. Evaluation of allelic abundance and communication analysis of microsatellite markers with some traits related to pre-harvest germination in rice cultivars. J. Agric. Sci. Iran, 18: 49-62.

[17]  Palanga, K.K., Traore, K., Bimpong, K., Jamshed, M. and Mkulama, A.P. 2016. Genetic diversity studies on selected rice varieties grown in Africa based on aroma, cooking and eating quality. Afr. J. Biotechnology, 15(23): 1136-1146.

[18]  Saghai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A. and Allard, R.W. 1984. Ribosomal DNA sepacer-length polymorphism in barley: Mendelian inheritance, chromosomal locus, and population dynamics. In: Proc. Natl. Acad. Sci. USA, 91: 4566-4570.

[19]  Seck, P. A., Diagne, A., Mohanty, S., & Wopereis, M. C. (2012). Crops that feed the world 7: Rice. Food security, 4(1), 7-24.

[20]  Verma, H., Pathak, K., Rathi, S. and Sarma, S.N. 2015. Association analysis for grain quality traits in rice. Indian J. Genet, 75(4): 506-509.

[21]  Victoria, C.L., Darshan, S.D., Toshinori, A. and Edilberto, D.R. 2007. Assessment of genetic diversity of Philippine rice cultivar carrying good quality traits using SSR markers. Breed. Sci, 57: 253-270.

[22]  Zhang, Z., Li, M., Fang, Y., Liu, F. and Lu, Y. 2012. Diversification of the waxy gene is closely related to variations in rice eating and cooking quality. Plant Mol. Biol. Rep, 30: 462-469.