Study of genetic variation of some Iranian rice (Oryza sativa) genotypes based on morphological traits, physicochemical properties and molecular markers

Document Type: Research Paper

Authors

1 Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran, P. O. Box 578

2 Department of Plant breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran, P. O. Box 578

Abstract

Assessment of genetic diversity and individual relationships in rice (Oryza sativa) germplasm collections seems to be necessary for future rice breeding program. In order to understand genetic relationships of 30 rice genotypes, nine morphological traits, seven physicochemical properties and twelve RAPD primers were used for study of 30 rice genotypes. Among morphological traits, number of unfilled grain, number of tiller, number of filled grain and plant height had the highest CV value that indicated the high range of genetic diversity for studied genotypes. Pairwise correlation of morphological traits and physicochemical properties showed plant height had a strong positive correlation with panicle length (r = 0.721, P< 0.0001). Also, ratio of white rice to paddy rice and milling ratio had a negative correlation with plant height and 1000-grain weight, respectively. Cluster analysis of physicochemical properties and morphological traits grouped all genotypes into three main clusters. A total of 105 obtained RAPD bands, a number of 35 bands were polymorphs which range 7 to 19 bands per primer. OPB-14 and OPH-12 primers shown that lowest and the highest number of bands per primers, respectively. Cluster analysis of molecular data based on UPGMA algorithm and Jaccard's similarity coefficient grouped 30 rice genotypes into three clusters. The findings of this study might provide valuable information about local rice cultivar relationships in terms of their genetic distance, and can be useful in rice breeding program.

Keywords

Main Subjects


[1]   Alizadeh, M., Nematzadeh, G., Ebrahimi, M., and Hashemi, S. 2013. Fingerprinting of Some Rice (Oryza sativa L.) Germplasm via AFLP Markers. Crop Biotech., 3(4): 53-60.
[2]   Allhgholipour, M., Farshdfar, E., and Rabiei, B. 2014. Molecular characterization and genetic diversity analysis of different rice cultivars by microsatellite markers. Genetika, 46(1): 187-198.
[3]   Babaei, A., Nematzadeh, G.-A., and Hashemi, H. 2011. An evaluation of genetic differentiation in rice mutants using semi-random markers and morphological characteristics. Australian Journal of Crop Science, 5(13): 1715.
[4]   Babaei, A., Nematzadeh, G.-A., and Hashemi, H. 2011. Molecular RAPD markers analysis of Sange-tarom and Taromhashemi cultivars (Oryza sativa L.) in M2 population. Annals Biol. Res, 2(4): 24-30.
[5]   Babaei, A., Nematzadeh, G.A., Avagyan, V., and Hashemi-Petrodi, S.H. 2010. Radio sensitivity studies of morpho-physiological characteristics in some Iranian rice varieties (Oryza sativa L.) in M1 generation. African Journal of Agricultural Research, 5(16): 2124-2130.
[6]   Bagheri, N., Babaeian, J.N., and HASAN, N.E. 2008. Genetic diversity of Iranian rice germplasm based on morphological traits.
[7]   Bagheri, N., Babaeian, N., and nataj, H. 2008. Genetic diversity of Iranian rice germplasm based on morphological traits. Iranian journal of field crops research, 6(2): 235-243.
[8]   Dellaporta, S.L., Wood, J., and Hicks, J.B. 1983. A plant DNA minipreparation: version II. Plant molecular biology reporter, 1(4): 19-21.
[9]   Ghareyazie, B., Huang, N., Second, G., Bennett, J., and Khush, G. 1995. Classification of rice germplasm. I. Analysis using ALP and PCR-based RFLP. TAG Theoretical and Applied Genetics, 91(2): 218-227.
[10] Haque, M., Islam, S., Banik, M., Khalequzzaman, M., Siddiquee, M., and Mian, M. 2013. Physicochemical and cooking properties of local aromatic rice gerplasm in Bangeladesh. Eco-friendly Agril. J., 6(11): 243-248.
[11] Hashemi-Petroudi, S.H., Maibody, S.A.M.M., Nematzadeh, G.A., and Arzani, A. 2010. Semi-random PCR markers for DNA fingerprinting of rice hybrids and theirs corresponding parents. African Journal of Biotechnology, 9(7): 979-985.
[12] Hashemi, S.H., Mirmohammadi-Maibody, S.A.M., Nematzadeh, G.A., and Arzani, A. 2009. Identification of rice hybrids using microsatellite and RAPD markers. African Journal of Biotechnology, 8(10).
[13] Huang, B.E., George, A.W., Forrest, K.L., Kilian, A., Hayden, M.J., Morell, M.K., and Cavanagh, C.R. 2012. A multiparent advanced generation inter‐cross population for genetic analysis in wheat. Plant biotechnology journal, 10(7): 826-839.
[14] Huang, Y.-F., Poland, J.A., Wight, C.P., Jackson, E.W., and Tinker, N.A. 2014. Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat. PloS one, 9(7): e102448.
[15] Jahani, M., Nematzadeh, G., Dolatabadi, B., Hashemi, S.H., and Mohammadi-Nejad, G. 2014. Identification and validation of functional markers in a global rice collection by association mapping. Genome, 57(6): 355-362.
[16] Jahani, M., Nematzadeh, G., Mohammadi-Nejad, G., Hashemi, S., Dolatabadi, B., and Hajipoor, A. 2013. Grain size diversity in rice (Oryza sativa L.) genotypes. International Journal of Agronomy and Plant Production, 4(8): 2024-2029.
[17] Juliano, B.O. and Villareal, C. 1993. Grain quality evaluation of world rices. Int. Rice Res. Inst.
[18] Kishine, M., Suzuki, K., Nakamura, S., and Ohtsubo, K.i. 2008. Grain qualities and their genetic derivation of 7 new rice for Africa (NERICA) varieties. Journal of agricultural and food chemistry, 56(12): 4605-4610.
[19] Lal, R. 2004. Soil carbon sequestration impacts on global climate change and food security. science, 304(5677): 1623-1627.
[20] Little, R.R. 1958. Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem., 35: 111-126.
[21] Mahjoob, B., Zarini, H., Hashemi, S., and Shamasbi, F. 2016. Comparison of ISSR, IRAP and REMAP markers for assessing genetic diversity in different species of Brassica sp. Russian Journal of Genetics, 52(12): 1272-1281.
[22] Majzoobi, M. and Farahnaky, A. 2010. The Physicochemical Properties of Starch Component of six Iranian Rice Cultivars. Iran Agricultural Research, 27(1.2): 113-122.
[23] Melchinger, A.E. and Gumber, R.K. 1998. Overview of heterosis and heterotic groups in agronomic crops. Concepts and breeding of heterosis in crop plants, (conceptsandbree): 29-44.
[24] Mohammadi, S. and Prasanna, B. 2003. Analysis of genetic diversity in crop plants—salient statistical tools and considerations. Crop science, 43(4): 1235-1248.
[25] Mullet, J.E. 2017. High-Biomass C 4 Grasses− Filling the Yield Gap. Plant Science.
[26] Nematzadeh, G. and Khush, G. 1993. Classification of rice germplasm from Iran through isozyme analysis. Intl. Rice Res. Newslett, 10.
[27] Neoh, W.T. 2011. Physicochemical characteristics of different rice varieties found in Sabah.
[28] Odenigbo, A.M., Ngadi, M., Ejebe, C., Woin, N., and Ndindeng, S.A. 2014. Physicochemical, cooking characteristics and textural properties of TOX 3145 milled rice. Journal of Food Research, 3(2): 82.
[29] Parsaeian, M., Mirlohi, A., and Saeidi, G. 2011. Study of genetic variation in sesame (Sesamum indicum L.) using agro-morphological traits and ISSR markers. Russian journal of genetics, 47(3): 314.
[30] Sajib, A.M., Hossain, M., Mosnaz, A., Hossain, H., Islam, M., Ali, M., and Prodhan, S.H. 2012. SSR marker-based molecular characterization and genetic diversity analysis of aromatic landreces of rice (Oryza sativa L.). Journal of BioScience & Biotechnology, 1(2).
[31] SES, I. 2002. Standard Evaluation System. International Rice Research Institute, Manila, Philippines: 11-30.
[32] Sorkheh, K., Masaeli, M., Chaleshtori, M.H., Adugna, A., and Ercisli, S. 2016. AFLP-based analysis of genetic diversity, population structure, and relationships with agronomic traits in rice germplasm from North region of Iran and world core germplasm set. Biochemical genetics, 54(2): 177-193.
[33] Stefanović, V.Ž., Filipović, N.K., and Jovanović, B.M. 2008. Undesirable metals content in wheat of different wheat varieties. Acta Periodica Technologica, (39): 69-76.
[34] Tabkhkar, N., Rabiei, B., and Sabouri, A. 2012. Genetic diversity of rice cultivars by microsatellite markers tightly linked to cooking and eating quality. Australian Journal of Crop Science, 6(6): 980.
[35] Vaesi, B., Rahamini Moghadam, N., Nematzadeh, G., Kazemitabar, S., and Gharahyazi, B. 2005. Determination of genetic diversity and classification of Iran rice germplasm with RAPD markers.
[36] Vazirzanjani, M., Sarhadi, W.A., NWE JJ, A.M., Siranet, R., and Trung, N. 2011. Characterization of Aromatic Rice Cultivars From Iran and Surrounding Regions for Aroma and Agronomic Traits. SABRAO J Breed Genet, 43: 15-26.
[37] Zaynali Nejad, K., Mirlohi, F., Nematzadeh, G., and Rezai, A. 2003. Genetic diversity in some of Iranian Rice (Oriza sativa L.) germplasm base on morphological traits. Journal of Science and Technology of Agriculture and Natural Resources, 7(4): 199-213.