Puji Lestari, Reflinur Reflinur, Dody Dwi Handoko, Mastur Mastur


PCR-based markers and evaluation of physicochemical properties should be addressed for the improvement of rice varieties with good eating dan eating quality (EQ). This study aimed to examine the genetic diversity of rice varieties based on DNA markers related to physicochemical properties determining EQ. A total of 46 rice varieties consisting of 22 japonica varieties and 24 indica varieties were examined using 43 PCR-based markers. The results showed that polymorphic information content (PIC) ranged from 0.04 to 0.38, in support of genetic diversity indices which ranged from 0.04 to 0.50 across total markers. Pairwise genetic similarity matrix ranged from 0.40 to 0.98 with the closest genetic distance was observed between two japonica varieties (Dongjin and Hwaseong) and the most distant one was between japonica and indica (Onnuri/Manmi with Cigeulis/Fatmawati). The unweighted neighbor-joining tree clustered the rice varieties into two major clades, indica and japonica, and subsequent subclades were differentiating according to the individual genetic background. The genetic diversity of rice from different subspecies and DNA markers for EQ can effectively be utilized for basic information and marker-assisted selection (MAS) for the development of improved varieties with good EQ in rice breeding program.


eating quality; genetic diversity; rice; japonica; indica; DNA marker

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Avaro MRA, Tong L, Yoshida T. 2009. A simple and low-cost method to classify amylose content of rice using a standard color chart. Plat Production Science. 12:97–99.

Bao JS, Corke H, Sun M. 2006a. Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.). Theoretical Applied Genetics. 113: 1185–1196.

Bao JS, Corke H, Sun M. 2006b. Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.). Theoretical Applied Genetics. 113: 1171–1183.

Bradbury PJ, Zhang Z, Kroon DF, Casstevens TN, Ramdoss Y, Buckler ES. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics. 23:2633–2635.

Cheng CY, Motohashi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, Ohtsubo E. 2003. Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Molecular Biology and Evolution. 20: 67–75.

Doi K, Sobrizal K, Ikeda K, Sanchez PL, Kurakazu TA. 2002. Developing and evaluating rice chromosome segment substitution lines, pp. 275–287 In IRRI Conference September, 16–19, 2002, International Rice Research Institute, Beijing, China.

Felsenstein J. 1985. Confident limit on phylogenies: An approach using the bootstrap. Evolution.39: 783–791.

Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch M. 2005. Genetic structure and diversity in Oryza sativa L. Genetics. 169: 1631–1638.

He Y, Han Y, Jiang L, Xu C, Lu J, Xu M. 2006. Functional analysis of starch-synthesis genes in determining rice eating and cooking qualities. Molecular Breeding.18:277–290.

Hori K, Suzuki K, Iijima K, Ebana K. 2016. Variation in cooking and eating quality traits in Japanese rice germplasm accessions. Breeding Science. 66(2): 309–318.

Johns MA and Mao L. 2007. Differentiation of two rice subspecies indica and japonica: a Gene Ontology perspective. Functional and Integrative. Genomics. 7(2): 135–151.

Kharabian-Masouleh A, Waters DL, Reinke RF,Henry RJ. 2011. Discovery of polymorphisms in starch-related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing. Plant Biotechnology Journal. 9:1074–1085.

Kharabian-Masouleh A, Waters DLE, Reinke RF, Ward R, Henry RJ. 2012. SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Scientific Report- Uk. 2:557–565.

Kobayashi A, Tomita K, Yu F, Takeuchi Y, Yano M. 2008. Verification of quantitative trait locus for stickiness of cooked rice and amylose content by developing near-isogenic lines. Breeding Science. 58: 235 –242.

Kohyama K, Sodhi NS, Suzuki K, Sasaki T. 2016. Texture evaluation of cooked rice prepared from Japanese cultivars using two-bite instrumental test and electromyography. Journal of Texture Studies. 47: 188–198.

Kubo M, Purevdorj M. 2004.The future of rice production and consumption. Journal of Food Distribution Research. 35: 128-142.

Lestari P, Ham TH, Lee HH, Woo MO, Jiang WJ, Chu SH, Kwon SK, Ma KH, Lee JH, Cho YC, Koh HJ. 2009. PCR marker-based evaluation of eating quality of cooked rice (Oryza sativa L,). Journal of Agriculture and Food Chemistry. 57 (7): 2754–2762.

Lestari P, Koh HJ. 2013. Evaluasi kandungan protein dan sifat pasta beras japonica dengan marka DNA. Berita Biologi. 12(2): 141–152.

Lestari P, Reflinur, Koh HJ. 2014. Prediction of physicochemical proeprties of Indonesian indica rice using molecular markers. HAYATI Journal of Biosciences. 21(2): 76–86.

Lestari P, Jiang W, Chu SH, Reflinur, Sutrisno, Kusbiantoro B, Kim B, Piao R, Cho YC, Koh HJ. 2015. DNA markers for eating quality of indica rice in Indonesia. Plant Breeding. 134: 40–48.

Liu J. 2001. Power Marker V3.25 Manual, http://www. powermarker. net.

Liu K, Muse SV. 2005. PowerMarker: integrated analysis of environment for genetic diversity in core collection accessions of wild barley, Hordeum vulgare ssp, spontaneum. Hereditas.136: 67–73.

Luo J, Jobling SA, Millar A, Morell MK, Li Z. 2015. Allelic affect on starch structure and properties of six starch biosynthesis genes in a rice recombinant inbred line population. Rice. 8: 15.

Matsuo T, Futsuhara Y, Kikuchi F, Yamaguchi H. 1997. Science of the Rice Plant, Food and Agriculture. Policy Research Center, Tokyo.

Murray MG, Thompson WF. 1980. Rapid isolation of high molecular weight DNA. Nucleic Acids Research. 8: 4321–4325.

Ohstubo K, Nakamura S, Imamura T. 2002. Development of the primer sets for identification of a rice variety, Koshihikari by PCR. Nippon Nogeikagaku Kaishi. 76: 388–397.

Ohstubo K, Nakamura S, Okadome H. 2003. Investigation on estimation of rice palatability by DNA analysis (studies on estimation of rice palatability by DNA analysis part I). Nippon Nogeikagaku Kaishi. 50:122–132.

Ohtsubo K, Nakamura S. 2007. Cultivar identification of rice (Oryza sativa L,) by PCR application to processed rice product. Journal of Agricultural Food and Chemistry. 55(4): 1501-1509.

Palanga KK, Traore K, Bimpong K, Jamshed M, Kulama MAP. 2016. Genetic diversity studies on selected rice varieties grown in Africa based on aroma, cooking and eating quality. African Journal of Biotechonology. 15:1136–1146.

Suprihatno B, Daradjat AA, Satoto. 2010. Deskripsi varietas padi. Balai Besar Penelitian Tanaman Padi, Sukamandi, Subang.

Tan Y, Sun M, Corke H. 2002. Physicochemical properties of an elite rice hybrid. Journal of the Science of Food and Agriculture. 82:1628–1636.

Tian ZX, Yan CJ, Qian QA, Yan S, Xie HL, Wang F, Xu JF, Liu GF, Wang YH, Liu QQ, Tang SZ, Li YJ, Gu MH. 2010. Development of gene-tagged molecular markers for starch synthesis-related genes in rice. Chinese Science Bulletin. 55:3768–3777.

Yan C, Tian S, Zhang Z, Han Y, Chen F, Li X, Gu M. 2007. The source of genes related to rice grain starch synthesis among cultivated varieties and its contribution to quality. Agricultural Sciences in China. 6:129–136.

Zeng D, Yan MX, Wang YH, Liu XF, Qian Q, Li JY. 2007. Du1, encoding a novel Prp 1 protein regulates starch biosynthesis through affecting the specificity of Wxb pre-mRNAs in rice (Oryza sativa L.). Plant Molecular Biology. 65: 501–509.

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