Morpho-molecular diversity study of rice cultivars in Bangladesh

Akter M.B., Mosab-Bin A., Kamruzzaman M., Reflinur R., Nahar N., Rana M.S., Hoque M.I., Islam M.S. (2022): Morpho-molecular diversity study of rice cultivars in Bangladesh. Czech J. Genet. Plant Breed., 58: 64−72.

download PDF

Rice is one of the frontline cereals in the world and the major cultivated crop in Bangladesh. A total of eleven simple sequence repeats (SSRs) and thirteen sequence-tagged site (STS) markers were used to characterize twenty-four rice cultivars in Bangladesh. Twenty-four markers generated 60 alleles with 2.5 alleles per locus. The average polymorphism information content (PIC) value was 0.40, while the mean value of heterozygosity, gene diversity, and major allele frequency were recorded as 0.10, 0.48 and 0.62, respectively. However, the SSR markers showed more specificity and a higher discrimination power than the STS markers. The cluster analysis displayed four major clusters with a genetic similarity coefficient value of 0.73. The morphological analyses of the grain identified that Binadhan-20 and BRRI dhan34 had the longest and the shortest seed size, respectively, with a variable correlation between the seed length, width and length/width ratio. The phenol reaction test distinguished seven cultivars as japonica and seventeen cultivars as indica or an intermediate type. All these results regarding the phenotypic data and marker information will be useful for parental selection in modern rice breeding programmes.

Akter M.B., Kim B., Lee Y., Koh E., Koh H-J. (2014): Fine mapping and candidate gene analysis of a new mutant gene for panicle apical abortion in rice. Euphytica, 197: 387–398.
Anupam A., Imam J., Quatadah S.M., Siddaiah A., Das S.P., Variar M., Mandal N.P. (2017): Genetic diversity analysis of rice germplasm in Tripura State of Northeast India using drought and blast linked markers. Rice Science, 24: 10–20.
Azeez M.A., Shafi M. (1966): Quality in Rice. Department of Agriculture, West Pakistan Technology Bulletin No.13.
Babu B.K., Meena V., Agarwal V., Agrawal P.K. (2014): Population structure and genetic diversity analysis of Indian and exotic rice (Oryza sativa L.) accessions using SSR markers. Molecular Biology Reports, 41: 4329–4339.
Botstein D., White R.L., Skolnick M., Davis R.W. (1980): Construction of a genetic linkage map in man using restriction fragment length polymorphisms. The American Journal of Human Genetics, 32: 314–331.
Caicedo A.L., Williamson S.H., Hernandez R.D., Boyko A., Fledel-Alon A., York T.L., Polato N.R., Olsen K.M., Niel-sen R., McCouch S.R. (2007): Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics, 3: e163.
Chin J.H., Kim J.H., Jiang W., Chu S.H., Woo M.O., Han L., Brar D., Koh H.J. (2007): Identification of subspecies-specific STS markers and their association with segregation distortion in rice (Oryza sativa L.). Journal of Crop Science and Biotechnology, 10: 175–184.
FAO (2019): FAOSTAT. Food and Agriculture Data. Available at
Felsenstein J. (1985): Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39: 783–791.
Fitzgerald M.A., Mccouch S.R., Hall R.D. (2009): Not just a grain of rice: The quest for quality. Trends in Plant Science, 14: 133–139.
Geist H. (2006): Our Earth’s Changing Land. Westport, Greenwood Press.
Gross B.L., Skare K.J., Olsen K.M. (2009): Novel Phr1 mutations and the evolution of phenol reaction variation in US weedy rice (Oryza sativa). New Phytologist, 184: 842–850.
IRRI (1998): Standard Evaluation System for Rice. Manila, International Rice Research Institute.
IRRI (2019): International Rice Genebank. Available at
Islam A., Touhidur R.A., Monjur H., Imtiaz U., Shahabuddin A. (2018): Genetic diversity analysis of some Bangladeshi aromatic rice (Oryza sativa L.) using simple sequence repeat markers (SSRM). Archives of Agriculture and Environmental Science, 3: 297–303.
Islam M., Begum H., Ali M., Kamruzzaman M., Hoque S., Hoque M. (2017): DNA fingerprinting and genetic diversities in some Bangladeshi aus rice (Oryza sativa L.) genotypes. SAARC Journal of Agriculture, 15: 123–137.
Li S., Zhang R., Chen J., Zou J., Liu T., Zhou G. (2017): Genetic analysis and fine mapping of the RK4 gene for round kernel in rice (Oryza sativa L.). Czech Journal of Genetics and Plant Breeding, 53: 153–158.
Lin H.Y., Wu Y.P., Hour A.L., Ho S.W., Wei F.J., Hsing Y.I.C., Lin Y.R. (2012): Genetic diversity of rice germplasm used in Taiwan breeding programs. Botanical Studies, 53: 363–376.
Liu K., Muse S.V. (2005): PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics, 21: 2128–2129.
Maji A.T., Shaibu A.A. (2012): Application of principal component analysis for rice germplasm characterization and evaluation. Journal of Plant Breeding and Crop Science, 4: 87–93.
McCouch S.R., Temnykh S., Lukashova A., Coburn J., Declerck G., Cartinhour S., Harrington S., Thomson M., Septiningsi E., Semon M., Moncada P., Jiming L. (2001): Microsatellite markers in rice: Abundance, diversity and applications. In: Rice Genetics IV. Manila, IRRI: 117–135.
McCouch S.R., Teytelman L., Xu Y., Lobos K.B., Clare K., Walton M., Fu B., Maghirang R., Li Z., Xing Y., Zhang Q., Kono I., Yano M., Fjellstrom R., DeClerck G., Schneider D., Cartinhour S., Ware D., Stein L. (2002): Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Research, 9: 199–207.
Oka H-I. (1958): Intervarietal variation and classification of cultivated rice. Indian Journal of Genetics and Plant Breeding, 18: 79–89.
Oka H.I. (1962): Rice varieties intermediate between wild and cultivated forms and the origin of the Japonica type. Botanical Bulletin of Academia Sinica, 3: 109–131.
Panaud O., Chen X., McCouch S.R. (1996): Development of microsatellite markers and characterization of simple sequence length polymorphism (SSR) in rice (Oryza sativa L.). Molecular and General Genetics, 252: 597–607.
Pathaichindachote W., Panyawut N., Sikaewtung K., Pata-rapuwadol S., Muangprom A. (2019): Genetic diversity and allelic frequency of selected Thai and exotic rice germplasm using SSR markers. Rice Science, 26: 393–403.
Rahman S.N., Islam M.S., Alam M.S., Nasiruddin K.M. (2007): Genetic polymorphism in rice (Oryza sativa) through RAPD analysis. Indian Journal of Biotechnology, 6: 230–233.
Reflinur, Kim B., Lestari P., Akter M.B., Koh H.-J. (2018): Identification of QTLs associated with indica-japonica differentiation-related traits in rice (Oryza sativa L.). Plant Breeding and Biotechnology, 6: 193–205.
Rita B., Sarawgi A.K. (2008): Agromorphological and quality characterization of badshah bhog group from aromatic rice germplasm of Chhattisgarh. Bangladesh Journal of Agriculture Research, 33: 479–492.
Rohlf F. J. (2002): Geometric morphometrics and phylogeny. In: MacLeod N., Forey P.L. (eds.): Morphology, Shape and Phylogeny, London, New York, Taylor & Francis: 175–193.
Sasaki T., Burr B. (2000): International rice genome sequencing project: the effort to completely sequence the rice genome. Current Opinion in Plant Biology, 3: 138–142.
Srivastava A.K., Jaiswal H.K. (2013): Grain characteristics and cooking quality of indigenous aromatic and non-aromatic genotypes of rice (Oryza sativa L.). International Journal of Scientific Research and Reviews, 2: 36–41.
Tiwari J.K., Rastogi N., Chandrakar P., Sarawgi A., Verul-kar S. (2013): Identification of rice varieties through chemical tests. Seed Research, 41: 83–90.
Wang X., Li R. (1997): Determination and classification of subspecies of Asian rice and their inter-subspecies hybrids. Chinese Science Bulletin, 42: 2596–2603.
Yadav S., Singh A., Singh M.R., Goel N., Vinod K.K., Mohapatra T., Singh A.K. (2013): Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): Use of random versus trait-linked microsatellite markers. Journal of Genetics, 92: 545–557.
Yang Y., Zhu K., Xia H., Chen L., Chen K. (2014): Comparative proteomic analysis of indica and japonica rice varieties. Genetics and Molecular Biology, 37: 652–661.
Yoon D.B., Kang K.H., Kim H.J., Ju H.G., Kwon S.J., Suh J.P., Ahn S.N. (2006): Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo. Theoretical and Applied Genetics, 112: 1052–1062.
Zhang J., Zhang D., Fan Y., Li C., Xu P., Li W., Sun Q., Huang X., Zhang C., Wu L. (2021): The identification of grain size genes by RapMap reveals directional selection during rice domestication. Nature Communications, 12: 1–18.
download PDF

© 2022 Czech Academy of Agricultural Sciences | Prohlášení o přístupnosti