Keywords: diversity, glutinous, molecular markers, pigmented rice, breeding


The challenge for making food for less is to make it healthier and with value-added traits i.e. glutinous and pigmented.  It is important in any crop breeding to increase heterosis by combining distant genotypes and this could be achieved through the use of molecular markers.  This study aimed to assess the genetic distance of 83 entries with 71 elite lines consisted of pigmented, glutinous and pigmented- glutinous rice, 9 parent lines and one check variety, NSIC Rc19. Preliminary survey of 300 genome-wide microsatellite markers led to 17 highly polymorphic markers. Overall diversity among the entries is 48% which is expected among sister lines. A 100% similarity was observed for two pairs of elite lines. Dendrogram generated based on UPGMA formed two major clusters with one elite line Line21 and Traditional4 and Traditional7 in one cluster while the rest of the entries formed the other cluster. Without markers, the breeding of special purpose rice including combination of pigmented and glutinous rice varieties would take longer but with highly polymorphic microsatellite markers could accelerate the development of new special purpose rice varieties.


Download data is not yet available.


Ahmad, F., Hanafi, MM., Hakim MA., Rafii MY., Arolu, IW., Abdullah, SNA. (2015). “Genetic divergence and heritability of 42 colored upland rice genotypes (Oryza sativa) as revealed by microsattelites marker and agro-morphological traits”. PLos ONE, vol. 10, no. 9, Article ID e0138246, 2015.

Anandan A, Anumalla M, Pradhan SK, Ali J. (2016). Population Structure, Diversity and Trait Association Analysis in Rice (Oryza sativa L.) Germplasm for Early Seedling Vigor (ESV) Using Trait Linked SSR Markers. PLoS ONE 11(3): e0152406. doi: 10.1371/journal.pone.0152406

Ashraf H, Husaini AM, Bhat MA, Parray GA, Khan S, Ganai N. (2016). SSR based genetic diversity of pigmented and aromatic rice (Oryza sativa L.) genotypes of the western Himalayan region of India. Physiol Mol Biol Plants (October–December 2016) 22(4):547–555 DOI 10.1007/s12298-016-0377-8

Brondani C, Borba TCO, Rangel PHN and Brondani RPV. (2006). “Determination of Genetic Variability of Traditional Varieties of Brazilian Rice Using Microsatellite Markers,” Genetics and Molecular Biology, Vol. 29, No. 4, 2006, pp. 676-684.

Das B, Sengupta S, Parida SK, Roy B, Ghosh M, Prasad M. (2013). Genetic Diversity and Population structure of rice landrances from Eastern and North Eastern States of India. BMC Genet. 14(1):71.

Giarocco LE, Marassi MA, Salerno GL. (2007). Assessment the genetic diversity in Argentina rice cultivars with SSR markers. Crop Sci 47:853–858

Hossain1 MZ, Rasul MG, Ali MS, Iftekharuddaula KM and Mian MAK. (2007). Molecular Characterization and Genetic Diversity in Fine Grain and Aromatic Landraces of Rice (Oryza Sativa L.) Using Microsatellite Markers. Bangladesh J. Genet Pl. Breed., 20(2): 01-10

Hue HT, Nghia LT, Minh HT, Anh LH, Trang LTT, Khanh TD. (2018). Evaluation of Genetic Diversity of Local-Colored Rice Landraces Using SSR Markers. International Letters of Natural Sciences. ISSN: 2300-9675, Vol. 67, pp 24-34.

Islam MZ, Khalequzzaman M, Prince MFRK, Siddique MA, Rashid ESMH, Ahmed MSU, et al. (2018) Diversity and population structure of red rice germplasm in Bangladesh. PLoS ONE 13 (5): e0196096.

Ji HC, Kim YI, Lee HB, Cho JW, Seo S, Yamakawa T. (2007). Genetic Diversity of Colored Rice Lines Based on Botanical Characteristics and Simple Sequence Repeat (SSR) Markers. J. Fac. Agr., Kyushu Univ., 52 (2), 287–293 (2007).

Jin L, Lu Y, Xiao P, Sun M, Corke H, Bao J. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theor Appl Genet. 2010;121(3):475–87. doi: 10.1007/s00122-010-1324-7.

Joshi RK, Behrea L (2006). Identification and differentiation of indigenous non-Basmati aromatic rice genotypes of India using microsatellite markers. African journal of Biotechnology 6, 348-354.

Kibria K, Nur F, Begum SN, Islam MM, Paul SK, Rahman KS, Azam SMM. (2009). Molecular Marker Based Genetic Diversity Analysis in Aromatic Ricgenotypes using SSR and RAPD Markers. Int. J. Sustain. Crop Prod. 4(1):23–34.

Lapitan VC, Brar DS, Abe T, Redoña ED. (2007). Assessment of Genetic Diversity of Philippine Rice Cultivars Carrying Good Quality Traits using SSR Markers. Breeding Science 57:263-270.

Nachimuthu VV, Muthurajan R, Duraialaguraja S, Sivakami R, Pandian BA, Ponniah G, Karthika G, Swaminathan M, Suji KK, and Sabariappan R. (2015). Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza sativa. Rice (N Y). 2015; 8: 30. doi: 10.1186/s12284-015-0062-5

Pathak K, Rathi S, Sarma RN, Baishya S. (2016). Assessment of Genetic Diversity of Indigenous Glutinous Pigmented Rice Genotypes of Assam using SSR Marker. Indian J Agric Biochem 29 (1), 54-61.

Patel S, Ravikiran R, Chakraborty S, Macwana S, Sasidharan N, Trivedi R and Aher B. (2014). Genetic diversity analysis of colored and white rice genotypes using Microsatellite (SSR) and Insertion-Deletion (INDEL) markers. Emir. J. Food Agric. 2014. 26 (6): 497-507 doi: 10.9755/ejfa. v26i6.15722

Phonsakhan W, Kong-Ngern K. (2015). A comparative proteomic study of white and black glutinous rice leaves. Science Direct Electric Journal of Biotechnology. 18:29-30.

Rani MG, Adilakshmi D. Genetic analysis of blast resistance in rice with simple sequence repeats (SSR) J Crop Improv. 2011; 25:232–238. doi: 10.1080/15427528.2011.555834.

Rajendrakumar P, Biswal AK, Sakthivel K, Madhav MS, Neeraja S, Balachandran SM, Srinivasarao K, Natarajkumar P, Hari Y, Sujatha K, Sundaram RM. (2009). Development and validation of class I SSR markers targeting (GATA)n repeat motifs in rice. Euphytica DOI 10.1007/s10681-009-9964-x

Sajib AM, Hossain MM, Mosnaz ATMJ, Hossain H, Islam MM, Ali MS, Prodhan SH. (2012). SSR marker-based molecular characterization and genetic diversity analysis of aromatic landreces of rice (Oryza sativa L.). J. BioSci. Biotech. 2012, 1(2): 107-116.

Salgotra RK, Gupta BB, Bhat JA, Sharma S (2015) Genetic Diversity and Population Structure of Basmati Rice (Oryza sativa L.) Germplasm Collected from North Western Himalayas Using Trait Linked SSR Markers. PLoS ONE 10(7): e0131858.

Sarao NK, Vikal Y, Singh K, Joshi MA and Sharma RC. (2010). SSR marker-based DNA fingerprinting and cultivar identification of rice (Oryza sativa L.) in Punjab State of India. Pl Genetics Res, 8, 42.

Sharma, S.D., J.M.R.Vellanki, K.L. Hakim, and R.K. Singh. (1971). Primitive and current cultivars of rice in Assam. A rich source of valuable genes, Curr. Sci. 40: 126-128.

Singh RK, Sharma RK, Singh AK, Singh VP, Singh NK, Tiwari SP, Mohapatara T. (2004). Suitability of mapped sequence tagged microatellite site markers for establishing distinctness, uniformity and stability in aromatic rice. Euphytica 135, 135-143

Singh VJ, Gampala S, Chakraborti SK and Singh AK. (2015). Molecular characterization and genetic diversity analysis of rice varieties and landraces based on SSR markers. The Ecoscan 9(1&2): 363-368.

Sivaranjani AKP, Pandey MK, Sudharshan I, Kumar GR, Madhav MS, Sundaram RM. et al (2010 ). Assessment of genetic diversity among basmati and non-basmati aromatic rices of India using SSR markers. Curr. Sci. 99 (2):221-226.

Sow M, Ndjiondjop M-N, Sido A, Mariac C, Laing M, Bezançon G. Genetic diversity, population structure and differentiation of rice species from Niger and their potential for rice genetic resources conservation and enhancement. Genet Resour Crop Evol. 2014;61(1):199–13. doi: 10.1007/s10722-013-0026-9.

Tu M, Lu BR, Zhu Y and Wang Y. (2007). Abundant within-varietal genetic diversity in rice germplasm from Yunnan Province of China revealed by SSR fingerprints. Biochem Genet, 45, 789

Zeng L, Kwon TR, Liu X, Wilson C, Grieve CM and Gregorio GB. (2004). Genetic diversity analyzed by microsatellite markers among rice (Oryza sativa L.) genotypes with different adaptations to saline soils. Plant Sci, 166, 1275.

How to Cite
Caguiat, X. G., Rañeses , M. A., Ticman, H., Chico, M., & Arocena, E. (2019). MOLECULAR ANALYSIS OF GLUTINOUS PIGMENTED RICE GERMPLASM THROUGH THE AID OF HIGHLY POLYMORPHIC MARKERS. International Journal For Research In Agricultural And Food Science (ISSN: 2208-2719), 5(5), 01-16. Retrieved from