Morpho-Molecular Diversity Analysis of Local Rice (Oryza sativa L.) Genotypes Using Microsatellite Markers

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S. K. Singh
Charupriya Singh
Mounika Korada
Sonali Habde
D. K. Singh
Amrutlal Khaire
Prasanta Kumar Majhi


Aim: The knowledge of genetic diversity and relationship among the genotypes play a significant role for genetic enhancement in breeding programmes to increase production, improve quality, biotic and abiotic stresses, and also for the selection of superior parental lines in rice. The present field experiment was conducted to study the diversity present in 29 local genotypes of rice using both morphological and molecular ways.

Methodology: The experiment was conducted at Agricultural Research Farm, Banaras Hindu University, during Kharif-2017 in an augmented block design with 29 rice genotypes including 3 checks. Mahalanobis’ D2 analysis was carried out to assess the morphological diversity present among the genotypes and molecular analysis was done with 21 polymorphic SSR markers using the NTSYSpc software.

Results: Mahalanobis’ D2 grouped the 29 genotypes into 6 clusters based on the inter-se genetic distance. The highest intra-cluster distance was recorded in the Cluster I (32.73), which comprised of 7 genotypes. The highest inter-cluster distance (65.86) was observed between Clusters IV and V. Molecular diversity analysis grouped the 29 rice genotypes into 2 main clusters i.e. cluster I and cluster II with dissimilarity coefficient of 0.34, which were further divided into sub-clusters. Polymorphic Information Content (PIC) value is an evidence of diversity and frequency among the varieties. The level of polymorphism varied from 0.164 to 0.694, with an average 0.521. The highest PIC value was observed for locus RM 5 (0.694) followed by RM 510 (0.692). All the 21 primers showed polymorphism and the number of alleles ranged from 2 to 4 with an average of 3.04. 

Conclusion: This study established the presence of considerable amount of genetic diversity among the genotypes studied, the most diverse genotypes being Anupam gold and HUR-1309 followed by Kalanamak-2 and HUR-1304. Breeders may attempt hybridization among the above genotypes which showed maximum diversity, for creating more variability in rice and can be used for planning further breeding programmes.

D2 analysis, dendrogram, molecular diversity, Oryza sativa, Polymorphic Information Content (PIC), microsatellite marker.

Article Details

How to Cite
Singh, S. K., Singh, C., Korada, M., Habde, S., Singh, D. K., Khaire, A., & Majhi, P. K. (2020). Morpho-Molecular Diversity Analysis of Local Rice (Oryza sativa L.) Genotypes Using Microsatellite Markers. Current Journal of Applied Science and Technology, 39(22), 92-104.
Original Research Article


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