Vegetos
(An International Journal of Plant Research & Biotechnology)
(eISSN: 2229-4473)
Assessment of genetic diversity in medium-duration rice (Oryza sativa L.) genotypes using clustering and principal component analysis
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Modi Sagar, Krishna Vemula Anjula, Bisane Ritik Digamber, Poudel Amrit Prasad, Singh Akansha, Singh Shravan Kumar
Research Articles | Published: 19 May, 2026
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Keywords: Crop breeding, Genetic diversity, Hierarchical cluster analysis, Principal component analysis, Rice
Abstract
Medium-duration rice genotypes are preferred in India for their efficient resource use, stress avoidance, and better fit in intensive cropping systems. Breeding for medium-duration, high-yielding, climate-resilient cultivars is crucial to enhance productivity and ensure sustainable rice production. With this aim, the present study was conducted to evaluate 85 genetically diverse medium-duration rice genotypes in an alpha lattice design with two replications during Kharif-2023 at the Agricultural Research Farm of Banaras Hindu University, Varanasi, Uttar Pradesh, India. The observations were recorded for 24 characters to determine the relationship and genetic divergence among the individuals by hierarchical cluster analysis and principal component analysis. Results from cluster analysis grouped 85 genotypes into five distinct clusters with minimum genotypes in Cluster III (5 genotypes) and maximum in Cluster IV (27 genotypes). The genotypes in Cluster II (intra-cluster distance: 5.928) showed maximum divergence. The maximum inter-cluster Euclidean distance was observed between Clusters II and III, followed by Clusters I and III, giving a scope for selection of parents for a hybridization programme from these clusters to realize high genetic variation and novel combinations for yield increment. Results from the PCA analysis revealed that the first nine principal components with eigenvalues greater than 1, explained a cumulative variance of 85.6%. PC1, contributing 20.8% of the total variance, was primarily associated with biomass, plot yield, and straw yield. Genotypes such as HL-19-WS-33 A-401, BHU-STM-2023-39, BHU-STM-2023-4, BHU-STM-2023-29, BHU-STM-2023-26, and HL-18-WS-39-24-25 exhibited superior performance for biomass, straw yield, plot yield, kernel length before cooking and test weight, making them valuable donors for yield improvement. Overall, the study offered valuable insights into the genetic diversity of medium-duration rice genotypes, identifying diverse parental lines suitable for hybridization and the development of advanced breeding lines to enhance genetic gain. It also highlighted key principal components that can be strategically targeted in future rice improvement programs.
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Author Information
Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India