Integrated multivariate analysis reveals genetic diversity for yield, grain quality, and stress tolerance in rice (Oryza sativa L.) genotypes

Abstract

Rice (Oryza sativa L.) is a major staple crop, and simultaneous improvement of yield, grain quality, and stress resistance is essential under changing climatic conditions. However, comprehensive diversity analyses that integrate agronomic, quality, and stress related traits remain limited in rice improvement programs. Therefore, the present study was conducted to evaluate 36 rice varieties during the Kharif season of 2025 at Nuthankal Farm, Hyderabad, using a Randomized Complete Block Design (RCBD) with two replications. Data on 22 traits, including six agronomic, 12 grain quality, and four biotic and abiotic stress-related parameters, were analyzed using analysis of variance (ANOVA), cluster analysis, and principal component analysis (PCA). The results revealed significant differences among the genotypes for all the measured parameters, indicating the presence of high genetic variability. The cluster analysis grouped the genotypes into four distinct clusters, with the highest number of genotypes in Cluster II and only one genotype in Cluster IV, which was highly divergent. The genotypes in Clusters II and III were found to be superior for yield, milling quality, and moderate stress resistance, whereas Cluster IV genotypes had unique characteristics such as early flowering and herbicide resistance. PCA revealed that the first six components explained 81.58 % of the total variation, with major contributions from yield, milling percentage, head rice recovery, amylose content, and stress scores. NP 10325-3-14, NP 7373, NP 9156, and NP 9558 exhibited resistance to bacterial leaf blight. Based on the identified trait-specific donor genotypes, NP 9156, NP 9153 and NP-9558 can be crossed with the genetically divergent and herbicide-tolerant HTM-N22 to combine high yield, superior grain quality, and herbicide tolerance. Likewise, NP 10325-3-11 or NP 10325-3-8 × NP 9156/NP 9153 are promising combinations for improving cooking quality with high yield, while NP 7373 or NP 10325-3-5 × NP 9156/NP 9153 may facilitate the development of high-yielding cultivars with improved head rice recovery.