Unveiling genetic diversity and population structure for nutraceutical and grain ionome profile in traditional rice cultivars

Fifty rice genotypes consisting of white, red and black coloured pericarp were evaluated for 15 distinct parameters, including nutraceutical and grain ionome levels. Significant variation was observed among all genotypes under study. The genetic diversity within genotypes was studied using 50 simple sequence repeats (SSR) markers. The marker-trait association study was conducted using 43 polymorphic SSR markers to find any relationship between the DNA markers and traits. Polymorphism Information Content (PIC) values of markers ranged from 0.13 to 0.49, and cluster analysis using NTSYSpc classified the landraces into two main clusters. Population structure analysis through STRUCTURE V2.3.4 revealed a k value of 3, suggesting that the population is divided into three subpopulations: red, black, and white rice. A total of 20 significant marker-trait associations (P < 0.05) were discovered with R² ranging from 8.97 to 25.67%. Recognizing the superior nutraceutical and mineral content in pigmented rice underscores their potential to address hidden hunger and enhance nutritional diversity.