Includes bibliographical references.

Rice consumption as a primary food source in the North East region of India (NER), a biodiversity hotspot with over 10,000 rice landraces, coincided with high iron (Fe) and zinc (Zn) deficiencies. Rising demand for quality rice and higher yields, coupled with extensive grain polishing, led to significant nutrient loss, worsening global micronutrient deficiencies. In our study evaluation of one hundred and thirty-three rice landraces and six checks (CAUS 107, CAUS124, Shahsarang, LR55, Protazin and Chakhao Poireiton) were carried out for 27 agro-morphological and grain quality traits, including grain Fe and Zn content. UM18 (18.45g), UM17 (17.56g) and UM 116 (16.62g) were the landraces identified for high Grain yield per plant. Majority of the examined rice landraces showed low protein content, but three landraces had moderate protein content, namely UM67 (9.01%), Chakhao Poireiton (9.31%), and UM9 (Chakhao Amubi) (9.63%). Majority of the landraces had low amylose content, while intermediate amylose genotypes, preferred in India, included UM30 (20.13%), UM2 (20.31%), and UM127 (20.45%), identified in this study. The study also revealed significant variability in iron and zinc concentrations among rice landraces. Iron levels ranged from 7.75 ppm (UM21) to 19.66 ppm (UM75), with an average of 11.40 ppm while Zinc levels ranged from 20.79 ppm (UM85) to 49.82 ppm (UM81), with an average of 29.88 ppm. UM81 (17.69ppm Fe, 49.82ppm Zn), UM82 (16.88ppm Fe, 48.69ppm Zn) and UM75 (19.66ppm Fe, 47.64ppm Zn) were some of the high iron and zinc containing landraces identified. Traits viz., PL, SF, G L:B, PH, Zn, Fe, HI, PC, PN, TN 60, SPP, AC, FGPP, BY, GYPP, and PY, which showed high GCV values, indicated effective selection due to observed variation, whereas traits like SB and GB, with low GCV, exhibited limited genetic diversity, making selection less effective. Amylose, Fe, and Zn content in grains showed high heritability, indicating effective selection. PCA and Ward’s clustering identified the same landraces for high Fe, Zn, and GYPP. Fe and Zn content were negatively correlated with grain yield. The anthocyanin content in sixteen coloured landraces was evaluated, revealing a range from 3.21 μg/100mg (UM35) to 0.11 μg/100mg (UM18). RM234, R1111, RM21975, RM26976, RM470, RM7488, RM3666, RM8210 and Badh2 were the markers identified to be significantly associated with iron and zinc content and RM234, RM470, RM21975, RM7488, RM1111, RM8210, RM26976, RM279 were the markers identified to be significantly associated with yield. The landraces identified with superior Fe and Zn content can be used as donors in breeding programme for rice biofortification and the validated markers can be used for marker assisted selection.