Includes bibliographical references.

Rice (Oryza sativa L.) is a staple food of Asia and the most significant cereal crop in India's North Eastern Hill Region (NEHR), which grows across an area of approximately 9.98 lakh hectares with an average productivity of 2.00 t/ha. Acidic soil leads to decreased productivity. The limitations of acid soils for plants are lower nitrogen use efficiency as well as suboptimal levels of available phosphorous. N and P are essential macro-elements for plant growth, including grain yield, grain quality, flowering time, root development, etc. The use of the wild species of Oryza and native landraces becomes imperative for exploiting the untapped reservoir of useful QTLs and genes, especially to broaden the genetic basis of rice and enrich existing varieties. It is important to study both mechanisms of plant tolerance to soil deficient in mineral nutrients and genes encoding the traits. Several genomic regions, including PSTOL1 and a 1.87 Mb region on chromosome 2 for tolerance of P deficiency and another region on chromosome 2 for nitrogen use efficiency, are reported in rice. Hence, the current study focused on the study of association of reported nitrogen use efficiency and low phosphorus tolerance loci in a panel of landraces from North East Hill Region. A total of 131 rice landraces from Northeast India, along with six checks (Caus107, Caus124, Shasarang, LR55, Chakhao poireiton, and Protazin), were evaluated at the CPGS-AS experimental farm under lowland acidic soil conditions. Based on traits like grain yield per plant, tiller number, and biological yield A set of thirty superior (e.g., UM18, UM17, UM22, UM96, UM133) and inferior (e.g., UM14, UM119, UM36, UM76, UM75) genotypes each were identified. The genotype UM18 (Naga Rei) was the best performing for grain yield per plant as well as biological yield. Based on ANOVA, all twelve traits measured were statistically significant. Vegetative stage screening using five extreme (both superior and inferior) genotypes out of 131 in a pot experiment with four treatments (N+P+, N+P-, N-P+, and N-P-) showed variation for tiller number. A set of reported markers (twenty-nine) for low P and nitrogen use efficiency were evaluated on a panel of 30 extreme genotypes. Twenty-one markers were polymorphic. Seven markers (RM12550, RM12558, RM12569, RM13201, RM169, RM495, and RM18076) showed a significant association with yield. Marker trait association analysis using a test revealed that maker RM169 was significantly associated with ten traits (GYPP, BY, DTF, PH, PL, SPP, FGPP, TW, SF, and HI), and marker RM18076 was significantly associated with most yield-contributing traits (GYPP, TN, PN, BY, PH, PL, SPP, and FGPP). These markers can be used in breeding programs for the selection of high nitrogen use efficiency (NUE) and low phosphorous tolerance.