Unlocking genetic hotspots: GWAS reveals key nitrogen responsive genomic regions and key genes for root and yield traits in indica rice

Abstract Enhanced Nitrogen Use Efficiency (NUE) for crop plant is important for the environment and cost of cultivation. Rice has the lowest NUE among the cereals, hence it is necessary to know the underlying genetic factors associated with it. To identify candidate genes and QTLs, a genome-wide association study (GWAS) was carried out involving 96 diverse indicarice genotypes. Plants were grown under contrasting nitrogen (N) regimes in hydroponics till the maturity for phenotyping the major N-responsive traits. Genotyping was carried out using 80K Affymetrix chip containing 47,686 curated SNP markers. The differential response of all N-responsive traits indicated separate breeding programme for each N-regime. The population structure analysis revealed two sub-populations with varying degrees of admixtures in the association panel. The linkage disequilibrium (LD) analysis revealed an LD block of 108.4 kb. GWAS using MLM, FarmCPU, and BLINK could identify 568 marker-trait associations (MTAs) across different traits and N-conditions. Out of 24 MTAs identified, 13 were novel with 156 candidate genes in the genomic region spanning the LD blocks. N-responsive genes showed either positive or negative role, and many of them were likely to be associated with other abiotic stresses like drought and salinity. Yield and root-related MTAs were found to be the most prominent. Candidate genes such as OsPRX59, OsPRX62, OsPSBS2, OsWAK14, OsWAK15, OsAMT3, OsNIN8,and OsHCT2 from the MTAs with major allelic effects also showed the differential responses under N-deficient conditions. These MTAs and candidate genes can serve as key resources for enhancement of NUE in rice.