Study on submergence tolerance of rice (Oryza sativa L.) in a core panel of North-East India using GWAS

Rice (Oryza sativa L.) being the major food crop of the north-eastern region, combating floods in rice fields for higher economic yield is a major challenge. A core panel, consisting of local rice landraces that have been cultivated in the flood-prone areas of this region for years, was used for this GWAS study to uncover possible genetic resistance sources to submergence. A study on GWAS was conducted to understand the mechanism of resistance of rice under water-submerged conditions through higher expression of genes. The GWAS analysis of a core panel of 400 rice landraces generated 38,723 filtered SNPs. The result showcased nine loci across the 12 rice chromosomes, one locus each in chromosome 2 and 4, five loci in chromosome 6, and two loci in chromosome 9. The two promising loci among these nine identified loci codes for zinc fingers, C3HC4 type domain-containing proteins, with FDR adjusted p-values of 0.04 each and allele effect of 4.60 and 4.57, respectively. These GWAS-identified association signals are a valuable source for allele mining and can be validated and introgressed into elite germplasms to decipher submergence tolerance in future breeding programs.