Identification of novel marker-trait associations and candidate genes for combined low phosphorus and nitrogen-deficient conditions in rice at seedling stage

Rice responds to individual N and P deficiencies through root traits’ modifications and characteristic starvation responses. The genomic regions associated with combined deficiencies of N and P are less reported, though the combinatorial regulation of N and P deficiencies is vital for seedling development. In this study, genome-wide association analysis (GWAS) using ~ 22 k SNPs was performed in one hundred and thirty rice genotypes for nine different traits at the seedling stage (21 days after sowing), and twenty-four statistically significant marker trait associations contributing to the phenotypic variation of 10–79% were identified. Further, except for 10% increase in root length, traits like shoot length, number of leaves, shoot area, shoot dry weight, and root dry weight decreased by 45%, 15%, 60%, 24%, and 45%, respectively, under N and P-deficient soils. Besides, candidate genes for root architecture remodeling (Dro1 and Sor1), P and N uptake (PTF1, PEPC), and amino acid transport and homeostasis (AAP7, BCAT2) were found within the genomic regions regulating the combined tolerance to low P and low N. Furthermore, three superior genotypes, namely ENT-62 (Root area, shoot area, and shoot dry weight), ENT-303 (shoot dry weight and root dry weight), and ENT-32 (no. of leaves and shoot area), were identified for regulating more than one trait under low P-low N conditions. Therefore, this study characterized the seedling stage trait response in rice genotypes and identified genomic regions regulating seedling traits for combined N and P deficient soils. The identified QTLs of these genes could be utilized in breeding programs for the combined improvement of nitrogen and phosphorus use efficiency under deficit soils.