Metabolomic study on the quality differences and physiological characteristics between rice cultivated in drought and flood conditions

•Amylase activity were lower after drought treatment than during flood cultivation.•The expression levels of related amylase genes in dry cultivation were different during grain filling.•Key period for quality formation of dry cultivation was from 8DAF to 15DAF.•At 8–15DAF, accumulation of metabolites in dry cultivation rice was higher than controls.•At 40DAF, metabolite consumption of dry cultivation rice was faster than control. The differences between dry- and flood-cultivated rice and the reason behind low-quality dry-cultivated rice were clarified. The physiological traits, starch synthase activity, and grain metabolomics of ‘Longdao 18′ were measured and analyzed at four growth stages. The brown, milled, and whole-milled rice rates and AGPase, SSS, and SBE activity were lower after drought treatment than during flood cultivation, while the chalkiness, chalky grain rate, amylose (16.57–20.999%), protein (7.99–12.09%), and GBSS activity were higher. Related enzymatic gene expression showed significant differences. Metabolic results showed pyruvate, glycine, and methionine upregulation at 8DAF and higher citric, pyruvic, and α-ketoglutaric acid content at 15DAF. Therefore, 8DAF-15DAF represented the crucial quality formation period for dry-cultivated rice. At 8DAF, the respiratory pathways used amino acids as signaling molecules and alternative substrates to adapt to energy shortages, arid environments and rapid protein accumulation and synthesis. Excessive amylose synthesis at 15DAF accelerated reproductive growth, promoting rapid premature aging.