Responses of rice (Oryza sativa L.) genotypes to zinc deficiency

This study aims to understand the responses of rice (Oryza sativa L.) genotypes to zinc (Zn) deficiency through determining the physiological and biochemical factors associated with Zn deficiency tolerance and identifying quantitative trait loci (QTL) controlling those tolerant mechanisms. A total of 465 rice genotypes composed of three sets: 251 accessions of an aus association panel, 200 lines of BC sub 1 F sub 6 QTL mapping population, and a core set of standard varieties and breeding lines, were used in the present study. Plants grown in Zn-deficient soil showed severe stress symptoms such as leaf bronzing, stunting, and delayed heading and maturity. Zn deficiency-tolerant and high-grain-Zn genotypes had over 90% survival rate with relatively lower leaf bronzing scores under Zn-deficient condition. On the other hand, sensitive genotypes showed high mortality rate with severe leaf bronzing. Physiological mechanisms of Zn deficiency tolerance demonstrated by these genotypes include higher root growth rate, ability to generate new roots, and maintain high root Zn concentration. One of the most tolerant genotypes, IR55179 showed higher Zn content in root than that of high-grain-Zn genotypes. Zn deficiency-induced oxidative stress (H sub 2 O sub 2 accumulation) was higher in sensitive genotypes than in tolerant genotypes. Phenolics concentration in roots was significantly reduced under Zn deficiency, with no significant differences among genotypes. Under hydroponics, bicarbonate toxicity (5 mM as NaHCO sub 3) caused more damage and stunted growth than Zn deficiency. In both stresses, IR55179 (tolerant) effectively maintained plant vigor and crown root generation and suppressed root solute leakage rate by less half than that in IR26. Twenty metabolites including amines, amino acids, fatty acids, sugars, and sterols (7 in root exudates, 19 in roots, and 6 in shoots) were identified using gas chromatography-mass spectrometry. Zn deficiency significantly increased the accumulation of silanol but depressed the D-fructose accumulation in all genotypes. Glutamine increased under Zn deficiency in IR55179 (tolerant) but not in IR26 (sensitive). The accumulation of deoxymugineic acid (DMA), a promising ligand related to efficient Zn uptake, was significantly higher in IR55179. The overall results of this study supports that IR55179 could be selected as a candidate variety for Zn-deficient rice paddy. Quantitative trait loci (QTL) analyses was conducted through QTL mapping and genome-wide association (GWA) mapping using 200 lines from a mapping population and 55 aus accessions. Most significant QTLs associated with root traits including qRN1W12.2 (enhancing root number; LOD of 7.7 and R2 of 17%) and qRDW12.1 (increasing root dry weight; LOD above 3.0 and R sup 2 of 25%) were located on the chromosome 12.qLBS5 (LOD of 6.7 and R sup 2 of 16%) on chromosome 5 and qVS3 (LOD of 5.0 and R sup 2 of 12%) on chromosome 3 were the most significant QTLs associated with leaf bronzing symptoms and plant vigor, respectively. These QTLs provide targets for further analyses and use in breeding.