PIF4 promotes water use efficiency during fluctuating light and drought resistance in rice

Molecular mechanism of intrinsic water use efficiency (iWUE) during fluctuating light (FL) was rarely understood. In this study, we investigated five parameters of iWUE under FL in 200 Minicore rice accessions. Among them, a novel trait, WUEFL (averaged iWUE during FL) has highest SNP heritability in these parameters. GWAS identifies six candidate genes, and PIF4 is highly expressed in high iWUEFL rice subgroup. Nine SNPs were significantly associated with iWUEFL, and v3 SNP located at -1,075 bp of PIF4 promoter shows highest sensitives to light. Deletion of v3 in a rice cultivar, WYG7 (PIF4v3m) leads to [~]20% reduction in iWUEFL, and overexpressing PIF4 causes 25% increase in iWUEFL under DS. There are 85% reduction in adenosine 3,5-diphosphate (PAP) amounts together with 73% increase in SAL1 gene abundance in PIF4v3m than WYG7. PIF4 transcriptionally repress and activate SAL1 and NHX1, respectively, through binding to G-box motifs of the two genes, which leads to 16% reduction and 5% increase in iWUEFL in co-overexpression rice lines of PIF4-SAL1 and PIF4-NHX1, respectively, relative to PIF4-OE under DS. We proposed that PIF4 promotes iWUEFL and stomatal adjustment via targeting the G-box motif of SAL1 and NHX1 genes during FL, eventually facilitating to drought resistance.