Alterations in stomatal response to fluctuating light increase biomass and yield of rice under drought conditions

The acceleration of stomatal closure upon high to low light transition could improve plant water use efficiency and drought tolerance. Herein, using genome-wide association study, we showed that the genetic variation in OsNHX1 was strongly associated with the changes in τ_cl , the time constant of stomatal closure, in 206 rice accessions. OsNHX1 overexpression in rice resulted in a decrease in τ_cl , and an increase in biomass, grain yield under drought. Conversely, OsNHX1 knockout by CRISPR/CAS9 shows opposite trends for these traits. We further found three haplotypes spanning the OsNHX1 promoter and CDS regions. Two among them, HapII and HapIII, were found to be associated with a high and low τ_cl , respectively. A near-isogenic line (NIL, S464) was developed through replacing the genomic region harboring HapII (~10 kb) from MH63 (recipient) rice cultivar by the same sized genomic region containing Hap III from 02428 (donor). Compared with MH63, S464 shows a reduction by 35% in τ_cl and an increase by 40% in the grain yield under drought. However, under normal conditions, S464 maintains closely similar grain yield as MH63. The global distribution of the two OsNHX1 haplotypes is associated with the local precipitation. Taken together, the natural variation in OsNHX1 could be utilized to manipulate the stomatal dynamics for an improved rice drought tolerance.