Natural variation in LONELY GUY-like 1 regulates rice grain weight under warmer nights

High nighttime temperature (HNT) stress affects rice yield by reducing grain weight, size and fertility. The genetic basis of grain weight regulation under HNT stress remains less explored. We have examined the natural variation for rice single grain weight (SGW) under HNT stress imposed during grain development. A genome wide association analysis identified several loci that regulate grain weight under HNT stress. A novel locus, qSGW1, specific to HNT conditions colocalized with LONELY GUY-LIKE 1 (LOGL1), which encodes a putative cytokinin activation enzyme. We demonstrate that LOGL1 contributes to variation at qSGW1. Accessions with lower LOGL1 transcript abundance have higher grain weight under HNT. This is supported by higher grain weight of logl1-mutants relative to wildtype under HNT. Compared to logl-mutants, LOGL1 over-expressers showed increased sensitivity to HNT. Disrupting LOGL1 alters genes associated with thiamine biosynthesis and circadian clock. Additionally, logl1-mutants showed enhanced accumulation of transcripts that are involved in trehalose and carbohydrate biosynthesis under HNT. These findings improve our mechanistic understanding of HNT stress and provide a genetic resource to enhance rice adaptation to warming nights.