Newly identified CSP41b gene localized in chloroplasts affects leaf color in rice

•A novel rice gene controlling leaf color (lgl1) was identified by map-based cloning.•The lgl1 mutant displayed reduced chlorophyll content and abnormal chloroplast morphology.•CSP41b was mainly expressed in leaves.•CSP41b is localized in chloroplasts.•The expression levels of some key genes involved in chlorophyll biosynthesis and photosynthesis were significantly changed in the lgl1 mutant.