The zinc‐finger transcription factor CcLOL1 controls chloroplast development and immature pepper fruit color in Capsicum chinense and its function is conserved in tomato

Summary Chloroplast development and chlorophyll content in the immature fruit has a major impact on the morphology and quality in pepper (Capsicum spp.) fruit. Two major quantitative trait loci (QTLs), pc1 and pc10 that affect chlorophyll content in the pepper fruit by modulation of chloroplast compartment size were previously identified in chromosomes 1 and 10, respectively. The pepper homolog of GOLDEN2‐LIKE transcription factor (CaGLK2) has been found as underlying pc10, similar to its effect on tomato chloroplast development. In the present study, we identified the pepper homolog of the zinc‐finger transcription factor LOL1 (LSD ONE LIKE1; CcLOL1) as the gene underlying pc1. LOL1 has been identified in Arabidopsis as a positive regulator of programmed cell death and we report here on its role in controlling fruit development in the Solanaceae in a fruit‐specific manner. The light‐green C. chinense parent used for QTL mapping was found to carry a null mutation in CcLOL1. Verification of the function of the gene was done by generating CRISPR/Cas9 knockout mutants of the orthologous tomato gene resulting in light‐green tomato fruits, indicating functional conservation of the orthologous genes in controlling chlorophyll content in the Solanaceae. Transcriptome profiling of light and dark‐green bulks differing for pc1, showed that the QTL affects multiple photosynthesis and oxidation‐reduction associated genes in the immature green fruit. Allelic diversity of three known genes CcLOL1, CaGLK2, and CcAPRR2 that influence pepper immature fruit color, was found to be associated with variation in chlorophyll content primarily in C. chinense. Significance Statement The genetic and molecular mechanisms controlling chlorophyll content in the fruit are only partially known. We discovered a zinc‐finger transcription factor, homologous to Arabidopsis LOL1, a regulator of oxidative stress‐induced cell death as affecting chlorophyll content and chloroplast development in pepper and tomato fruits. Allelic diversity in CcLOL1 and in other genes with similar function in affecting chloroplast development is associated with natural variation in immature color of pepper fruit.