Pankratov, I., Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
McQuinn, R., Boyce Thompson Institute for Plant Research, Tower Rd, Ithaca, NY, United States, U.S. Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, United States
Schwartz, J., Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Bar, E., Institute of Field and Vegetable Crops, Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, Israel
Fei, Z., Boyce Thompson Institute for Plant Research, Tower Rd, Ithaca, NY, United States
Lewinsohn, E., Institute of Field and Vegetable Crops, Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, Israel
Zamir, D., Robert H. Smith Institute of Plant Sciences and Genetics, Faculty of Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
Giovannoni, J.J., Boyce Thompson Institute for Plant Research, Tower Rd, Ithaca, NY, United States, U.S. Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, United States
Hirschberg, J., Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel

Isoprenoids consist of a large class of compounds that are present in all living organisms. They are derived from the 5C building blocks isopentenyl diphosphate (IDP) and its isomer dimethylallyl diphosphate (DMADP). In plants, IDP is synthesized in the cytoplasm from mevalonic acid via the MVA pathway, and in plastids from 2-C-methyl-d-erythritol-4-phosphate through the MEP pathway. The enzyme IDP isomerase (IDI) catalyzes the interconversion between IDP and DMADP. Most plants contain two IDI enzymes, the functions of which are characteristically compartmentalized in the cells. Carotenoids are isoprenoids that play essential roles in photosynthesis and provide colors to flowers and fruits. They are synthesized in the plastids via the MEP pathway. Fruits of Solanum lycopersicum (tomato) accumulate high levels of the red carotene lycopene. We have identified mutations in tomato that reduce overall carotenoid accumulation in fruits. Four alleles of a locus named FRUIT CAROTENOID DEFICIENT 1 (fcd1) were characterized. Map-based cloning of fcd1 indicated that this gene encodes the plastidial enzyme IDI1. Lack of IDI1 reduced the concentration of carotenoids in fruits, flowers and cotyledons, but not in mature leaves. These results indicate that the plastidial IDI plays an important function in carotenoid biosynthesis, thus highlighting its role in optimizing the ratio between IDP and DMADP as precursors for different downstream isoprenoid pathways. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd