Global Analysis of Gene Expression Profiles in Developing Physic Nut (Jatropha curcas L.) Seeds Huawu Jiang 1 , Pingzhi Wu1, Sheng Zhang1,2, Chi Song 3 , Yaping Chen1, Meiru Li1, Yongxia Jia1, Xiaohua Fang4, Fan Chen4*, Guojiang Wu 1 * 1 Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People’s Republic of China, 2 Graduate University of the Chinese Academy of Sciences, Beijing, People’s Republic of China, 3 BGI-Shenzhen, Shenzhen, People’s Republic of China, 4 National Center for Plant Gene Research, Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, People’s Republic of China Abstract Background: Physic nut (Jatropha curcas L.) is an oilseed plant species with high potential utility as a biofuel. Furthermore, following recent sequencing of its genome and the availability of expressed sequence tag (EST) libraries, it is a valuable model plant for studying carbon assimilation in endosperms of oilseed plants. There have been several transcriptomic analyses of developing physic nut seeds using ESTs, but they have provided limited information on the accumulation of stored resources in the seeds. Methodology/Principal Findings: We applied next-generation Illumina sequencing technology to analyze global gene expression profiles of developing physic nut seeds 14, 19, 25, 29, 35, 41, and 45 days after pollination (DAP). The acquired profiles reveal the key genes, and their expression timeframes, involved in major metabolic processes including: carbon flow, starch metabolism, and synthesis of storage lipids and proteins in the developing seeds. The main period of storage reserves synthesis in the seeds appears to be 29–41 DAP, and the fatty acid composition of the developing seeds is consistent with relative expression levels of different isoforms of acyl-ACP thioesterase and fatty acid desaturase genes. Several transcription factor genes whose expression coincides with storage reserve deposition correspond to those known to regulate the process in Arabidopsis. Conclusions/Significance: The results will facilitate searches for genes that influence de novo lipid synthesis, accumulation and their regulatory networks in developing physic nut seeds, and other oil seeds. Thus, they will be helpful in attempts to modify these plants for efficient biofuel production. Citation: Jiang H, Wu P, Zhang S, Song C, Chen Y, et al. (2012) Global Analysis of Gene Expression Profiles in Developing Physic Nut (Jatropha curcas L.) Seeds. PLoS ONE 7(5): e36522. doi:10.1371/journal.pone.0036522 Editor: Joshua L. Heazlewood, Lawrence Berkeley National Laboratory, United States of America Received January 7, 2012; Accepted April 3, 2012; Published May 4, 2012 Copyright: 2012 Jiang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The research work was supported by grants from the National Basic Research Program of China (973 Program) (2010CB126603) (http://www.973.gov. cn/) and the NSFC-Guangdong Joint Fund of Natural Sciences (U0733005) (http://www.nsfc.gov.cn/Portal0/default152.htm). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: fchen@genetics.ac.cn (FC); wugj@scbg.ac.cn (GW) Introduction Physic nut (Jatropha curcas L.) is a drought-resistant, non-food oilseed plant that meets many of the requirements for commercial biodiesel production [1–4]. Further, following the recent sequenc- ing of its genome and the development of expressed sequence tag (EST) libraries by ourselves and other research groups [5–6] it is now a valuable model plant for studying carbon assimilation in the endosperms of oilseeds such as castor bean. In mature physic nut seeds, triacylglycerols (TAGs) are the major storage compounds [4]. In oilseed plants such as Brassica napus L. and Arabidopsis, starch is synthesized at an early stage, while TAGs and storage proteins are mainly synthesized during the seed-filling phase of seed development [7–8]. The biosynthesis and accumulation of TAGs from sugars involves hundreds of enzymes acting in several metabolic pathways. The common flux model for TAG synthesis in oilseeds includes the absorption of sugars into seed cells, their breakdown through both cytosolic and plastidic glycolytic pathways, exchange of the intermediates between the cytosol and organelles (such as plastids and the endoplasmic reticulum), starch turnover, malonyl–CoA and fatty acid (FA) synthesis, TAG assembly and oil body formation [9]. In the model plant species Arabidopsis, there are over 800 genes encoding lipid metabolism-related proteins [10–11]. Several transcription factor genes involved in seed development and reserve substance accumulation have been identified in Arabidopsis. WRINKLED11 (WRI) regulates several genes encoding late glycolysis enzymes and the plastidial FA biosynthetic machinery [8,12–13]. ABSCISIC ACID INSENSITIVE 3 (ABI3), LEAFY COTYLEDON 1 (LEC1), LEC2 and FUSCA 3 (FUS3) interactively form complex networks that regulate multiple aspects of seed development, including storage reserve accumulation [13– 20]. ABI4 regulates lipid breakdown in Arabidopsis seed germination [21] and the transcription of acyl-CoA:diacylglycerol acyltransferase 1 (which catalyzes formation of triglycerides from PLoS ONE | www.plosone.org 1 May 2012 | Volume 7 | Issue 5 | e36522