Dataset Information

ESTs from Seeds to Assist the Selective Breeding of Jatropha curcas L. for Oil and Active Compounds.

ABSTRACT: We report here on the characterization of a cDNA library from seeds of Jatropha curcas L. at three stages of fruit maturation before yellowing. We sequenced a total of 2200 clones and obtained a set of 931 non-redundant sequences (unigenes) after trimming and quality control, ie, 140 contigs and 791 singlets with PHRED quality ?10. We found low levels of sequence redundancy and extensive metabolic coverage by homology comparison to GO. After comparison of 5841 non-redundant ESTs from a total of 13193 reads from GenBank with KEGG, we identified tags with nucleotide variations among J. curcas accessions for genes of fatty acid, terpene, alkaloid, quinone and hormone pathways of biosynthesis. More specifically, the expression level of four genes (palmitoyl-acyl carrier protein thioesterase, 3-ketoacyl-CoA thiolase B, lysophosphatidic acid acyltransferase and geranyl pyrophosphate synthase) measured by real-time PCR proved to be significantly different between leaves and fruits. Since the nucleotide polymorphism of these tags is associated to higher level of gene expression in fruits compared to leaves, we propose this approach to speed up the search for quantitative traits in selective breeding of J. curcas. We also discuss its potential utility for the selective breeding of economically important traits in J. curcas.

SUBMITTER: Gomes KA

PROVIDER: S-EPMC4510598 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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ESTs from Seeds to Assist the Selective Breeding of Jatropha curcas L. for Oil and Active Compounds.

Gomes Kleber A KA Almeida Tiago C TC Gesteira Abelmon S AS Lôbo Ivon P IP Guimarães Ana Carolina R AC de Miranda Antonio B AB Van Sluys Marie-Anne MA da Cruz Rosenira S RS Cascardo Júlio Cm JC Carels Nicolas N

Genomics insights 20101028

We report here on the characterization of a cDNA library from seeds of Jatropha curcas L. at three stages of fruit maturation before yellowing. We sequenced a total of 2200 clones and obtained a set of 931 non-redundant sequences (unigenes) after trimming and quality control, ie, 140 contigs and 791 singlets with PHRED quality ≥10. We found low levels of sequence redundancy and extensive metabolic coverage by homology comparison to GO. After comparison of 5841 non-redundant ESTs from a total of ...[more]

PMID: 26217103

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Project description:According to IPCC Annual Report (AR-5), environmental impact assessment of any product prototype is recommended before its large-scale commercialization; however, no environmental profile analysis of any biodiesel prototype has been conducted in Pakistan. Therefore, objective of this study was to conduct a comprehensive life cycle assessment (LCA), water footprint and cumulative energy demand (CED) of biodiesel production from Jatropha curcas L. (JC) seeds oil in Pakistan. A cradle-to-gate LCA approach was applied for 400 liter (L) JC biodiesel produced in Pakistan. JC biodiesel production chain was divided into three stages i.e., 1). cultivation of JC crop 2). crude oil extraction from JC seeds and 3). crude oil conversion to biodiesel. Primary data for all the stages were acquired through questionnaire surveys, field visits and measurements in the field. Potential environmental impacts were calculated in SimaPro v.9.2 software using Eco-indicator 99 methodology. Results showed that crude oil extraction stage accounted for highest emissions (77%) to the overall environmental impact categories evaluated, followed by oil conversion stage (21%) and JC cultivation stage (02%), respectively. The three stages of JC biodiesel production chain are major contributor to ecotoxicity with a contribution of 57% to this impact category. Higher contribution to ecotoxicity was due to agrochemicals used in the JC cultivation. Similarly, fossil fuels impact category was responsible for 38% of overall environmental impacts. In addition, water footprint of JC biodiesel production chain was 2632.54 m3/reference unit. Cumulative energy required for 400L JC biodiesel production chain was 46745.70 MJ in Pakistan. Fossil diesel consumption, synthetic fertilizers use and purchased electricity were major hotspot sources to environmental burdens caused by JC biodiesel production in Pakistan. By performing sensitivity analysis at 20% reduction of the baseline values of fossil diesel used, synthetic fertilizers and purchased electricity, a marked decrease in environmental footprint was observed. It is highly recommended that use of renewable energy instead of fossil energy would provide environmental benefits such as lower greenhouse gases and other toxic emissions as compared to conventional petroleum fuels. It is also recommended that JC as a biofuel plant, has been reported to have many desired characteristics such as quick growth, easy cultivation, drought resistance, pest and insect resistance, and mainly great oil content in JC seeds (27-40%). Therefore, JC plant is highly recommended to Billion Tree Afforestation Project (BTAP) for plantation on wasteland because it has multipurpose benefits.

Project description:BackgroundJatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as biodiesel. Genetic improvement in jatropha is needed to increase the seed yield, oil content, drought and pest resistance, and to modify oil composition so that it becomes a technically and economically preferred source for biodiesel production. However, genetic improvement efforts in jatropha could not take advantage of genetic engineering methods due to lack of cloned genes from this species. To overcome this hurdle, the current gene discovery project was initiated with an objective of isolating as many functional genes as possible from J. curcas by large scale sequencing of expressed sequence tags (ESTs).ResultsA normalized and full-length enriched cDNA library was constructed from developing seeds of J. curcas. The cDNA library contained about 1 × 10(6) clones and average insert size of the clones was 2.1 kb. Totally 12,084 ESTs were sequenced to average high quality read length of 576 bp. Contig analysis revealed 2258 contigs and 4751 singletons. Contig size ranged from 2-23 and there were 7333 ESTs in the contigs. This resulted in 7009 unigenes which were annotated by BLASTX. It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins. The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes. Functional classification revealed unigenes related to broad range of cellular, molecular and biological functions. Among the 7009 unigenes, 6233 unigenes were identified to be potential full-length genes.ConclusionsThe high quality normalized cDNA library was constructed from developing seeds of J. curcas for the first time and 7009 unigenes coding for diverse biological functions including oil biosynthesis were identified. These genes will serve as invaluable genetic resource for crop improvement in jatropha to make it an ideal and profitable crop for biodiesel production.

Project description:Jatropha curcas L. is a non-edible oilseed containing almost 40% of seed oil and is famous as the best source of raw material for biofuel production. J. curcas seeds contain three main tissues, such as inner integument, endosperm, and embryo. To best understand the physiological events related to specific tissues, it is important to perform the proteome analysis of these tissues. Previously we have explored the pattern of reserves deposition and tissue-specific biological pathways by analyzing the proteome of the inner integument and endosperm and organelles, such as plastids and gerontoplasts isolated from these tissues. The focus of the present study was to perform the proteomic analysis of embryo isolated from the mature seeds of J. curcas. This analysis resulted in the identification of 564 proteins of which 206 are not identified previously from any other tissue of this plant. The identified proteins were functionally classified using the MapMan classification system revealing various proteins involved in different functionalities. The proteins involved in transport functions and those with proteolytic activity were determined through the Transporter Classification Database (TCDB) and MEROPS database, respectively. In addition to identify a large number of proteins participating in various metabolic processes, we found several proteins involved in defense functions, such as the members of chaperones and the ubiquitin-proteasome system. Similarly, members of the legumin and vicilin family of seed storage proteins (SSPs) were identified which in addition to their storage function, are involved in defense. In addition, we have reported that proteases belonging to different mechanistic classes and are involved in diverse physiological functions. Last but not the least, several classes of transport-related proteins were identified that are discussed concerning their function in the transportation of different nutrients across the embryo. To the best of our knowledge, this study reported the highest number of proteins identified from the embryo of mature J. curcas seeds, most of which are essential for seed germination, reflecting the fact that many proteins required for germination are already present in the mature embryo.

Dataset Information

ESTs from Seeds to Assist the Selective Breeding of Jatropha curcas L. for Oil and Active Compounds.

Publications

ESTs from Seeds to Assist the Selective Breeding of Jatropha curcas L. for Oil and Active Compounds.

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