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Turck D, Bohn T, Castenmiller J, De Henauw S, Hirsch‐Ernst KI, Maciuk A, Mangelsdorf I, McArdle HJ, Naska A, Pelaez C, Pentieva K, Siani A, Thies F, Tsabouri S, Vinceti M, Cubadda F, Frenzel T, Heinonen M, Marchelli R, Neuhäuser‐Berthold M, Poulsen M, Prieto Maradona M, Schlatter JR, van Loveren H, Colombo P, Knutsen HK. Safety of hydrothermally treated kernels from edible Jatropha curcas L. (Chuta) as a novel food pursuant to Regulation (EU) 2015/2283. EFSA J 2022; 20:e06998. [PMID: 35079277 PMCID: PMC8777556 DOI: 10.2903/j.efsa.2022.6998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Following a request from the European Commission, the EFSA Panel on Nutrition, Novel Foods and Food Allergens (NDA) was asked to deliver an opinion on hydrothermally treated kernels from edible Jatropha curcas (Chuta) as a novel food (NF) pursuant to Regulation (EU) 2015/2283. Although Jatropha curcas is generally considered a toxic plant due to the presence of phorbol esters (PEs), edible varieties exist in Central America. The applicant has developed a breeding programme for an edible cultivar and proposes the kernels from this cultivar as an NF as whole kernels or fragments thereof to be used as a snack or as a food ingredient. Procedures are in place to avoid commingling with non-edible kernels, with the last steps being the analytical control of PEs concentrations in all produced batches. The Panel considers that the production process of the NF is sufficiently described and that the information provided on the composition of the NF is sufficient for its characterisation. Components of the NF were tested for genotoxicity applying the standard in vitro test battery and no genotoxic concerns have been identified. In a conservative scenario for exposure to PEs from the NF, it was assumed that all kernels contain PEs at the level of detection of the analytical method. When comparing the estimated maximum exposure to PEs with a reference point from a subchronic study in pigs, a margin of exposure ≥ 900 is obtained, which is considered sufficiently large. The presence of anti-nutritional factors does not pose safety concerns as they are within the ranges found in vegetables. The Panel concludes that the NF is safe under the proposed conditions of use.
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Yu L, Nie Y, Jiao J, Jian L, Zhao J. The Sequencing-Based Mapping Method for Effectively Cloning Plant Mutated Genes. Int J Mol Sci 2021; 22:ijms22126224. [PMID: 34207582 PMCID: PMC8226582 DOI: 10.3390/ijms22126224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/05/2021] [Indexed: 11/23/2022] Open
Abstract
A forward genetic approach is a powerful tool for identifying the genes underlying the phenotypes of interest. However, the conventional map-based cloning method is lengthy, requires a large mapping population and confirmation of many candidate genes in a broad genetic region to clone the causal variant. The whole-genome sequencing method clones the variants with a certain failure probability for multiple reasons, especially for heterozygotes, and could not be used to clone the mutation of epigenetic modifications. Here, we applied the highly complementary characteristics of these two methods and developed a sequencing-based mapping method (SBM) for identifying the location of plant variants effectively with a small population and low cost, which is very user-friendly for most popular laboratories. This method used the whole-genome sequencing data of two pooled populations to screen out enough markers. These markers were used to identify and narrow the candidate region by analyzing the marker-indexes and recombinants. Finally, the possible mutational sites were identified using the whole-genome sequencing data and verified in individual mutants. To elaborate the new method, we displayed the cloned processes in one Arabidopsis heterozygous mutant and two rice homozygous mutants. Thus, the sequencing-based mapping method could clone effectively different types of plant mutations and was a powerful tool for studying the functions of plant genes in the species with known genomic sequences.
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de Almeida NP, Neto DFM, Carneiro GRA, de Farias ARB, Domont GB, de Paiva Campos FDA, Nogueira FCS. Monitoring casbene synthase in Jatropha curcas tissues using targeted proteomics. PLANT METHODS 2021; 17:15. [PMID: 33549129 PMCID: PMC7868020 DOI: 10.1186/s13007-021-00716-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Casbene synthase (CS) is responsible for the first committed step in the biosynthesis of phorbol esters (PE) in the Euphorbiaceae. PE are abundant in the seeds of the biofuel crop Jatropha curcas and its toxicity precludes the use of the protein-rich cake obtained after oil extraction as an animal feed and the toxicity of the fumes derived from burning PE containing biofuel is also a matter of concern. This toxicity is a major hindrance to exploit the potential of this crop as a source of raw material to produce biodiesel. For this reason, the current research on J. curcas is mainly focused on the understanding of the biosynthesis and site of synthesis of PE, as an avenue for the development of genotypes unable to synthesize PE in its seeds. RESULTS Here, we present targeted proteomics assays (SRM and PRM) to detect and quantify CS in leaves, endosperm, and roots of two J. curcas genotypes with contrasting levels of PE. These assays were based on the use of reference isotopic labeled synthetic peptides (ILSP) predicted from 12 gene models of CS from the J. curcas genome. CONCLUSION Our targeted proteomics methods were able to detect and quantify, for the first time, CS gene products and demonstrate the distribution of CS isoforms only in roots from J. curcas genotypes with a high and low concentration of PE. These methods can be expanded to monitor CS, at the protein level, in different tissues and genotypes of J. curcas.
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Affiliation(s)
- Natália Pinto de Almeida
- Laboratory of Proteomics/LADETEC, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
- Proteomics Unit, Institute of Chemistry, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Gabriel Reis Alves Carneiro
- Laboratory of Proteomics/LADETEC, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
- Proteomics Unit, Institute of Chemistry, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Gilberto Barbosa Domont
- Proteomics Unit, Institute of Chemistry, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Fábio César Sousa Nogueira
- Laboratory of Proteomics/LADETEC, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
- Proteomics Unit, Institute of Chemistry, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
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Maghuly F, Deák T, Vierlinger K, Pabinger S, Tafer H, Laimer M. Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas. BMC Genomics 2020; 21:290. [PMID: 32272887 PMCID: PMC7146973 DOI: 10.1186/s12864-020-6666-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/11/2020] [Indexed: 11/10/2022] Open
Abstract
Background Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronomic performance, a two-step approach was performed in six different maturation stages of seeds: 1) generation of the entire transcriptome of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels using a custom Agilent 8x60K oligonucleotide microarray. Results A total of 793,875 high-quality reads were assembled into 19,382 unique full-length contigs, of which 13,507 could be annotated with Gene Ontology (GO) terms. Microarray data analysis identified 9111 probes (out of 57,842 probes), which were differentially expressed between the six maturation stages. The expression results were validated for 75 selected transcripts based on expression levels, predicted function, pathway, and length. Result from cluster analyses showed that transcripts associated with fatty acid, flavonoid, and phenylpropanoid biosynthesis were over-represented in the early stages, while those of lipid storage were over-represented in the late stages. Expression analyses of different maturation stages of J. curcas seed showed that most changes in transcript abundance occurred between the two last stages, suggesting that the timing of metabolic pathways during seed maturation in J. curcas occurs in late stages. The co-expression results showed that the hubs (CB5-D, CDR1, TT8, DFR, HVA22) with the highest number of edges, associated with fatty acid and flavonoid biosynthesis, are showing a decrease in their expression during seed maturation. Furthermore, seed development and hormone pathways are significantly well connected. Conclusion The obtained results revealed differentially expressed sequences (DESs) regulating important pathways related to seed maturation, which could contribute to the understanding of the complex regulatory network during seed maturation with the focus on lipid, flavonoid and phenylpropanoid biosynthesis. This study provides detailed information on transcriptional changes during J. curcas seed maturation and provides a starting point for a genomic survey of seed quality traits. The results highlighted specific genes and processes relevant to the molecular mechanisms involved in Jatropha seed maturation. These data can also be utilized regarding other Euphorbiaceae species.
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Affiliation(s)
- Fatemeh Maghuly
- Plant Functional Genomics, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Tamás Deák
- Department of Viticulture, Szent István University, Villányi út 29-43, 1118 Budapest, Hungary
| | - Klemens Vierlinger
- Center for Health and Bioresources, Molecular Diagnostics, Austrian Institute of Technology (AIT), Giefinggasse 4, 1210, Vienna, Austria
| | - Stephan Pabinger
- Center for Health and Bioresources, Molecular Diagnostics, Austrian Institute of Technology (AIT), Giefinggasse 4, 1210, Vienna, Austria
| | - Hakim Tafer
- Austrian Center of Biological Resources (ACBR), Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Margit Laimer
- Plant Biotechnology Unit, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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Vandepitte K, Valdés-Rodríquez OA, Sánchez-Sánchez O, De Kort H, Martinez-Herrera J, García-Pérez E, De Meyer T, Pérez-Vázquez A, Muys B, Honnay O. High SNP diversity in the non-toxic indigenous Jatropha curcas germplasm widens the potential of this upcoming major biofuel crop species. ANNALS OF BOTANY 2019; 124:645-652. [PMID: 30715120 PMCID: PMC6821362 DOI: 10.1093/aob/mcz008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 01/08/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS Jatropha curcas (jatropha) is an oil crop cultivated in (sub)tropical regions around the world, and holds great promise as a renewable energy source. However, efforts to fully commercialize jatropha are currently hampered by the lack of genetic diversity in the extant breeding germplasm, and by the toxicity of its seeds meaning that its seed cake cannot be used as a protein source in animal feed, among other constraints. In Mexico, the species' native range, there are jatropha plants whose seeds are used to prepare traditional meals. This non-toxic jatropha 'type' is considered to harbour low genetic variation due to a presumed domestication bottleneck and therefore to be of limited breeding value; yet, very little is known regarding its origin and genetic diversity. METHODS Using genotyping-by-sequencing (GBS), we extensively genotyped both indigenous toxic and non-toxic jatropha collected along roads and home gardens throughout southern Mexico. KEY RESULTS Single nucleotide polymorphism diversity in non-toxic jatropha is relatively high, particularly in northern Veracruz state, the probable origin of this germplasm. Genetic differences between toxic and non-toxic indigenous genotypes are overall quite small. A a genome-wide association study supported a genomic region (on LG 8, scaffold NW_012130064), probably involved in the suppression of seed toxicity. CONCLUSIONS Conservation actions are urgently needed to preserve this non-toxic indigenous, relatively wild germplasm, having potential as a fuel feedstock, animal feed and food source among other uses. More generally, this work demonstrates the value of conservation genomic research on the indigenous gene pool of economically important plant species.
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Affiliation(s)
- K Vandepitte
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Leuven, Belgium
| | | | - O Sánchez-Sánchez
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Xalapa, Ver. México
| | - H De Kort
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Leuven, Belgium
| | | | - E García-Pérez
- Colegio de Postgraduados, Campus Veracruz, Veracruz, México
| | - T De Meyer
- Laboratory for Bioinformatics and Computational Genomics, Mathematical Modelling, Statistics & Bioinformatics Department, Ghent University, Ghent, Belgium
| | | | - B Muys
- Division of Forest, Nature and Landscape, KU Leuven, Leuven, Belgium
| | - O Honnay
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Leuven, Belgium
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Identification and validation of SNP markers linked to seed toxicity in Jatropha curcas L. Sci Rep 2019; 9:10220. [PMID: 31308439 PMCID: PMC6629616 DOI: 10.1038/s41598-019-46698-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 06/05/2019] [Indexed: 12/21/2022] Open
Abstract
Edible/non-toxic varieties of Jatropha curcas L. are gaining increasing attention, providing both oil as biofuel feedstock or even as edible oil and the seed kernel meal as animal feed ingredient. They are a viable alternative to the limitation posed by the presence of phorbol esters in toxic varieties. Accurate genotyping of toxic/non-toxic accessions is critical to breeding management. The aim of this study was to identify SNP markers linked to seed toxicity in J. curcas. For SNP discovery, NGS technology was used to sequence the whole genomes of a toxic and non-toxic parent along with a bulk of 51 toxic and 30 non-toxic F2 plants. To ascertain the association between SNP markers and seed toxicity trait, candidate SNPs were genotyped on 672 individuals segregating for seed toxicity and two collections of J. curcas composed of 96 individuals each. In silico SNP discovery approaches led to the identification of 64 candidate SNPs discriminating non-toxic and toxic samples. These SNPs were mapped on Chromosome 8 within the Linkage Group 8 previously identified as a genomic region important for phorbol ester biosynthesis. The association study identified two new SNPs, SNP_J22 and SNP_J24 significantly linked to low toxicity with R2 values of 0.75 and 0.54, respectively. Our study released two valuable SNP markers for high-throughput, marker-assisted breeding of seed toxicity in J. curcas.
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Ha J, Shim S, Lee T, Kang YJ, Hwang WJ, Jeong H, Laosatit K, Lee J, Kim SK, Satyawan D, Lestari P, Yoon MY, Kim MY, Chitikineni A, Tanya P, Somta P, Srinives P, Varshney RK, Lee S. Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:517-530. [PMID: 30059608 PMCID: PMC6335072 DOI: 10.1111/pbi.12995] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/26/2018] [Indexed: 05/02/2023]
Abstract
Jatropha curcas (physic nut), a non-edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up-regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.
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Affiliation(s)
- Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
| | - Sangrea Shim
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Taeyoung Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Yang J. Kang
- Division of Applied Life Science (BK21 plus program) DepartmentGyeongsang National UniversityPMBBRCJinju‐siKorea
- Division of Life Science DepartmentGyeongsang National UniversityJinju‐siKorea
| | | | - Haneul Jeong
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Kularb Laosatit
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Jayern Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Sue K. Kim
- Department of ChemistryCollege of Natural ScienceDankook UniversityCheonanSouth Korea
| | - Dani Satyawan
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD‐IAARD)BogorIndonesia
| | - Puji Lestari
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD‐IAARD)BogorIndonesia
| | - Min Y. Yoon
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Moon Y. Kim
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelangana StateIndia
| | - Patcharin Tanya
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Prakit Somta
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Peerasak Srinives
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelangana StateIndia
| | - Suk‐Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
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Maghuly F, Pabinger S, Krainer J, Laimer M. The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:524. [PMID: 29774036 PMCID: PMC5944264 DOI: 10.3389/fpls.2018.00524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/04/2018] [Indexed: 05/31/2023]
Abstract
Mutagenesis in combination with Genotyping by Sequencing (GBS) is a powerful tool for introducing variation, studying gene function and identifying causal mutations underlying phenotypes of interest in crop plant genomes. About 400 million paired-end reads were obtained from 82 ethylmethane sulfonate (EMS) induced mutants and 14 wild-type accessions of Jatropha curcas for the detection of Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletions (InDels) by two different approaches (nGBS and ddGBS) on an Illumina HiSeq 2000 sequencer. Using bioinformatics analyses, 1,452 induced SNPs and InDels were identified in coding regions, which were distributed across 995 genes. The predominantly observed mutations were G/C to A/T transitions (64%), while transversions were observed at a lower frequency (36%). Regarding the effect of mutations on gene function, 18% of the mutations were located in intergenic regions. In fact, mutants with the highest number of heterozygous SNPs were found in samples treated with 0.8% EMS for 3 h. Reconstruction of the metabolic pathways showed that in total 16 SNPs were located in six KEGG pathways by nGBS and two pathways by ddGBS. The most highly represented pathways were ether-lipid metabolism and glycerophospholipid metabolism, followed by starch and sucrose metabolism by nGBS and triterpenoid biosynthesis as well as steroid biosynthesis by ddGBS. Furthermore, high genome methylation was observed in J. curcas, which might help to understand the plasticity of the Jatropha genome in response to environmental factors. At last, the results showed that continuously vegetatively propagated tissue is a fast, efficient and accurate method to dissolve chimeras, especially for long-lived plants like J. curcas. Obtained data showed that allelic variations and in silico analyses of gene functions (gene function prediction), which control important traits, could be identified in mutant populations using nGBS and ddGBS. However, the handling of GBS data is more difficult and more challenging than the traditional TILLING strategy in mutated plants, since the Jatropha genome sequence is incomplete, which makes alignment and variant analysis of target sequence reads challenging to perform and interpret. Therefore, providing a complete Jatropha reference genome sequence with high quality should be a priority for any breeding program.
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Affiliation(s)
- Fatemeh Maghuly
- Plant Biotechnology Unit, Department of Biotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stephan Pabinger
- Molecular Diagnostics, Center for Health & Bioresources, Austrian Institute of Technology, Vienna, Austria
| | - Julie Krainer
- Molecular Diagnostics, Center for Health & Bioresources, Austrian Institute of Technology, Vienna, Austria
| | - Margit Laimer
- Plant Biotechnology Unit, Department of Biotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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Gomes TG, Hadi SIIA, Costa Alves GS, Mendonça S, De Siqueira FG, Miller RNG. Current Strategies for the Detoxification of Jatropha curcas Seed Cake: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2510-2522. [PMID: 29498277 DOI: 10.1021/acs.jafc.7b05691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Jatropha curcas is an important oilseed plant, with considerable potential in the development of biodiesel. Although Jatropha seed cake, the byproduct of oil extraction, is a residue rich in nitrogen, phosphorus, potassium, and carbon, with high protein content suitable for application in animal feed, the presence of toxic phorbol esters limits its application in feed supplements and fertilizers. This review summarizes the current methods available for detoxification of this residue, based upon chemical, physical, biological, or combined processes. The advantages and disadvantages of each process are discussed, and future directions involving genomic and proteomic approaches for advancing our understanding of biodegradation processes involving microorganisms are highlighted.
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Affiliation(s)
- Taisa G Gomes
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
| | - Sámed I I A Hadi
- Universidade Federal de Minas Gerais , Instituto de Ciências Biológicas - ICB , Av. Pres. Antônio Carlos, 6627 , 31270-010 , Belo Horizonte , MG , Brazil
| | - Gabriel S Costa Alves
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
| | - Simone Mendonça
- Embrapa Agroenergia, STN-70297-400 , 70297-400 , Brasília , DF , Brazil
| | | | - Robert N G Miller
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
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Xia Z, Zhang S, Wen M, Lu C, Sun Y, Zou M, Wang W. Construction of an ultrahigh-density genetic linkage map for Jatropha curcas L. and identification of QTL for fruit yield. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:3. [PMID: 29321812 PMCID: PMC5759280 DOI: 10.1186/s13068-017-1004-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/22/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND As an important biofuel plant, the demand for higher yield Jatropha curcas L. is rapidly increasing. However, genetic analysis of Jatropha and molecular breeding for higher yield have been hampered by the limited number of molecular markers available. RESULTS An ultrahigh-density linkage map for a Jatropha mapping population of 153 individuals was constructed and covered 1380.58 cM of the Jatropha genome, with average marker density of 0.403 cM. The genetic linkage map consisted of 3422 SNP and indel markers, which clustered into 11 linkage groups. With this map, 13 repeatable QTLs (reQTLs) for fruit yield traits were identified. Ten reQTLs, qNF-1, qNF-2a, qNF-2b, qNF-2c, qNF-3, qNF-4, qNF-6, qNF-7a, qNF-7b and qNF-8, that control the number of fruits (NF) mapped to LGs 1, 2, 3, 4, 6, 7 and 8, whereas three reQTLs, qTWF-1, qTWF-2 and qTWF-3, that control the total weight of fruits (TWF) mapped to LGs 1, 2 and 3, respectively. It is interesting that there are two candidate critical genes, which may regulate Jatropha fruit yield. We also identified three pleiotropic reQTL pairs associated with both the NF and TWF traits. CONCLUSION This study is the first to report an ultrahigh-density Jatropha genetic linkage map construction, and the markers used in this study showed great potential for QTL mapping. Thirteen fruit-yield reQTLs and two important candidate genes were identified based on this linkage map. This genetic linkage map will be a useful tool for the localization of other economically important QTLs and candidate genes for Jatropha.
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Affiliation(s)
- Zhiqiang Xia
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Shengkui Zhang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Mingfu Wen
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Cheng Lu
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Yufang Sun
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Meiling Zou
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Wenquan Wang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
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11
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Amkul K, Laosatit K, Somta P, Shim S, Lee SH, Tanya P, Srinives P. Mapping of QTLs for Seed Phorbol Esters, a Toxic Chemical in Jatropha curcas (L.). Genes (Basel) 2017; 8:genes8080205. [PMID: 28820491 PMCID: PMC5575668 DOI: 10.3390/genes8080205] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/12/2017] [Accepted: 08/17/2017] [Indexed: 11/30/2022] Open
Abstract
Jatropha (Jatropha curcas L.) is an oil-bearing plant that has potential to be cultivated as a biodiesel crop. The seed cake after oil extraction has 40–50% protein that can be used in animal feeds. A major limitation in utilizing the cake is the presence of phorbol esters (PE), a heat-tolerant toxic chemical. To identify the quantitative trait loci (QTLs) for PE, we constructed a genetic linkage map from an F2 population of 95 individuals from a cross “Chai Nat” × “M10” using 143 simple sequence repeat (SSR) markers. M10 is low in seed PE while Chai Nat is high. Seeds from each F2 individual were quantified for PE content by high performance liquid chromatography. A single marker analysis revealed five markers from linkage group 3 (LG3) and nine markers from LG8 associated with seed PE. Inclusive composite interval mapping identified two QTLs, each on LG3 (qPE3.1) and LG8 (qPE8.1) responsible for the PE. qPE3.1 and qPE8.1 accounted for 14.10%, and 15.49% of total variation in seed PE, respectively. Alelle(s) from M10 at qPE3.1 increased seed PE, while at qPE8.1 decreased seed PE. qPE3.1 is a new loci for PE, while qPE8.1 is the same locus with that reported recently for PE.
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Affiliation(s)
- Kitiya Amkul
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand.
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand.
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand.
| | - Sangrea Shim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
| | - Patcharin Tanya
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand.
| | - Peerasak Srinives
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand.
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Vásquez-Mayorga M, Fuchs EJ, Hernández EJ, Herrera F, Hernández J, Moreira I, Arnáez E, Barboza NM. Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica. PeerJ 2017; 5:e2931. [PMID: 28289556 PMCID: PMC5345823 DOI: 10.7717/peerj.2931] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/21/2016] [Indexed: 11/20/2022] Open
Abstract
We estimated the genetic diversity of 50 Jatropha curcas samples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values for J. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f = − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of the Jatropha curcas germplasm bank in Costa Rica.
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Affiliation(s)
- Marcela Vásquez-Mayorga
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica , San Pedro , San José , Costa Rica
| | - Eric J Fuchs
- Escuela de Biología, Universidad de Costa Rica , San Pedro , San José , Costa Rica
| | - Eduardo J Hernández
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica , San Pedro , San José , Costa Rica
| | - Franklin Herrera
- Estación Experimental Fabio Baudrit Moreno, Universidad de Costa Rica , Alajuela , Costa Rica
| | - Jesús Hernández
- Ministerio de Agricultura y Ganadería , San José , Costa Rica
| | - Ileana Moreira
- Escuela de Biología, Instituto Tecnológico de Costa Rica , Cartago , Costa Rica
| | - Elizabeth Arnáez
- Escuela de Biología, Instituto Tecnológico de Costa Rica , Cartago , Costa Rica
| | - Natalia M Barboza
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro, San José, Costa Rica; Escuela de Tecnología de Alimentos, Universidad de Costa Rica, San Pedro, San José, Costa Rica; Centro Nacional en Ciencia y Tecnología de Alimentos, Universidad de Costa Rica, San Pedro, San José, Costa Rica
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13
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Martínez-Díaz Y, González-Rodríguez A, Rico-Ponce HR, Rocha-Ramírez V, Ovando-Medina I, Espinosa-García FJ. Fatty Acid Diversity is Not Associated with Neutral Genetic Diversity in Native Populations of the Biodiesel Plant Jatropha curcas
L. Chem Biodivers 2016; 14. [DOI: 10.1002/cbdv.201600188] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/28/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Yesenia Martínez-Díaz
- Posgrado en Ciencias Biológicas; Universidad Nacional Autónoma de México; Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta CP 58190 Morelia Michoacán México
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad; Universidad Nacional Autónoma de México; Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta CP 58190 Morelia Michoacán México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad; Universidad Nacional Autónoma de México; Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta CP 58190 Morelia Michoacán México
| | - Héctor Rómulo Rico-Ponce
- Centro de Investigación Regional Pacífico Centro; Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias; Campo experimental Valle de Apatzingán, Km. 17.5, Carretera Apatzingán-Cuatro Caminos Km 17.5 CP 6078 Apatzingán Michoacán México
| | - Víctor Rocha-Ramírez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad; Universidad Nacional Autónoma de México; Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta CP 58190 Morelia Michoacán México
| | - Isidro Ovando-Medina
- Instituto de Biociencias; Universidad Autónoma de Chiapas; Carretera a Puerto Madero Km 2.0 CP 30798 Tapachula Chiapas México
| | - Francisco J. Espinosa-García
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad; Universidad Nacional Autónoma de México; Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta CP 58190 Morelia Michoacán México
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Montes JM, Melchinger AE. Domestication and Breeding of Jatropha curcas L. TRENDS IN PLANT SCIENCE 2016; 21:1045-1057. [PMID: 27639951 DOI: 10.1016/j.tplants.2016.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 07/14/2016] [Accepted: 08/17/2016] [Indexed: 05/27/2023]
Abstract
Jatropha curcas L. (jatropha) has a high, untapped potential to contribute towards sustainable production of food and bioenergy, rehabilitation of degraded land, and reduction of atmospheric carbon dioxide. Tremendous progress in jatropha domestication and breeding has been achieved during the past decade. This review: (i) summarizes current knowledge about the domestication and breeding of jatropha; (ii) identifies and prioritizes areas for further research; and (iii) proposes strategies to exploit the full genetic potential of this plant species. Altogether, the outlook is promising for accelerating the domestication of jatropha by applying modern scientific methods and novel technologies developed in plant breeding.
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Affiliation(s)
- Juan M Montes
- JatroSolutions GmbH, Echterdinger Straße 30, 70599 Stuttgart, Germany.
| | - Albrecht E Melchinger
- Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, Fruwirth Straße 21, 70593 Stuttgart, Germany
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15
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Shah M, Soares EL, Lima MLB, Pinheiro CB, Soares AA, Domont GB, Nogueira FCS, Campos FAP. Deep proteome analysis of gerontoplasts from the inner integument of developing seeds of Jatropha curcas. J Proteomics 2016; 143:346-352. [PMID: 26924298 DOI: 10.1016/j.jprot.2016.02.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/15/2016] [Accepted: 02/22/2016] [Indexed: 01/17/2023]
Abstract
UNLABELLED The inner integument of Jatropha curcas seeds is a non-photosynthetic tissue that acts primarily as a conduit for the delivery of nutrients to the embryo and endosperm. In this study we performed a histological and transmission electron microscopy analysis of the inner integument in stages prior to fertilization to 25days after pollination, to establish the structural changes associated with the plastid to gerontoplast transition. This study showed that plastids are subjected to progressive changes, which include the dismantling of the internal membrane system, matrix degradation and the formation of stromule-derived vesicles. A proteome analysis of gerontoplasts isolated from the inner integument at 25days after pollination, resulted in the identification of 1923 proteins, which were involved in a myriad of metabolic functions, such as synthesis of amino acids and fatty acids. Among the identified proteins, were also a number of hydrolases (peptidases, lipases and carbohydrases), which presumably are involved in the ordered dismantling of this organelle to provide additional sources of nutrients for the growing embryo and endosperm. The dataset we provide here may provide a foundation for the study of the proteome changes associated with the plastid to gerontoplast transition in non-photosynthetic tissues. SIGNIFICANCE We describe ultrastructural features of gerontoplasts isolated from the inner integument of developing seeds of Jatropha curcas, together with a deep proteome analysis of these gerontoplasts. This article explores a new aspect of the biology of plastids, namely the ultrastructural and proteome changes associated with the transition plastid to gerontoplast in a non-photosynthetic tissue.
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Affiliation(s)
- Mohibullah Shah
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60455-900, Ceara, Brazil
| | - Emanoella L Soares
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60455-900, Ceara, Brazil
| | - Magda L B Lima
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60455-900, Ceara, Brazil
| | - Camila B Pinheiro
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60455-900, Ceara, Brazil
| | - Arlete A Soares
- Department of Biology, Federal University of Ceara, Fortaleza 60455-900, Ceara, Brazil
| | - Gilberto B Domont
- Proteomic Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Fabio C S Nogueira
- Proteomic Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil.
| | - Francisco A P Campos
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60455-900, Ceara, Brazil.
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16
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Li C, Ng A, Xie L, Mao H, Qiu C, Srinivasan R, Yin Z, Hong Y. Engineering low phorbol ester Jatropha curcas seed by intercepting casbene biosynthesis. PLANT CELL REPORTS 2016; 35:103-114. [PMID: 26441058 DOI: 10.1007/s00299-015-1871-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 08/31/2015] [Accepted: 09/21/2015] [Indexed: 06/05/2023]
Abstract
Casbene is a precursor to phorbol esters and down-regulating casbene synthase effectively reduces phorbol ester biosynthesis. Seed-specific reduction of phorbol ester (PE) helps develop Jatropha seed cake for animal nutrition. Phorbol esters (PEs) are diterpenoids present in some Euphorbiaceae family members like Jatropha curcas L. (Jatropha), a tropical shrub yielding high-quality oil suitable as feedstock for biodiesel and bio jet fuel. Jatropha seed contains up to 40 % of oil and can produce oil together with cake containing high-quality proteins. However, skin-irritating and cancer-promoting PEs make Jatropha cake meal unsuitable for animal nutrition and also raise some safety and environmental concerns on its planting and processing. Two casbene synthase gene (JcCASA163 and JcCASD168) homologues were cloned from Jatropha genome and both genes were highly expressed during seed development. In vitro functional analysis proved casbene synthase activity of JcCASA163 in converting geranylgeranyl diphosphate into casbene which has been speculated to be the precursor to PEs. A seed-specific promoter driving inverted repeats for RNAi interference targeting at either JcCASA163 or both genes could effectively down-regulate casbene synthase gene expression with concurrent marked reduction of PE level (by as much as 85 %) in seeds with no pleiotropic effects observed. Such engineered low PE in seed was heritable and co-segregated with the transgene. Our work implicated casbene synthase in Jatropha PE biosynthesis and provided evidence for casbene being the precursor for PEs. The success in reducing seed PE content through down-regulation of casbene synthase demonstrates the feasibility of intercepting PE biosynthesis in Jatropha seed to help address safety concerns on Jatropha plantation and seed processing and facilitate use of its seed protein for animal nutrition.
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Affiliation(s)
- Chunhong Li
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
| | - Ailing Ng
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Lifen Xie
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
| | - Huizhu Mao
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
| | - Chengxiang Qiu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
| | - Ramachandran Srinivasan
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
| | - Zhongchao Yin
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
| | - Yan Hong
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
- JOil (S) Pte Ltd, 1 Research Link, Singapore, 117604, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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Wu P, Zhou C, Cheng S, Wu Z, Lu W, Han J, Chen Y, Chen Y, Ni P, Wang Y, Xu X, Huang Y, Song C, Wang Z, Shi N, Zhang X, Fang X, Yang Q, Jiang H, Chen Y, Li M, Wang Y, Chen F, Wang J, Wu G. Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:810-21. [PMID: 25603894 DOI: 10.1111/tpj.12761] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 12/18/2014] [Accepted: 01/06/2015] [Indexed: 05/08/2023]
Abstract
The family Euphorbiaceae includes some of the most efficient biomass accumulators. Whole genome sequencing and the development of genetic maps of these species are important components in molecular breeding and genetic improvement. Here we report the draft genome of physic nut (Jatropha curcas L.), a biodiesel plant. The assembled genome has a total length of 320.5 Mbp and contains 27,172 putative protein-coding genes. We established a linkage map containing 1208 markers and anchored the genome assembly (81.7%) to this map to produce 11 pseudochromosomes. After gene family clustering, 15,268 families were identified, of which 13,887 existed in the castor bean genome. Analysis of the genome highlighted specific expansion and contraction of a number of gene families during the evolution of this species, including the ribosome-inactivating proteins and oil biosynthesis pathway enzymes. The genomic sequence and linkage map provide a valuable resource not only for fundamental and applied research on physic nut but also for evolutionary and comparative genomics analysis, particularly in the Euphorbiaceae.
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Affiliation(s)
- Pingzhi Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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18
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King AJ, Montes LR, Clarke JG, Itzep J, Perez CAA, Jongschaap REE, Visser RGF, van Loo EN, Graham IA. Identification of QTL markers contributing to plant growth, oil yield and fatty acid composition in the oilseed crop Jatropha curcas L. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:160. [PMID: 26413159 PMCID: PMC4583170 DOI: 10.1186/s13068-015-0326-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/25/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Economical cultivation of the oilseed crop Jatropha curcas is currently hampered in part due to the non-availability of purpose-bred cultivars. Although genetic maps and genome sequence data exist for this crop, marker-assisted breeding has not yet been implemented due to a lack of available marker-trait association studies. To identify the location of beneficial alleles for use in plant breeding, we performed quantitative trait loci (QTL) analysis for a number of agronomic traits in two biparental mapping populations. RESULTS The mapping populations segregated for a range of traits contributing to oil yield, including plant height, stem diameter, number of branches, total seeds per plant, 100-seed weight, seed oil content and fatty acid composition. QTL were detected for each of these traits and often over multiple years, with some variation in the phenotypic variance explained between different years. In one of the mapping populations where we recorded vegetative traits, we also observed co-localization of QTL for stem diameter and plant height, which were both overdominant, suggesting a possible locus conferring a pleotropic heterosis effect. By using a candidate gene approach and integrating physical mapping data from a recent high-quality release of the Jatropha genome, we were also able to position a large number of genes involved in the biosynthesis of storage lipids onto the genetic map. By comparing the position of these genes with QTL, we were able to detect a number of genes potentially underlying seed traits, including phosphatidate phosphatase genes. CONCLUSIONS The QTL we have identified will serve as a useful starting point in the creation of new varieties of J. curcas with improved agronomic performance for seed and oil productivity. Our ability to physically map a significant proportion of the Jatropha genome sequence onto our genetic map could also prove useful in identifying the genes underlying particular traits, allowing more controlled and precise introgression of desirable alleles and permitting the pyramiding or stacking of multiple QTL.
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Affiliation(s)
- Andrew J. King
- />Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Luis R. Montes
- />Biocombustibles de Guatemala, Guatemala Ciudad, Guatemala
- />Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, The Netherlands
- />Graduate School of Experimental Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Jasper G. Clarke
- />Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Jose Itzep
- />Biocombustibles de Guatemala, Guatemala Ciudad, Guatemala
| | - Cesar A. A. Perez
- />Facultad de Agronomia, Universidad de San Carlos de Guatemala, Edifico T-8 y T-9 Ciudad Universitaria zona 12, Guatemala Cuidad, Guatemala
| | - Raymond E. E. Jongschaap
- />Wageningen UR Agrosystems Research, Wageningen University and Research Centre, PO Box 16, 6708 AP Wageningen, The Netherlands
| | - Richard G. F. Visser
- />Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Eibertus N. van Loo
- />Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Ian A. Graham
- />Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
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19
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Economic and Social Sustainability Performance of Jatropha Projects: Results from Field Surveys in Mozambique, Tanzania and Mali. SUSTAINABILITY 2014. [DOI: 10.3390/su6096203] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Genetic Diversity in Jatropha curcas L. Assessed with SSR and SNP Markers. DIVERSITY-BASEL 2014. [DOI: 10.3390/d6030551] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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King AJ, Brown GD, Gilday AD, Larson TR, Graham IA. Production of bioactive diterpenoids in the euphorbiaceae depends on evolutionarily conserved gene clusters. THE PLANT CELL 2014; 26:3286-98. [PMID: 25172144 PMCID: PMC4371829 DOI: 10.1105/tpc.114.129668] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/01/2014] [Accepted: 08/11/2014] [Indexed: 05/18/2023]
Abstract
The Euphorbiaceae produce a diverse range of diterpenoids, many of which have pharmacological activities. These diterpenoids include ingenol mebutate, which is licensed for the treatment of a precancerous skin condition (actinic keratosis), and phorbol derivatives such as resiniferatoxin and prostratin, which are undergoing investigation for the treatment of severe pain and HIV, respectively. Despite the interest in these diterpenoids, their biosynthesis is poorly understood at present, with the only characterized step being the conversion of geranylgeranyl pyrophosphate into casbene. Here, we report a physical cluster of diterpenoid biosynthetic genes from castor (Ricinus communis), including casbene synthases and cytochrome P450s from the CYP726A subfamily. CYP726A14, CYP726A17, and CYP726A18 were able to catalyze 5-oxidation of casbene, a conserved oxidation step in the biosynthesis of this family of medicinally important diterpenoids. CYP726A16 catalyzed 7,8-epoxidation of 5-keto-casbene and CYP726A15 catalyzed 5-oxidation of neocembrene. Evidence of similar gene clustering was also found in two other Euphorbiaceae, including Euphorbia peplus, the source organism of ingenol mebutate. These results demonstrate conservation of gene clusters at the higher taxonomic level of the plant family and that this phenomenon could prove useful in further elucidating diterpenoid biosynthetic pathways.
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Affiliation(s)
- Andrew J King
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Geoffrey D Brown
- Department of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
| | - Alison D Gilday
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Tony R Larson
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Ian A Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
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Soares EL, Shah M, Soares AA, Costa JH, Carvalho P, Domont GB, Nogueira FCS, Campos FAP. Proteome analysis of the inner integument from developing Jatropha curcas L. seeds. J Proteome Res 2014; 13:3562-70. [PMID: 25010673 DOI: 10.1021/pr5004505] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this study, we performed a systematic proteomic analysis of the inner integument from developing seeds of Jatropha curcas and further explored the protein machinery responsible for generating the carbon and nitrogen sources to feed the growing embryo and endosperm. The inner integument of developing seeds was dissected into two sections called distal and proximal, and proteins were extracted from these sections and from the whole integument and analyzed using an EASY-nanoLC system coupled to an ESI-LTQ-Orbitrap Velos mass spectrometer. We identified 1526, 1192, and 1062 proteins from the proximal, distal, and whole inner integuments, respectively. The identifications include those of peptidases and other hydrolytic enzymes that play a key role in developmental programmed cell death and proteins associated with the cell-wall architecture and modification. Because many of these proteins are differentially expressed within the integument cell layers, these findings suggest that the cells mobilize an array of hydrolases to produce carbon and nitrogen sources from proteins, carbohydrates, and lipids available within the cells. Not least, the identification of several classes of seed storage proteins in the inner integument provides additional evidence of the role of the seed coat as a transient source of reserves for the growing embryo and endosperm.
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Affiliation(s)
- Emanoella L Soares
- Department of Biochemistry and Molecular Biology, Federal University of Ceara , Campus do Pici - Bl. 907, Fortaleza 60455-900, Brazil
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