Inhibition of flowering by gibberellins in the woody plant Jatropha curcas is restored by overexpression of JcFT.

Jatropha curcas (J. curcas) is a perennial oil-seed plant with vigorous vegetative growth but relatively poor reproductive growth and low seed yield. Gibberellins (GAs) promotes flowering in most annual plants but inhibits flowering in many woody plants, including J. curcas. However, the underlying mechanisms of GA inhibits flowering in perennial woody plants remain unclear. Here, we found that overexpression of the GA biosynthesis gene JcGA20ox1 inhibits flowering in J. curcas and in J. curcas × J. integerrima hybrids. Consistent with this finding, overexpression of the GA catabolic gene JcGA2ox6 promotes flowering in J. curcas. qRTPCR revealed that inhibits floral transition by overexpressing JcGA20ox1 resulted from a decrease in the expression of JcFT and other flowering-related genes, which was restored by overexpressing JcFT in J. curcas. Overexpression of JcGA20ox1 or JcGA2ox6 reduced seed yield, but overexpression of JcFT significantly increased seed yield. Furthermore, hybridization experiments showed that the reduction in seed yield caused by overexpression of JcGA20ox1 or JcGA2ox6 was partially restored by the overexpression of JcFT. In addition, JcGA20ox1, JcGA2ox6 and JcFT were also found to be involved in the regulation of seed oil content and endosperm development. In conclusion, our study revealed that the inhibitory effect of GA on flowering is mediated through JcFT and demonstrated the effects of JcGA20ox1, JcGA2ox6 and JcFT on agronomic traits in J. curcas. This study also indicates the potential value of GA metabolism genes and JcFT in the breeding of new varieties of woody oil-seed plants.

A comparative appraisal of three important oil yielding plants for their biodiesel potential.

In the present scenario, alternative energy sources are required to achieve the future economic prosperity where shortage of fossil fuels will be a limiting factor and hamper the global economic growth. Therefore, interest in biofuel is increasing continuously. The best way of sustainable development is fossil fuel supplementation with biodiesel to reduce the fossil fuel demand. Biodiesel is a clean burning, ester-based, oxygenated fuel derived from natural and renewable sources. Till now, majority of the people have worked on the biodiesel derived from edible oil. Instead of using edible oil, non-edible oil needs to be explored as feedstock for biofuel because half of the world's population is unable to afford the food oil as feedstock for fuel production. Looking at the significance of biodiesel and the resources of biofuel, in this paper, a comparative exhaustive study has been reported with for three important plants, namely Jatropha curcas, Pongemia pinnata and Balanites aegyptiaca. These plants were selected based on their biodiesel potential, availability, cultivation practices and general information available. The present study involves scientometric publications, comparison of fatty acid composition and biodiesel parameters. We have also compared climatic conditions for the growth of the plants, economic feasibility of biodiesel production and other ecological services. The study paves a way for sustainable solution to policy makers and foresters looking for selection of plant species as bioenergy resource.

Increasing selection gain and accuracy of harvest prediction models in Jatropha through genome-wide selection.

Genome-wide selection (GWS) has been becoming an essential tool in the genetic breeding of long-life species, as it increases the gain per time unit. This study had a hypothesis that GWS is a tool that can decrease the breeding cycle in Jatropha. Our objective was to compare GWS with phenotypic selection in terms of accuracy and efficiency over three harvests. Models were developed throughout the harvests to evaluate their applicability in predicting genetic values in later harvests. For this purpose, 386 individuals of the breeding population obtained from crossings between 42 parents were evaluated. The population was evaluated in random block design, with six replicates over three harvests. The genetic effects of markers were predicted in the population using 811 SNP's markers with call rate = 95% and minor allele frequency (MAF) > 4%. GWS enables gains of 108 to 346% over the phenotypic selection, with a 50% reduction in the selection cycle. This technique has potential for the Jatropha breeding since it allows the accurate obtaining of GEBV and higher efficiency compared to the phenotypic selection by reducing the time necessary to complete the selection cycle. In order to apply GWS in the first harvests, a large number of individuals in the breeding population are needed. In the case of few individuals in the population, it is recommended to perform a larger number of harvests.

Genome-wide characterization of bZIP transcription factors and their expression patterns in response to drought and salinity stress in Jatropha curcas.

The basic leucine zipper (bZIP) family is one of the largest families of transcription factors (TFs) in plants and is responsible for various functions, including regulating development and responses to abiotic/biotic stresses. However, the roles of bZIPs in the regulation of responses to drought stress and salinity stress remain poorly understood in Jatropha curcas L., a biodiesel crop. In the present study, 50 JcbZIP genes were identified and classified into ten groups. Cis-element analysis indicated that JcbZIP genes are associated with abiotic stress. Gene expression patterns and quantitative real-time PCR (qRT-PCR) showed that four JcbZIP genes (JcbZIPs 34, 36, 49 and 50) are key resistance-related genes under both drought and salinity stress conditions. On the basis of the results of cis-element and phylogenetic analyses, JcbZIP49 and JcbZIP50 are likely involved in responses to drought and salinity stress; moreover, JcbZIP34 and JcbZIP36 might also play important roles in seed development and response to abiotic stress. These findings advance our understanding of the comprehensive characteristics of JcbZIP genes and provide new insights for functional validation in the further.

Jatropha curcas, a Novel Crop for Developing the Marginal Lands.

Jatropha curcas L. has more attention from researchers and policymakers as an inexpensive source for produce biofuel to reduce environmental pollution by fossil fuel in the next decades without competing for lands and freshwater currently used for food production. Jatropha is a perennial deciduous, succulent oilseed shrub, belonging to family Euphorbiaceae. It is native to Central and South America. It is a multipurpose shrub, each part of the plant can be used for various purposes, Jatropha produces flowers throughout the year and enables multiple harvests, while, in arid and semi-arid regions it is harvesting twice time per year.Jatropha is a drought-tolerant plant that could be growing under malnutrition conditions, and in different climatic conditions; therefore, it is proper plant for developing marginal lands and rural areas.Due to the growing demand for biofuel, jatropha cultivation has received more attention to providing seeds. While, there are various aspects of using jatropha include use as a traditional medicine for treating skin ailments, as a hedge for protecting other crops, to reduce soil degradation, combating desertification, and deforestation, also, jatropha cultivation protects the environment through using wastewater in irrigation and reduce sequester carbon dioxide.Conventional propagation of Jatropha propagated by seeds or stem cutting which is a more satisfactory technique to produce high-yielding seedlings, while, tissue culture method used in propagation but on small scale.Jatropha curcas L. contains mixtures of numerous active substances in all parts of the plant, which are used as biopesticides, larvicides, fungicide, and nematicide; also extracts are used as pesticides for whiteflies and termites.Jatropha crude oil is used for industrial purposes like manufacturing candles, soaps, varnishes, and as a lubricant; also press seedcake is used to produce biogas and organic fertilizers. Jatropha propagated by seeds or stem cutting which is more applicable techniques to produce high-yielding seedlings, also, tissue culture method used in propagation but on small scale for scientific work.

Multiple-trait model through Bayesian inference applied to Jatropha curcas breeding for bioenergy.

Multiple-trait model tends to be the best alternative for the analysis of repeated measures, since they consider the genetic and residual correlations between measures and improve the selective accuracy. Thus, the objective of this study was to propose a multiple-trait Bayesian model for repeated measures analysis in Jatropha curcas breeding for bioenergy. To this end, the grain yield trait of 730 individuals of 73 half-sib families was evaluated over six harvests. The Markov Chain Monte Carlo algorithm was used to estimate genetic parameters and genetic values. Genetic correlation between pairs of measures were estimated and four selective intensities (27.4%, 20.5%, 13.7%, and 6.9%) were used to compute the selection gains. The full model was selected based on deviance information criterion. Genetic correlations of low (ρg ≤ 0.33), moderate (0.34 ≤ ρg ≤ 0.66), and high magnitude (ρg ≥ 0.67) were observed between pairs of harvests. Bayesian analyses provide robust inference of genetic parameters and genetic values, with high selective accuracies. In summary, the multiple-trait Bayesian model allowed the reliable selection of superior Jatropha curcas progenies. Therefore, we recommend this model to genetic evaluation of Jatropha curcas genotypes, and its generalization, in other perennials.

Silencing of the Ortholog of DEFECTIVE IN ANTHER DEHISCENCE 1 Gene in the Woody Perennial Jatropha curcas Alters Flower and Fruit Development.

DEFECTIVE IN ANTHER DEHISCENCE 1 (DAD1), a phospholipase A1, utilizes galactolipids (18:3) to generate α-linolenic acid (ALA) in the initial step of jasmonic acid (JA) biosynthesis in Arabidopsis thaliana. In this study, we isolated the JcDAD1 gene, an ortholog of Arabidopsis DAD1 in Jatropha curcas, and found that it is mainly expressed in the stems, roots, and male flowers of Jatropha. JcDAD1-RNAi transgenic plants with low endogenous jasmonate levels in inflorescences exhibited more and larger flowers, as well as a few abortive female flowers, although anther and pollen development were normal. In addition, fruit number was increased and the seed size, weight, and oil contents were reduced in the transgenic Jatropha plants. These results indicate that JcDAD1 regulates the development of flowers and fruits through the JA biosynthesis pathway, but does not alter androecium development in Jatropha. These findings strengthen our understanding of the roles of JA and DAD1 in the regulation of floral development in woody perennial plants.

Identification and characterization of long non-coding RNA (lncRNA) in the developing seeds of Jatropha curcas.

Long non-coding RNAs (lncRNAs) play critical roles in plant development. However, the information of lncRNAs in Jatropha curcas remains largely unexplored. Thus, an attempt has been made in J. curcas to identify 1,850 lncRNAs based on deep sequencing of developing seeds at three typical stages. About ten percent lncRNAs (196 lncRNAs) were differentially expressed lncRNAs during seed developing process. Together with reverse transcription quantitative real-time PCR, the lncRNA expression analyses revealed the stage-specific expression patterns of some novel lncRNAs in J. curcas. The target genes of lncRNAs were annotated for their roles in various biological processes such as gene expression, metabolism, and cell growth. Besides, 10 lncRNAs were identified as the precursors of microRNAs and 26 lncRNAs were predicted to be the targets of Jatropha miRNAs. A total of 31 key lncRNAs play critical roles in the seed developing process in the context of cell growth and development, lipid metabolism, and seed maturation. Our study provides the first systematic study of lncRNAs in the developing seeds of J. curcas and facilitates the functional research of plant lncRNAs and the regulation of seed development.

Genome-wide characterization of the SPL gene family involved in the age development of Jatropha curcas.

BACKGROUND: SPL (SQUAMOSA-promoter binding protein-like) proteins form a large family of plant-specific transcription factors that play essential roles in various aspects of plant growth and development. They are potentially important candidates for genetic improvement of agronomic traits. However, there were limited information about the SPL genes in Jatropha curcas, an important biofuel plant. RESULTS: In Jatropha, 15 JcSPL genes were identified. Phylogenetic analysis revealed that most of the JcSPLs were closely related to SPLs from woody plant rather than herbaceous plant and distantly related to monocotyledon SPLs. Gene structure, conserved motif and repetitive sequence analysis indicated diverse and specific functions of some JcSPL genes. By combination of target prediction and degradome sequencing analysis, 10 of the 15 JcSPLs were shown to be targets of JcmiR156. Quantitative PCR analysis showed diversified spatial-temporal expression patterns of JcSPLs. It is interesting that the expression levels of JcSPL3 were the highest in all tissues examined in 7- or 10-year-old plants and exhibited increasing trend with plant age, suggesting its important role in the regulation of age development in Jatropha. Overexpression of JcSPL3 in Arabidopsis resulted in earlier flowering time, shorter silique length and reduced biomass of roots. CONCLUSIONS: Through comprehensive and systematic analysis of phylogenetic relationships, conserved motifs, gene structures, chromosomal locations, repetitive sequence and expression patterns, 15 JcSPL genes were identified in Jatropha and characterized in great detail. These results provide deep insight into the evolutionary origin and biological significance of plant SPLs and lay the foundation for further functional characterization of JcSPLs with the purpose of genetic improvement in Jatropha.

Quantitative Proteome Analysis of Jatropha curcas L. Genotypes with Contrasting Levels of Phorbol Esters.

The phorbol esters in the seeds of Jatropha curcas are a major hindrance to the full exploitation of the potential of this oil crop as a source of raw material for the production of biodiesel. Here, various quantitative proteomic strategies are used to establish the proteomes of roots, leaves, and endosperm of two genotypes of J. curcas with contrasting levels of phorbol esters in the seeds. In total 4532, 1775, and 503 proteins are identified respectively in roots, leaves, and endosperm, comprising 5068 unique proteins; of this total, 185 are differentially abundant in roots, 72 in leaves, and 20 in the endosperm. The biosynthetic pathways for flavonoids and terpenoids are well represented in roots, including the complete set of proteins for the mevalonate and non-mevalonate/Deoxyxylulose 5-Phosphate pathways, and proteins involved in the branches which lead to the synthesis tricyclic diterpenoids and gibberellins. Also, casbene synthase which catalyzes the first committed step in the biosynthesis of tigliane-type diterpenes is identified in roots of both genotypes, but not in leaves and endosperm. This dataset will be a valuable resource to explore the biochemical basis of the low toxicity of Jatropha genotypes with low concentration of phorbol esters in the seeds.

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas.

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.

De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas.

BACKGROUND: Chromatin architecture is an essential factor regulating gene transcription in different cell types and developmental phases. However, studies on chromatin architecture in perennial woody plants and on the function of chromatin organization in sex determination have not been reported. RESULTS: Here, we produced a chromosome-scale de novo genome assembly of the woody plant Jatropha curcas with a total length of 379.5 Mb and a scaffold N50 of 30.7 Mb using Pacific Biosciences long reads combined with genome-wide chromosome conformation capture (Hi-C) technology. Based on this high-quality reference genome, we detected chromatin architecture differences between monoecious and gynoecious inflorescence buds of Jatropha. Differentially expressed genes were significantly enriched in the changed A/B compartments and topologically associated domain regions and occurred preferentially in differential contact regions between monoecious and gynoecious inflorescence buds. Twelve differentially expressed genes related to flower development or hormone synthesis displayed significantly different genomic interaction patterns in monoecious and gynoecious inflorescence buds. These results demonstrate that chromatin organization participates in the regulation of gene transcription during the process of sex differentiation in Jatropha. CONCLUSIONS: We have revealed the features of chromatin architecture in perennial woody plants and investigated the possible function of chromatin organization in Jatropha sex differentiation. These findings will facilitate understanding of the regulatory mechanisms of sex determination in higher plants.

Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas.

BACKGROUND: In higher plants, inflorescence architecture is an important agronomic trait directly determining seed yield. However, little information is available on the regulatory mechanism of inflorescence development in perennial woody plants. Based on two inflorescence branching mutants, we investigated the transcriptome differences in inflorescence buds between two mutants and wild-type (WT) plants by RNA-Seq to identify the genes and regulatory networks controlling inflorescence architecture in Jatropha curcas L., a perennial woody plant belonging to Euphorbiaceae. RESULTS: Two inflorescence branching mutants were identified in germplasm collection of Jatropha. The duo xiao hua (dxh) mutant has a seven-order branch inflorescence, and the gynoecy (g) mutant has a three-order branch inflorescence, while WT Jatropha has predominantly four-order branch inflorescence, occasionally the three- or five-order branch inflorescences in fields. Using weighted gene correlation network analysis (WGCNA), we identified several hub genes involved in the cytokinin metabolic pathway from modules highly associated with inflorescence phenotypes. Among them, Jatropha ADENOSINE KINASE 2 (JcADK2), ADENINE PHOSPHORIBOSYL TRANSFERASE 1 (JcAPT1), CYTOKININ OXIDASE 3 (JcCKX3), ISOPENTENYLTRANSFERASE 5 (JcIPT5), LONELY GUY 3 (JcLOG3) and JcLOG5 may participate in cytokinin metabolic pathway in Jatropha. Consistently, exogenous application of cytokinin (6-benzyladenine, 6-BA) on inflorescence buds induced high-branch inflorescence phenotype in both low-branch inflorescence mutant (g) and WT plants. These results suggested that cytokinin is an important regulator in controlling inflorescence branching in Jatropha. In addition, comparative transcriptome analysis showed that Arabidopsis homologous genes Jatropha AGAMOUS-LIKE 6 (JcAGL6), JcAGL24, FRUITFUL (JcFUL), LEAFY (JcLFY), SEPALLATAs (JcSEPs), TERMINAL FLOWER 1 (JcTFL1), and WUSCHEL-RELATED HOMEOBOX 3 (JcWOX3), were differentially expressed in inflorescence buds between dxh and g mutants and WT plants, indicating that they may participate in inflorescence development in Jatropha. The expression of JcTFL1 was downregulated, while the expression of JcLFY and JcAP1 were upregulated in inflorescences in low-branch g mutant. CONCLUSIONS: Cytokinin is an important regulator in controlling inflorescence branching in Jatropha. The regulation of inflorescence architecture by the genes involved in floral development, including TFL1, LFY and AP1, may be conservative in Jatropha and Arabidopsis. Our results provide helpful information for elucidating the regulatory mechanism of inflorescence architecture in Jatropha.

Ecophysiological responses of Jatropha curcas L. seedlings to simulated acid rain under different soil types.

Acid rain is a global environmental problem. Acid rain can affect plants directly by damaging the leaves and indirectly by soil acidifying. Many studies have been conducted to investigate the impacts of acid rain on plant under a single soil type. However, there is little information on the effect of acid rain on plant under different soil types. Jatropha curcas L. is an energy plant widely distributed in acid rain pollution area with various soil types. In this study, we investigated the effects of acid rain (pH2.5, pH3.5, pH4.5, pH5.6) on the growth, physiology, nutrient elements and bacterial community of J. curcas seedlings under different soil types [Red soils (RS), Yellow soils (YS), Yellow-brown soils (YBS), and Purplish soils (PS)]. Acid rain and soil types significantly influence the growth of J. curcas seedlings, and there was a significant interaction between acid rain and soil types. Acid rain (pH 4.5) was beneficial to the growth of J. curcas seedlings, whereas acid rain (pH 2.5 or 3.5) inhibited growth of J. curcas seedlings. The growth of J. curcas seedlings could resist the stress of acid rain by scavenging and detoxification of active oxygen species in leaves. Combined with the increase in relative growth rate of seedlings treated with simulated acid rain at pH 4.5, we inferred that K can stimulate the growth of seedlings. The lower soil pH, cation exchange capacity and base saturation had stronger inhibitory effects on growth of J. curcas seedlings. YBS and PS were beneficial for growth of J. curcas seedlings by higher buffering capacity under acid rain treatments. The phylum Proteobacteria was found to predominate in rhizosphere soils. YBS was favorable to support Proteobacteria growth and reproduction. The redundancy analysis showed that the Cyanobacteria were favorable to growth of J. curcas seedlings.

Ectopic Expression of Jatropha curcas TREHALOSE-6-PHOSPHATE PHOSPHATASE J Causes Late-Flowering and Heterostylous Phenotypes in Arabidopsis but not in Jatropha.

Trehalose-6-phosphate (T6P) phosphatase (TPP), a dephosphorylating enzyme, catalyzes the dephosphorylation of T6P, generating trehalose. In Jatropha, we found six members of the TPP family. Five of them JcTPPA, JcTPPC, JcTPPD, JcTPPG, and JcTPPJ are highly expressed in female flowers or male flowers, or both, suggesting that members of the JcTPP family may participate in flower development in Jatropha. The wide expression of JcTPPJ gene in various organs implied its versatile roles and thus was chosen for unraveling its biological functions during developmental process. We constructed an overexpression vector of JcTPPJ cDNA driven by the cauliflower mosaic virus (CaMV) 35S promoter for genetic transformation. Compared with control Arabidopsis plants, 35S:JcTPPJ transgenic Arabidopsis plants presented greater sucrose contents in their inflorescences and displayed late-flowering and heterostylous phenotypes. Exogenous application of sucrose to the inflorescence buds of wild-type Arabidopsis repressed the development of the perianth and filaments, with a phenocopy of the 35S:JcTPPJ transgenic Arabidopsis. These results suggested that the significantly increased sucrose level in the inflorescence caused (or induced) by JcTTPJ overexpression, was responsible for the formation of heterostylous flower phenotype. However, 35S:JcTPPJ transgenic Jatropha displayed no obvious phenotypic changes, implying that JcTPPJ alone may not be sufficient for regulating flower development in Jatropha. Our results are helpful for understanding the function of TPPs, which may regulate flower organ development by manipulating the sucrose status in plants.

Identifying High Confidence microRNAs in the Developing Seeds of Jatropha curcas.

MicroRNAs (miRNAs) are endogenously short noncoding regulatory RNAs implicated in plant development and physiology. Nine small RNA (sRNA) libraries from three typical seed developmental stages (young, intermediate, and mature) were generated by deep sequencing to identify the miRNAs of J. curcas, a potential oilseed crop for the production of renewable oil. Strict criteria were adopted to identify 93 high confidence miRNAs including 48 conserved miRNAs and 45 novel miRNAs. Target genes of these miRNAs were involved in a broad range of physiological functions, including gene expression regulation, primary & secondary metabolism, growth & development, signal transduction, and stress response. About one third (29 out of 93) miRNAs showed significant changes in expression levels during the seed developmental process, indicating that the miRNAs might regulate its targets by their changes of transcription levels in seed development. However, most miRNAs were found differentially expressed in the late stage of seed development, suggesting that miRNAs play more important roles in the stage when seed accumulating organic matters and suffering dehydration stress. This study presents the first large scale identification of high confidence miRNAs in the developing seeds of J. curcas.

Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits.

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.

miR172 Regulates both Vegetative and Reproductive Development in the Perennial Woody Plant Jatropha curcas.

Jatropha curcas is a promising feedstock for biofuel production because its oil is highly suitable for processing bio-jet fuels and biodiesel. However, Jatropha exhibits a long juvenile stage in subtropical areas. miR172, a conserved small non-protein-coding RNA molecule with 21 nucleotides, regulates a wide range of developmental processes. To date, however, no studies have examined the function of miR172 in Jatropha. There are five miR172 precursors encoding two mature miR172s in Jatropha, which are expressed in all tissues, with the highest expression level in leaves, and the levels are up-regulated with age. Overexpression of JcmiR172a resulted in early flowering, abnormal flowers, and altered leaf morphology in transgenic Arabidopsis and Jatropha. The expression levels of miR172 target genes were down-regulated, and the flower identity genes were up-regulated in the JcmiR172a-overexpressing transgenic plants. Interestingly, we showed that JcmiR172 might be involved in regulation of stem vascular development through manipulating the expression of cellulose and lignin biosynthesis genes. Overexpression of JcmiR172a enhanced xylem development and reduced phloem and pith development. This study helped elucidate the functions of miR172 in perennial plants, a known age-related miRNA involved in the regulation of perennial plant phase change and organ development.

Genome-wide Identification of Jatropha curcas MAPK, MAPKK, and MAPKKK Gene Families and Their Expression Profile Under Cold Stress.

Mitogen-activated protein kinase (MAPK) cascades are fundamental signal transduction modules in all eukaryotic organisms, controlling cell division, growth, development, and hormone signaling. Additionally, they can be activated in response to a variety of biotic and abiotic stressors. Although the evolution and expression patterns of MAPK cascade families have been systematically investigated in several model plants (e.g., Arabidopsis, rice, and poplar), we still know very little about MAPK, MAPKK, and MAPKKK families in Jatropha curcas, an economically important species. Therefore, this study performed genome-wide identification and transcriptional expression analysis of these three families in J. curcas. We identified 12 J. curcas MAPK (JcMAPKs), 5 JcMAPKKs, and 65 JcMAPKKKs. Phylogenetic analysis classified all JcMAPKs and JcMAPKKs into four subgroups, whereas JcMAPKKKs were grouped into three subfamilies (MEKK, RAF, and ZIK). Similarities in exon/intron structures supported the evolutionary relationships within subgroups and subfamilies. Conserved motif analysis indicated that all J. curcas MAPK cascades possessed typical, 200-300 amino-acid protein kinase domains. MAPK cascade genes were presented throughout all 11 chromosomes. Gene duplication analysis suggested that after JcMAPK and JcMAPKKK diverged, 3 and 19 tandem duplicates occurred under strong purifying selection. Furthermore, RNA-seq and qRT-PCR analyses revealed that some MAPK cascade genes are predominantly expressed in specific tissues. Moreover, their expression levels significantly increased under cold treatment. Our results should provide insight into the roles of MAPK cascade genes in regulating J. curcas stress responses and in hormonal signal transduction. Furthermore, these data have important applications in the genetic improvement of J. curcas.

Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut.

Auxin response factors (ARF) are important transcription factors which mediate the transcription of auxin responsive genes by binding directly to auxin response elements (AuxREs) found in the promoter regions of these genes. To date, no information has been available about the genome-wide organization of the ARF transcription factor family in physic nut. In this study, 17 ARF genes (JcARFs) are identified in the physic nut genome. A detailed investigation into the physic nut ARF gene family is performed, including analysis of the exon-intron structure, conserved domains, conserved motifs, phylogeny, chromosomal locations, potential small RNA targets and expression profiles under various conditions. Phylogenetic analysis suggests that the 17 JcARF proteins are clustered into 6 groups, and most JcARF proteins from the physic nut reveal closer relationships with those from Arabidopsis than those from rice. Of the 17 JcARF genes, eight are predicted to be the potential targets of small RNAs; most of the genes show differential patterns of expression among four tissues (root, stem cortex, leaf, and seed); and qRT-PCR indicates that the expression of all JcARF genes is inhibited or induced in response to exogenous auxin. Expression profile analysis based on RNA-seq data shows that in leaves, 11 of the JcARF genes respond to at least one abiotic stressor (drought and/or salinity) at, as a minimum, at least one time point. Our results provide valuable information for further studies on the roles of JcARF genes in regulating physic nut's growth, development and responses to abiotic stress.