Transcriptome Analysis Revealed the Dynamic Oil Accumulation in \u3ci\u3eSymplocos paniculata\u3c/i\u3e Fruit

Background Symplocos paniculata, asiatic sweetleaf or sapphire berry, is a widespread shrub or small tree from Symplocaceae with high oil content and excellent fatty acid composition in fruit. It has been used as feedstocks for biodiesel and cooking oil production in China. Little transcriptome information is available on the regulatory molecular mechanism of oil accumulation at different fruit development stages. Results The transcriptome at four different stages of fruit development (10, 80,140, and 170 days after flowering) of S. paniculata were analyzed. Approximately 28 million high quality clean reads were generated. These reads were trimmed and assembled into 182,904 non-redundant putative transcripts with a mean length of 592.91 bp and N50 length of 785 bp, respectively. Based on the functional annotation through Basic Local Alignment Search Tool (BLAST) with public protein database, the key enzymes involved in lipid metabolism were identified, and a schematic diagram of the pathway and temporal expression patterns of lipid metabolism was established. About 13,939 differentially expressed unigenes (DEGs) were screened out using differentially expressed sequencing (DESeq) method. The transcriptional regulatory patterns of the identified enzymes were highly related to the dynamic oil accumulation along with the fruit development of S. paniculata. In addition, quantitative real-time PCR (qRT-PCR) of six vital genes was significantly correlated with DESeq data. Conclusions The transcriptome sequences obtained and deposited in NCBI would enrich the public database and provide an unprecedented resource for the discovery of the genes associated with lipid metabolism pathway in S. paniculata. Results in this study will lay the foundation for exploring transcriptional regulatory profiles, elucidating molecular regulatory mechanisms, and accelerating genetic engineering process to improve the yield and quality of seed oil of S. paniculata. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3275-0) contains supplementary material, which is available to authorized users

Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit

BACKGROUND: Symplocos paniculata, asiatic sweetleaf or sapphire berry, is a widespread shrub or small tree from Symplocaceae with high oil content and excellent fatty acid composition in fruit. It has been used as feedstocks for biodiesel and cooking oil production in China. Little transcriptome information is available on the regulatory molecular mechanism of oil accumulation at different fruit development stages. RESULTS: The transcriptome at four different stages of fruit development (10, 80,140, and 170 days after flowering) of S. paniculata were analyzed. Approximately 28 million high quality clean reads were generated. These reads were trimmed and assembled into 182,904 non-redundant putative transcripts with a mean length of 592.91 bp and N50 length of 785 bp, respectively. Based on the functional annotation through Basic Local Alignment Search Tool (BLAST) with public protein database, the key enzymes involved in lipid metabolism were identified, and a schematic diagram of the pathway and temporal expression patterns of lipid metabolism was established. About 13,939 differentially expressed unigenes (DEGs) were screened out using differentially expressed sequencing (DESeq) method. The transcriptional regulatory patterns of the identified enzymes were highly related to the dynamic oil accumulation along with the fruit development of S. paniculata. In addition, quantitative real-time PCR (qRT-PCR) of six vital genes was significantly correlated with DESeq data. CONCLUSIONS: The transcriptome sequences obtained and deposited in NCBI would enrich the public database and provide an unprecedented resource for the discovery of the genes associated with lipid metabolism pathway in S. paniculata. Results in this study will lay the foundation for exploring transcriptional regulatory profiles, elucidating molecular regulatory mechanisms, and accelerating genetic engineering process to improve the yield and quality of seed oil of S. paniculata. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3275-0) contains supplementary material, which is available to authorized users

Transcriptome-based Gene Networks for Systems-level Analysis of Plant Gene Functions

Present day genomic technologies are evolving at an unprecedented rate, allowing interrogation of cellular activities with increasing breadth and depth. However, we know very little about how the genome functions and what the identified genes do. The lack of functional annotations of genes greatly limits the post-analytical interpretation of new high throughput genomic datasets. For plant biologists, the problem is much severe. Less than 50% of all the identified genes in the model plant Arabidopsis thaliana, and only about 20% of all genes in the crop model Oryza sativa have some aspects of their functions assigned. Therefore, there is an urgent need to develop innovative methods to predict and expand on the currently available functional annotations of plant genes. With open-access catching the ‘pulse’ of modern day molecular research, an integration of the copious amount of transcriptome datasets allows rapid prediction of gene functions in specific biological contexts, which provide added evidence over traditional homology-based functional inference. The main goal of this dissertation was to develop data analysis strategies and tools broadly applicable in systems biology research. Two user friendly interactive web applications are presented: The Rice Regulatory Network (RRN) captures an abiotic-stress conditioned gene regulatory network designed to facilitate the identification of transcription factor targets during induction of various environmental stresses. The Arabidopsis Seed Active Network (SANe) is a transcriptional regulatory network that encapsulates various aspects of seed formation, including embryogenesis, endosperm development and seed-coat formation. Further, an edge-set enrichment analysis algorithm is proposed that uses network density as a parameter to estimate the gain or loss in correlation of pathways between two conditionally independent coexpression networks

Recent Advances in Genetics and Breeding of Major Staple Food Crops

To meet the global food demand of an increasing population, food production has to be increased by 60% by 2050. The main production constraints, such as climate change, biotic stresses, abiotic stresses, soil nutrition deficiency problems, problematic soils, etc., have to be addressed on an urgent basis. More than 50% of human calories are from three major cereals: rice, wheat, and maize. The harnessing of genetic diversity by novel allele mining assisted by recent advances in biotechnological and bioinformatics tools will enhance the utilization of the hidden treasures in the gene bank. Technological advances in plant breeding will provide some solutions for the biofortification, stress resistance, yield potential, and quality improvement in staple crops. The elucidation of the genetic, physiological, and molecular basis of useful traits and the improvement of the improved donors containing multiple traits are key activities for variety development. High-throughput genotyping systems assisted by bioinformatics and data science provide efficient and easy tools for geneticists and breeders. Recently, new breeding techniques applied in some food crops have become game-changers in the global food crop market. With this background, we invited 18 eminent researchers working on food crops from across the world to contribute their high-quality original research manuscripts. The research studies covered modern food crop genetics and breeding

Fruit dehiscence in Brassicas

Dehiscence is a means by which some wild plants release their seeds. In Brassicas the mature fruit or 'pod', strictly a silique, releases seed by a sometimes explosive mechanism triggered by mechanical pressure and referred to as 'shatter'. This mechanism is a problem in Brassica crop plants and results in loss of seed, and hence loss of revenue, during harvesting. This problem is further compounded by the distribution of volunteers which contaminate future crops and the environment. The post-fertilisation development of the carpel wall of a number of Brassica species has been examined including, a range of Arabidopsis ecotypes and mutants, and fruits from two other Brassicas, Brassica napus and Brassica juncea, which exhibit differences in the dehiscence characteristic. These have been studied by a combination of cytological, cytochemical and molecular techniques. Following fertilisation, dehiscence zones form at the carpel margins, separating the carpel walls from the replum and forming two valves. Cells within the dehiscence zone exhibit reduced cellular cohesion due to breakdown of the middle lamella. Differentiation of the carpel wall layers results in a thickened exocarp, a senescing mesocarp, and modification of the endocarp layers in which the inner layer Enϸ lignifies whilst Enα collapses. It is proposed that the patterns of differentiation result in the development of the dehiscence mechanism. The dehiscence mechanism and pod 'shatter' is a result of; 1) weakening of valve attachment due to reduced cell cohesion in the dehiscence zone, and, 2) tensions which develop within the carpel walls due to desiccation and shrinkage of the mesocarp which is attached to a thickened, non-shrinking endocarp.The fruits from all of the Arabidopsis ecotypes examined exhibited a similar pattern of carpel wall development and similar dehiscence characteristics. Light microscopical examination of the fruits of Brassica napus and Brassica juncea which do not shatter as easily as those of Arabidopsis showed a different pattern of endocarp development in the post fertilised fruit. Enα tangential walls thickened considerably in the post-fertilised Brassica napus and Brassica juncea fruit, prior to the collapse of this cell layer. In Indian mustard, the Brassica juncea variety which had a non-shattering phenotype, the lignified walls of En6 were surrounded by a highly pectinised layer. This deposition of pectins confers more elasticity to the carpel walls, hence reducing the tensions which normally result in dehiscence and cause pod shatter. The model of the shattering and non-shattering phenotypes described in this study suggest a number of strategies which may be used to reduce the problems of pod shatter. These include modification of the separation layer to increase cellular cohesion, and modifications to the patterns of differentiation in the carpel wall to reduce the tensions which normally develop during fruit ripening

insights from the coding and non-coding transcriptomes

"In a context of increasing wood demand from the forest industry worldwide, maritime pine (Pinus pinaster) breeding programs have been putting their focus on wood traits, resilience to abiotic stresses and to biotic agents. Ultimately, one of the main goals is to produce large numbers of clonal trees from the ones selected with the improved traits. Currently, the clonal propagation of the genotypes selected in breeding programs is already being applied to several forest tree species for commercial purposes, namely by using a type of vegetative propagation technology called somatic embryogenesis. P. pinaster is not yet among the forest tree species which have been successfully clonally propagated on a large commercial scale by somatic embryogenesis.(...)

Proteomic profiling of fatty acid biosynthetic enzymes from oil palm chromoplast

Plant fatty acid metabolism has proven to be amenable to manipulation by conventional breeding, genetic and metabolic engineering to enhance the fatty acid profile. This can be done by engineering palm fruit to synthesise more oleic acid at the expense of palmitic acid. This would produce an oil with greater perceived nutritional quality and higher market value. Although the biochemistry of fatty acid biosynthesis in plants is well described, crosstalk between transcriptional and metabolic controls in regulating fatty acid composition remains poorly understood. Our hypothesis is that phosphorylation is one of the main regulators of acetyl-CoA carboxylase, fatty acid synthase complex and stearoyl-ACP-desaturase in increasing the oleic acid level between oil palm (Elaeis guineensis Jacq. var. Tenera) low and high oleic acid varieties. This study utilised advanced proteomic techniques to isolate, detect and identify chromoplast-based phosphorylated proteins associated with the fatty acid biosynthesis pathway. Sub-organelle isolation using differential centrifugation enriched the chromoplast fraction that contained the fatty acid biosynthetic enzymes before their protein extraction. Gel-based and non-gel based mass spectrometry techniques were then employed to separate and improve the identification of key fatty acid biosynthetic enzymes. Protein expression was analysed using isobaric labelling strategy. Five key enzymes, namely the β-ketoacyl-ACP reductase (EC 1.1.1.100), β-hydroxyacyl-ACP dehydrogenase (EC 4.2.1.58 and 4.2.1.59), 3-enoyl-ACP reductase (EC 1.3.19), β-ketoacyl-ACP synthase (EC 2.3.1.41) and stearoyl-ACP desaturase (EC 1.14.99.6) were identified using GeLC-MS/MS strategy. An additional two subunits of acetyl-CoA carboxylase (EC 6.4.1.2) were identified from the 2DLC-MS/MS strategy. The expression of β-hydroxyacyl-ACP dehydrogenase and β-ketoacyl-ACP synthase was up-regulated in the high oleic acid variety. In contrast, 3-enoyl-ACP reductase was down-regulated in the high oleic acid variety. The existence of other differentially regulated metabolic enzymes associated with fatty acid biosynthesis suggested that the control of fatty acid production, particularly the synthesis of oleic acid, involves more than just the main fatty acid biosynthetic enzymes. Subsequently, the role of phosphorylation in regulating these fatty acid biosynthetic enzymes was investigated using a novel combination of neutral loss-triggered MS3 and Selected Reaction Monitoring. Acetyl-CoA carboxylase and 3-enoyl-ACP reductase were postulated to be phosphorylated in both low oleic acid and high oleic acid-producing oil palms during the fruit maturation stage of 20th week after anthesis. However, other fatty acid biosynthetic enzymes from these oil palm varieties did not show any indication of phosphorylation despite the prediction of phosphoserine-containing peptides. The location of the phosphorylated serine residues in the protein domains of acetyl-CoA carboxylase and 3-enoyl-ACP reductase suggested that phosphorylation could have regulated their enzyme activities. This study has produced a robust method to capture and identify chromoplast-based enzymes that are related to plant fatty acid biosynthesis. The differences in their protein expression levels suggested that fatty acid biosynthetic enzymes were differentially regulated and phosphorylation might be involved in this regulation, at least in the enzyme activity. The outcomes reported in this thesis have significantly improved the knowledge of the possible regulation mechanisms in plant fatty acid biosynthesis. The logical extension of this work in future efforts will be to determine the biological significance of this differential protein expression and to understand the exact role of phosphorylation in the regulation of these enzymes

Plant Genetics and Molecular Biology

This book reviews the latest advances in multiple fields of plant biotechnology and the opportunities that plant genetics, genomics and molecular biology have offered for agriculture improvement. Advanced technologies can dramatically enhance our capacity in understanding the molecular basis of traits and utilizing the available resources for accelerated development of high yielding, nutritious, input-use efficient and climate-smart crop varieties. In this book, readers will discover the significant advances in plant genetics, structural and functional genomics, trait and gene discovery, transcriptomics, proteomics, metabolomics, epigenomics, nanotechnology and analytical & decision support tools in breeding. This book appeals to researchers, academics and other stakeholders of global agriculture