Analysis of expression sequence tags from a full-length-enriched cDNA library of developing sesame seeds (Sesamum indicum)

Analysis of genes specific to the early maturation stage of Sesamum indicum seeds by subtraction method*,*

The mechanisms regulating the content ratio of unsaturated fatty acid in sesame oil need to be clarified in order to breed novel varieties with high contents of unsaturated fatty acids. Full-length cDNA libraries prepared from sesame seeds 1 to 3 weeks after flowering were subtracted with cDNAs from plantlets of 4 weeks after germination. A total of 1545 cDNA clones was sequenced. The functions of novel genes expressed specifically during the early maturation of sesame seeds were investigated by the transformation of Arabidopsis thaliana. Thirteen genes for a transcription factor were identified, four of which were involved in ethylene signaling. Fifty-nine genes, including those for the aquaporin-like protein and ethylene response factor, were analyzed by overexpression in A. thaliana. The overexpression of novel genes and the aquaporin-like protein gene in A. thaliana increased the content of unsaturated fatty acids. The localization of these products was investigated by the induction of the expression vectors for the GFP fusion protein into onion epidermal cells and sesame root cells with a particle gun. As a result, two cDNA clones were identified as good candidate genes to clarify the regulation in the yield and the ratio of unsaturated fatty acids in sesame seeds. Sein60414 (Accession No. LC603128), an intrinsic membrane protein, may be involved in the increase of unsaturated fatty acids, and Sein61074 (Accession No. LC709278) MAP3K δ-1 protein kinase in the regulation of the total ratio of unsaturated fatty acids in sesame seeds.

Fine Mapping of a Major Pleiotropic QTL Associated with Sesamin and Sesamolin Variation in Sesame (Sesamum indicum L.)

Deciphering the genetic basis of quantitative agronomic traits is a prerequisite for their improvement. Herein, we identified loci governing the main sesame lignans, sesamin and sesamolin variation in a recombinant inbred lines (RILs, F8) population under two environments. The content of the two lignans in the seeds was investigated by HPLC. The sesamin and sesamolin contents ranged from 0.33 to 7.52 mg/g and 0.36 to 2.70 mg/g, respectively. In total, we revealed 26 QTLs on a linkage map comprising 424 SSR markers, including 16 and 10 loci associated with sesamin and sesamolin variation, respectively. Among them, qSmin_11.1 and qSmol_11.1 detected in both the two environments explained 67.69% and 46.05% of the phenotypic variation of sesamin and sesamolin, respectively. Notably, qSmin11-1 and qSmol11-1 were located in the same interval of 127-127.21cM on LG11 between markers ZMM1776 and ZM918 and acted as a pleiotropic locus. Furthermore, two potential candidate genes (SIN_1005755 and SIN_1005756) at the same locus were identified based on comparative transcriptome analysis. Our results suggest the existence of a single gene of large effect that controls expression, both of sesamin and sesamolin, and provide genetic information for further investigation of the regulation of lignan biosynthesis in sesame.

Characterization of the Genetic Diversity Present in a Diverse Sesame Landrace Collection Based on Phenotypic Traits and EST-SSR Markers Coupled With an HRM Analysis

A selection of sesame (Sesamum indicum L.) landraces of different eco-geographical origin and breeding history have been characterized using 28 qualitative morpho-physiological descriptors and seven expressed sequence tag-simple sequence repeat (EST-SSR) markers coupled with a high-resolution melting (HRM) analysis. The most variable qualitative traits that could efficiently discriminate landraces, as revealed by the correlation analyses, were the plant growth type and position of the branches, leaf blade width, stem pubescence, flowering initiation, capsule traits and seed coat texture. The agglomerative hierarchical clustering analysis based on a dissimilarity matrix highlighted three main groups among the sesame landraces. An EST-SSR marker analysis revealed an average polymorphism information content (PIC) value of 0.82, which indicated that the selected markers were highly polymorphic. A principal coordinate analysis and dendrogram reconstruction based on the molecular data classified the sesame genotypes into four major clades. Both the morpho-physiological and molecular analyses showed that landraces from the same geographical origin were not always grouped in the same cluster, forming heterotic groups; however, clustering patterns were observed for the Greek landraces. The selective breeding of such traits could be employed to unlock the bottleneck of local phenotypic diversity and create new cultivars with desirable traits.

Transcriptome Dynamics during Black and White Sesame (Sesamum indicum L.) Seed Development and Identification of Candidate Genes Associated with Black Pigmentation

Seed coat color is a crucial agronomic trait in sesame (Sesamum indicum L.) since it is strongly linked to seed oil, proteins, and lignans contents, and also influences consumer preferences. In East Asia, black sesame seed is used in the treatment and the prevention of various diseases. However, in sesame, little is known about the establishment of the seed coat color, and only one gene has been reported to control black pigmentation. This study provides an overview of developing seeds transcriptome of two varieties of sesame "Zhongfengzhi No.1" (white seed) and "Zhongzhi No.33" (black seed) and shed light on genes involving in black seed formation. Until eight days post-anthesis (DPA), both the seeds of the two varieties were white. The black sesame seed turned to yellow between 9 and 11 DPA and then black between 12 and 14 DPA. The black and white sesame showed similar trend-expressed genes with the numbers increased at the early stages of seed development. The differentially expressed genes (DEGs) number increased with seed development in the two sesame varieties. We examined the DEGs and uncovered that more were up-regulated at the early stages. The DEGs between the black and white sesame were mainly enriched in 37 metabolic pathways, among which the flavonoid biosynthesis and biosynthesis of secondary metabolites were dominants. Furthermore, we identified 20 candidate genes associated with pigment biosynthesis in black sesame seed, among which 10 were flavonoid biosynthesis and regulatory genes. These genes also include isochorismate and polyphenol oxidase genes. By comparing the phenotypes and genes expressions of the black and white sesame seed at different development stages, this work revealed the important role of 8-14 DPA in black pigment biosynthesis and accumulation. Moreover, it unfolded candidate genes associated with black pigmentation in sesame. These findings provide a vast transcriptome dataset and list of genes that will be targeted for functional studies related to the molecular mechanism involved in biosynthesis and regulation of seed coat color in sesame.

Gene isolation, heterologous expression, purification and functional confirmation of sesamin synthase from Sesamum indicum L

Members of Cytochromes P450 super family of enzymes catalyse important biochemical reactions in plants. Some of these reactions are so important that they contribute to enormous chemical diversity seen in plants. Many unique secondary metabolites formed by mediation of these enzymes play key role in plant defence and often contribute to maintenance of human health. In oilseed crop Sesamum indicum, the reaction leading to the formation of clinically important sesamin is catalyzed by a unique methylene-di-oxy bridge forming Cytochrome P450 enzyme sesamin synthase. It is encoded by the gene CYP81Q1. In order to elucidate the structure - function relationship of this enzyme and to apply biotechnological tools for enhancing the production of sesamin in the crop, it was intended to clone and express the enzyme in a heterologous system. In this paper we present our results on synthesis of cDNA, cloning, expression and purification of CYP81Q1 from the developing seeds of sesame crop. Following the same procedure we have also cloned a CYP reductase1 (CPR1) gene (CPR1) to facilitate transfer of electron from NADPH to CYP81Q1 enzyme from the same crop. Functional characterization was performed by expressing the recombinant proteins in E. coli (pET28a/BL21-DE3 codon plus) and its activity was evaluated in vitro by HPLC. We demonstrate that purified CYP81Q1 enzyme, on its own, has limited level of activity in the conversion of pinoresinol to sesamin. Its activity gets considerably enhanced in the presence of CPR1.

Gene expression profiles that shape high and low oil content sesames

Background

Sesame (Sesamum indicum) can accumulate over 60% oil in its seed. However, low oil content genotypes with an oil content of less than 50% are also observed. To gain insights into how genes shape this variation, we examined 22 seed and carpel transcriptomes from 3 varieties of sesame with high and low oil content.

Results

A total of 34.6~52.2% of the sesame genes were expressed with a RPKM greater than 5 in the 22 tissue samples. The expressed gene numbers tended to decrease in the seed but fluctuated in the carpels from 10 to 30 days post-anthesis (DPA). Compared with that of the low oil content sesames, the high oil content sesame exhibited more positive gene expression during seed development. Typically, genes involved in lipid biosynthesis were enriched and could distinguish the high and low genotypes at 30 DPA, suggesting the pivotal role of seed oil biosynthesis in the later stages. Key homologous lipid genes that function in TAG biosynthesis, including those that encoded glycerol-3-phosphate acyltransferase (GPAT), acyl-CoA:diacylglycerol acyltransferase (DGAT), and phospholipid:diacylglycerol acyltransferase (PDAT), were strengthened asynchronously at different stages, but the lipid transfer protein (LTP)-encoding genes, including SIN_1019175, SIN_1019172 and SIN_1010009, usually were highlighted in the high oil content sesames. Furthermore, a list of 23 candidate genes was identified and predicted to be beneficial for higher oil content accumulation. Despite the different gene expression patterns between the seeds and carpels, the two tissues showed a cooperative relationship during seed development, and biological processes, such as transport, catabolic process and small molecule metabolic process, changed synchronously.

Conclusions

The study elucidated the different expression profiles in high and low oil content sesames and revealed key stages and a list of candidate genes that shaped oil content variation. These findings will accelerate dissection of the genetic mechanism of sesame oil biosynthesis.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0747-7) contains supplementary material, which is available to authorized users.

The Emerging Oilseed Crop Sesamum indicum Enters the "Omics" Era

Sesame (Sesamum indicum L.) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, web-based functional databases and diverse daft genome sequences. The availability of these tools in association with the discovery of candidate genes and quantitative trait locis for key agronomic traits including high oil content and quality, waterlogging and drought tolerance, disease resistance, cytoplasmic male sterility, high yield, pave the way to the development of some new strategies for sesame genetic improvement. As a result, sesame has graduated from an "orphan crop" to a "genomic resource-rich crop." With the limited research teams working on sesame worldwide, more synergic efforts are needed to integrate these resources in sesame breeding for productivity upsurge, ensuring food security and improved livelihood in developing countries. This review retraces the evolution of sesame research by highlighting the recent advances in the "Omics" area and also critically discusses the future prospects for a further genetic improvement and a better expansion of this crop.

Tracking sesamin synthase gene expression through seed maturity in wild and cultivated sesame species--a domestication footprint

Sesamin and sesamolin are the major oil-soluble lignans present in sesame seed, having a wide range of biological functions beneficial to human health. Understanding sesame domestication history using sesamin synthase gene expression could enable delineation of the sesame putative progenitor. This report examined the functional expression of sesamin synthase (CYP81Q1) during capsule maturation (0-40 days after flowering) in three wild Sesamum species and four sesame cultivars. Among the cultivated accessions, only S. indicum (CO-1) exhibited transcript abundance of sesamin synthase along with high sesamin content similar to S. malabaricum, while the other cultivated sesame showed low expression. The sesamin synthase expression analysis, coupled with quantification of sesamin level, indicates that sesamin synthase was not positively favoured during domestication. The sesamin synthase expression pattern and lignan content, along with phylogenetic analysis suggested a close relationship of cultivated sesame and the wild species S. malabaricum. The high genetic identity between the two species S. indicum and S. malabaricum points towards the role of the putative progenitor S. malabaricum in sesame breeding programmes to broaden the genetic base of sesame cultivars. This study emphasises the need to investigate intraspecific and interspecific variation in the primary, secondary and tertiary gene pools to develop superior sesame genotypes.

ocsESTdb: a database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism

BACKGROUND

Oil crop seeds are important sources of fatty acids (FAs) for human and animal nutrition. Despite their importance, there is a lack of an essential bioinformatics resource on gene transcription of oil crops from a comparative perspective. In this study, we developed ocsESTdb, the first database of expressed sequence tag (EST) information on seeds of four large-scale oil crops with an emphasis on global metabolic networks and oil accumulation metabolism that target the involved unigenes.

DESCRIPTION

A total of 248,522 ESTs and 106,835 unigenes were collected from the cDNA libraries of rapeseed (Brassica napus), soybean (Glycine max), sesame (Sesamum indicum) and peanut (Arachis hypogaea). These unigenes were annotated by a sequence similarity search against databases including TAIR, NR protein database, Gene Ontology, COG, Swiss-Prot, TrEMBL and Kyoto Encyclopedia of Genes and Genomes (KEGG). Five genome-scale metabolic networks that contain different numbers of metabolites and gene-enzyme reaction-association entries were analysed and constructed using Cytoscape and yEd programs. Details of unigene entries, deduced amino acid sequences and putative annotation are available from our database to browse, search and download. Intuitive and graphical representations of EST/unigene sequences, functional annotations, metabolic pathways and metabolic networks are also available. ocsESTdb will be updated regularly and can be freely accessed at http://ocri-genomics.org/ocsESTdb/ .

CONCLUSION

ocsESTdb may serve as a valuable and unique resource for comparative analysis of acyl lipid synthesis and metabolism in oilseed plants. It also may provide vital insights into improving oil content in seeds of oil crop species by transcriptional reconstruction of the metabolic network.

Association mapping of seed oil and protein content in Sesamum indicum L. using SSR markers

Sesame is an important oil crop for the high oil content and quality. The seed oil and protein contents are two important traits in sesame. To identify the molecular markers associated with the seed oil and protein contents in sesame, we systematically performed the association mapping among 369 worldwide germplasm accessions under 5 environments using 112 polymorphic SSR markers. The general linear model (GLM) was applied with the criteria of logP≥3.0 and high stability under all 5 environments. Among the 369 sesame accessions, the oil content ranged from 27.89%–58.73% and the protein content ranged from 16.72%–27.79%. A significant negative correlation of the oil content with the protein content was found in the population. A total of 19 markers for oil content were detected with a R² value range from 4% to 29%; 24 markers for protein content were detected with a R² value range from 3% to 29%, of which 19 markers were associated with both traits. Moreover, partial markers were confirmed using mixed linear model (MLM) method, which suggested that the oil and protein contents are controlled mostly by major genes. Allele effect analysis showed that the allele associated with high oil content was always associated with low protein content, and vice versa. Of the 19 markers associated with oil content, 17 presented near the locations of the plant lipid pathway genes and 2 were located just next to a fatty acid elongation gene and a gene encoding Stearoyl-ACP Desaturase, respectively. The findings provided a valuable foundation for oil synthesis gene identification and molecular marker assistant selection (MAS) breeding in sesame.

Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using insertion-deletion (InDel) and simple sequence repeat (SSR) markers

Background

Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars. Domestication and modern plant breeding have presumably narrowed the genetic basis of cultivated sesame. Several modern sesame cultivars were bred with a limited number of landrace cultivars in their pedigree. The genetic variation was subsequently reduced by genetic drift and selection. Characterization of genetic diversity of these cultivars by molecular markers is of great value to assist parental line selection and breeding strategy design.

Results

Three hundred and forty nine simple sequence repeat (SSR) and 79 insertion-deletion (InDel) markers were developed from cDNA library and reduced-representation sequencing of a sesame cultivar Zhongzhi 14, respectively. Combined with previously published SSR markers, 88 polymorphic markers were used to assess the genetic diversity, phylogenetic relationships, population structure, and allele distribution among 130 Chinese sesame accessions including 82 cultivars, 44 landraces and 4 wild germplasm accessions. A total of 325 alleles were detected, with the average gene diversity of 0.432. Model-based structure analysis revealed the presence of five subgroups belonging to two main groups, which were consistent with the results from principal coordinate analysis (PCA), phylogenetic clustering and analysis of molecular variance (AMOVA). Several missing or unique alleles were identified from particular types, subgroups or families, even though they share one or both parental/progenitor lines.

Conclusions

This report presented a by far most comprehensive characterization of the molecular and genetic diversity of sesame cultivars in China. InDels are more polymorphic than SSRs, but their ability for deciphering genetic diversity compared to the later. Improved sesame cultivars have narrower genetic basis than landraces, reflecting the effect of genetic drift or selection during breeding processes. Comparative analysis of allele distribution revealed genetic divergence between improved cultivars and landraces, as well as between cultivars released in different years. These results will be useful for assessing cultivars and for marker-assisted breeding in sesame.

Genome sequencing of the important oilseed crop Sesamum indicum L

The Sesame Genome Working Group (SGWG) has been formed to sequence and assemble the sesame (Sesamum indicum L.) genome. The status of this project and our planned analyses are described.