Dynamic transcriptome landscape of sesame (Sesamum indicum L.) under progressive drought and after rewatering.
ABSTRACT: Drought is one of the most important abiotic stresses that impair sesame (Sesamum indicum L.) productivity mainly when it occurs at flowering stage. However up to now, very few studies have attempted to investigate the molecular responses of sesame to drought stress. In this experiment, two genotypes having contrasting responses to drought (tolerant and sensitive) were submitted to progressive drought followed by recovering stage at flowering stage. RNAs were isolated from roots of plants before drought stress, at 3-time points during progressive drought, after rewatering, and sequenced using Illumina HiSeq 4000 platform. These RNA-Seq resources (BioSample IDs: SAMN06130606 and SAMN06130607) provided an opportunity to elucidate the molecular responses of sesame to drought and find out some candidate genes for drought tolerance improvement.
Project description:The NAM, ATAF1/2, and CUC2 (NAC) family constitutes a large family of plant-specific transcription factors, involved in many aspects of physiological processes and a variety of abiotic stresses. There is little information concerning the NAC family in Sesamum indicum. In this study, 87 sesame NAC genes were identified and phylogenetically clustered into 12 groups with Arabidopsis NAC genes. A total of 83 SiNAC genes were distributed non-randomly on the 16 linkage groups in sesame. Four and 49 SiNACs were found to be tandemly and segmentally duplicated, respectively. Expression profiles of SiNAC genes in different tissues (root, stem, leaf, flower, seed, and capsule) and in response to drought and waterlogging stresses by using RNA-seq data demonstrated that 23 genes were highly expressed in all tissues, 18 and 31 SiNACs respond strongly to drought and waterlogging stresses, respectively. In addition, the expression of 30 SiNAC genes distributed in different subgroups was analyzed with quantitative real-time RT-PCR under cold, osmotic, and salt stresses, revealed that their expression patterns vary in response to abiotic stresses. SiNAC genes displayed diverse expression patterns among the different tissues and stress treatments, suggested that their contribution to plant growth and development in sesame and multiple stress resistance in sesame. In this study, NAC transcription factors were analyzed in sesame and some specific candidate SiNAC genes in response to abiotic stress for functional study were identified. This study provides valuable information to deepen our understanding of the abiotic stress responses by NAC transcription factors in sesame.
Project description: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.
Project description: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.
Project description:The effect of plant population density (PPD) and root-induced leaf cytokinin on the compensatory growth of potted corn seedlings during post-drought rewatering was investigated. The study design comprised four treatments: (1) wetness with low PPD, (2) wetness with high PPD, (3) rewatering with low PPD, and (4) rewatering with high PPD. Results showed that drought stress restrained the growth of corns. By contrast, rewatering enhanced the net photosynthetic rate and growth of corns. During the 8 days of rewatering, compensatory growth during post-drought rewatering occurred in corns with high PPD; however, such compensatory growth did not occur in corns with low PPD. Zeatin riboside concentrations in leaves and xylem saps were significantly higher under rewatering treatment than those under wet treatment. High leaf cytokinin concentration accelerated corn growth. The coefficients of variation and Gini-coefficient of wet treatment were significantly higher than those of rewatering treatment under high PPD, demonstrating that intense intraspecific competition occurred in the wet treatment. Extreme intraspecific competition negatively affected net photosynthetic rate. In brief, the interactions between root-induced leaf cytokinin and weak intraspecific competition promoted the compensatory growth under high PPD.
Project description:Unlike most of the important food crops, sesame can survive drought but severe and repeated drought episodes, especially occurring during the reproductive stage, significantly curtail the productivity of this high oil crop. Genome-wide association study was conducted for traits related to drought tolerance using 400 diverse sesame accessions, including landraces and modern cultivars. Ten stable QTLs explaining more than 40% of the phenotypic variation and located on four linkage groups were significantly associated with drought tolerance related traits. Accessions from the tropical area harboured higher numbers of drought tolerance alleles at the peak loci and were found to be more tolerant than those from the northern area, indicating a long-term genetic adaptation to drought-prone environments. We found that sesame has already fixed important alleles conferring survival to drought which may explain its relative high drought tolerance. However, most of the alleles crucial for productivity and yield maintenance under drought conditions are far from been fixed. This study also revealed that pyramiding the favourable alleles observed at the peak loci is of high potential for enhancing drought tolerance in sesame. In addition, our results highlighted two important pleiotropic QTLs harbouring known and unreported drought tolerance genes such as SiABI4, SiTTM3, SiGOLS1, SiNIMIN1 and SiSAM. By integrating candidate gene association study, gene expression and transgenic experiments, we demonstrated that SiSAM confers drought tolerance by modulating polyamine levels and ROS homeostasis, and a missense mutation in the coding region partly contributes to the natural variation of drought tolerance in sesame.
Project description:Three iridoids (lamalbid (I1), sesamoside (I2) and shanzhiside methyl ester (I3)) and seven polyphenols (cistanoside F (P1), chlorogenic acid (P2), pedalitin-6-O-laminaribioside (P3), pedaliin (P4), isoacteoside (P6), pedalitin (P7) and martynoside (P8)) were identified in young sesame leaves (Sesamum indicum L.) other than the acteoside (P5) reported previously. P3 was a new compound, and I1, I3, P2 and P8 were found in a species of Sesamum for the first time. HPLC analyses revealed that the compounds I1 (0.29-1.75% of dry leaves), I2 (0.38-0.87%), I3 (0.04-1.07%), P4 (0.01-2.05%) and P5 (0.13-4.86%) were present primarily in young sesame leaves and were found in plants cultivated on different farms (plant height, 30-70 cm). Of the identified compounds, P5 and P6 showed high 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging, oxygen radical absorbance capacity (ORAC), and in vitro antiglycation activities. Given its content, P5 makes a major contribution to the biological activities of young sesame leaves. The compounds were examined at six different growth stages of plants cultured in a greenhouse to determine the optimum harvest stage and for end-use assessment. P5 accumulated in the leaves during growth, and the content reached a maximum of 12.9% of dry leaves in the 4th stage (plant height, 74.5±9.7 cm), which is one of the highest percentages reported in plants from nature.
Project description:Sesame (Sesamum indicum L.) is one of the oldest oilseed crops. In order to investigate the evolutionary characters according to the Sesame Genome Project, apart from sequencing its nuclear genome, we sequenced the complete chloroplast genome of S. indicum cv. Yuzhi 11 (white seeded) using Illumina and 454 sequencing. Comparisons of chloroplast genomes between S. indicum and the 18 other higher plants were then analyzed. The chloroplast genome of cv. Yuzhi 11 contains 153,338 bp and a total of 114 unique genes (KC569603). The number of chloroplast genes in sesame is the same as that in Nicotiana tabacum, Vitis vinifera and Platanus occidentalis. The variation in the length of the large single-copy (LSC) regions and inverted repeats (IR) in sesame compared to 18 other higher plant species was the main contributor to size variation in the cp genome in these species. The 77 functional chloroplast genes, except for ycf1 and ycf2, were highly conserved. The deletion of the cp ycf1 gene sequence in cp genomes may be due either to its transfer to the nuclear genome, as has occurred in sesame, or direct deletion, as has occurred in Panax ginseng and Cucumis sativus. The sesame ycf2 gene is only 5,721 bp in length and has lost about 1,179 bp. Nucleotides 1-585 of ycf2 when queried in BLAST had hits in the sesame draft genome. Five repeats (R10, R12, R13, R14 and R17) were unique to the sesame chloroplast genome. We also found that IR contraction/expansion in the cp genome alters its rate of evolution. Chloroplast genes and repeats display the signature of convergent evolution in sesame and other species. These findings provide a foundation for further investigation of cp genome evolution in Sesamum and other higher plants.
Project description:The present study was designed to investigate the duration-dependent changes in the biochemical attributes of sesame in response to waterlogging stress. Sesame plants (Sesamum indicum L. cv. BARI Til-4) were subjected to waterlogging for 2, 4, 6, and 8 days during the vegetative stage and data were measured following waterlogging treatment. The present study proves that waterlogging causes severe damage to different attributes of the sesame plant. The plants showed an increasing trend in lipid peroxidation as well as hydrogen peroxide (H2O2) and methylglyoxal contents that corresponded to increased stress duration. A prolonged period of waterlogging decreased leaf relative water content and proline content. Photosynthetic pigments, like chlorophyll (chl) a, b, and chl (a+b) and carotenoid contents, also decreased over time in stressed plants. Glutathione (GSH) and oxidized glutathione (GSSG) contents increased under waterlogging, while the GSH/GSSG ratio and ascorbate content decreased, indicating the disruption of redox balance in the cell. Ascorbate peroxidase, monodehydroascorbate reductase, and glutathione peroxidase activity increased under waterlogging, while dehydroascorbate reductase, glutathione reductase, and catalase activity mostly decreased. Waterlogging modulated the glyoxalase system mostly by enhancing glyoxalase II activity, with a slight increase in glyoxalase I activity. The present study also demonstrates the induction of oxidative stress via waterlogging in sesame plants and that stress levels increase with increased waterlogging duration.
Project description:BACKGROUND:Sesame (Sesamum indicum L.) is one of the world's most important oil crops. However, it is susceptible to abiotic stresses in general, and to waterlogging and drought stresses in particular. The molecular mechanisms of abiotic stress tolerance in sesame have not yet been elucidated. The WRKY domain transcription factors play significant roles in plant growth, development, and responses to stresses. However, little is known about the number, location, structure, molecular phylogenetics, and expression of the WRKY genes in sesame. RESULTS:We performed a comprehensive study of the WRKY gene family in sesame and identified 71 SiWRKYs. In total, 65 of these genes were mapped to 15 linkage groups within the sesame genome. A phylogenetic analysis was performed using a related species (Arabidopsis thaliana) to investigate the evolution of the sesame WRKY genes. Tissue expression profiles of the WRKY genes demonstrated that six SiWRKY genes were highly expressed in all organs, suggesting that these genes may be important for plant growth and organ development in sesame. Analysis of the SiWRKY gene expression patterns revealed that 33 and 26 SiWRKYs respond strongly to waterlogging and drought stresses, respectively. Changes in the expression of 12 SiWRKY genes were observed at different times after the waterlogging and drought treatments had begun, demonstrating that sesame gene expression patterns vary in response to abiotic stresses. CONCLUSIONS:In this study, we analyzed the WRKY family of transcription factors encoded by the sesame genome. Insight was gained into the classification, evolution, and function of the SiWRKY genes, revealing their putative roles in a variety of tissues. Responses to abiotic stresses in different sesame cultivars were also investigated. The results of our study provide a better understanding of the structures and functions of sesame WRKY genes and suggest that manipulating these WRKYs could enhance resistance to waterlogging and drought.
Project description:Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world's population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (?5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding.