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Major crops are generally sensitive to waterlogging, but our limited understanding of the waterlogging gene regulatory network hinders the efforts to develop waterlogging-tolerant cultivars. We generated high-resolution temporal transcriptome data from root of two contrasting sesame genotypes over a 48 h period waterlogging and drainage treatments. Three distinct chronological transcriptional phases were identified, including the earlywaterlogging, late-waterlogging and drainage responses. We identified 47 genes representing the core waterlogging-responsive genes. Waterlogging/drainage-induced transcriptional changes were mainly driven by ERF and WRKY transcription factors (TF). The major difference between the two genotypes resides in the early transcriptional phase. A chronological transcriptional network model predicting putative causal regulations between TFs and downstream waterlogging-responsive genes was constructed and some interactions were validated through yeast one-hybrid assay. Overall, this study unveils the architecture and dynamic regulation of the waterlogging/drainage response in a non-model crop and helps formulate new hypotheses on stress sensing, signaling and sophisticated adaptive responses.

An increasing number of candidate genes related to abiotic stress tolerance are being discovered and proposed to improve the existing cultivars of the high oil-bearing crop sesame (Sesamum indicum L.). However, the in planta functional validation of these genes is remarkably lacking. In this study, we cloned a novel sesame R2-R3 MYB gene SiMYB75 which is strongly induced by drought, sodium chloride (NaCl), abscisic acid (ABA) and mannitol. SiMYB75 is expressed in various sesame tissues, especially in root and its protein is predicted to be located in the nucleus. Ectopic over-expression of SiMYB75 in Arabidopsis notably promoted root growth and improved plant tolerance to drought, NaCl and mannitol treatments. Furthermore, SiMYB75 over-expressing lines accumulated higher content of ABA than wild-type plants under stresses and also increased sensitivity to ABA. Physiological analyses revealed that SiMYB75 confers abiotic stress tolerance by promoting stomatal closure to reduce water loss; inducing a strong reactive oxygen species scavenging activity to alleviate cell damage and apoptosis; and also, up-regulating the expression levels of various stress-marker genes in the ABA-dependent pathways. Our data suggested that SiMYB75 positively modulates drought, salt and osmotic stresses responses through ABA-mediated pathways. Thus, SiMYB75 could be a promising candidate gene for the improvement of abiotic stress tolerance in crop species including sesame.

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.

Sesame is a source of a healthy vegetable oil, attracting a growing interest worldwide. Abiotic stresses have devastating effects on sesame yield; hence, studies have been performed to understand sesame molecular responses to abiotic stresses, but the core abiotic stress-responsive genes (CARG) that the plant reuses in response to an array of environmental stresses are unknown. We performed a meta-analysis of 72 RNA-Seq datasets from drought, waterlogging, salt and osmotic stresses and identified 543 genes constantly and differentially expressed in response to all stresses, representing the sesame CARG. Weighted gene co-expression network analysis of the CARG revealed three functional modules controlled by key transcription factors. Except for salt stress, the modules were positively correlated with the abiotic stresses. Network topology of the modules showed several hub genes predicted to play prominent functions. As proof of concept, we generated over-expressing Arabidopsis lines with hub and non-hub genes. Transgenic plants performed better under drought, waterlogging, and osmotic stresses than the wild-type plants but did not tolerate the salt treatment. As expected, the hub gene was significantly more potent than the non-hub gene. Overall, we discovered several novel candidate genes, which will fuel investigations on plant responses to multiple abiotic stresses.

Sesame is poised to become a major oilseed crop owing to its high oil quality and adaptation to various ecological areas. However, the seed yield of sesame is very low and the underlying genetic basis is still elusive. Here, we performed genome-wide association studies of 39 seed yield-related traits categorized into five major trait groups, in three different environments, using 705 diverse lines. Extensive variation was observed for the traits with capsule size, capsule number and seed size-related traits, found to be highly correlated with seed yield indexes. In total, 646 loci were significantly associated with the 39 traits (p < 10−7) and resolved to 547 quantitative trait loci QTLs. We identified six multi-environment QTLs and 76 pleiotropic QTLs associated with two to five different traits. By analyzing the candidate genes for the assayed traits, we retrieved 48 potential genes containing significant functional loci. Several homologs of these candidate genes in Arabidopsis are described to be involved in seed or biomass formation. However, we also identified novel candidate genes, such as SiLPT3 and SiACS8, which may control capsule length and capsule number traits. Altogether, we provided the highly-anticipated basis for research on genetics and functional genomics towards seed yield improvement in sesame.

Sesame has great potential as an industrial crop but its production is challenged by drought and salt stresses. To unravel the genetic variants leading to salinity and drought tolerances at the germination stage, genome-wide association studies of stress tolerance indexes related to NaCl-salt and polyethylene glycol-drought induced stresses were performed with a diversity panel of 490 sesame accessions. An extensive variation was observed for drought and salt responses in the population and most of the accessions were moderately tolerant to both stresses. A total of 132 and 120 significant Single Nucleotide Polymorphisms (SNPs) resolved to nine and 15 Quantitative trait loci (QTLs) were detected for drought and salt stresses, respectively. Only two common QTLs for drought and salt responses were found located on linkage groups 5 and 7, respectively. This indicates that the genetic bases for drought and salt responses in sesame are different. A total of 13 and 27 potential candidate genes were uncovered for drought and salt tolerance indexes, respectively, encoding transcription factors, antioxidative enzymes, osmoprotectants and involved in hormonal biosynthesis, signal transduction or ion sequestration. The identified SNPs and potential candidate genes represent valuable resources for future functional characterization towards the enhancement of sesame cultivars for drought and salt tolerances.

DNA methylation is a heritable epigenetic mechanism that participates in gene regulation under abiotic stresses in plants. Sesame (Sesamum indicum) is typically considered a drought-tolerant crop but highly susceptible to waterlogging, probably because of its origin in Africa or India. Understanding DNA methylation patterns under drought and waterlogging conditions can provide insights into the regulatory mechanisms underlying sesame contrasting responses to these abiotic stresses. We combined Methylation-Sensitive Amplified Polymorphism and transcriptome analyses to profile cytosine methylation patterns, transcript accumulation, and their interplay in drought-tolerant and waterlogging-tolerant sesame genotypes. Drought stress strongly induced de novo methylation (DNM) whereas most of the loci were demethylated (DM) during the recovery phase. In contrast, waterlogging stress decreased the level of methylation but during the recovery phase, both DM and DNM were concomitantly deployed. In both stresses, the levels of the differentially accumulated transcripts (DATs) highly correlated with the methylation patterns. We observed that DM was associated with an increase of DAT levels while DNM was correlated with a decrease of DAT levels. Altogether, sesame has divergent epigenetic programs that respond to drought and waterlogging stresses and an interplay among DNA methylation and transcript accumulation may partly modulate the contrasting responses to these stresses.

Sesame is an important oilseed crop with a high oil quality. It is prone to drought stress in the arid and semi-arid areas where it is widely grown. This study aims to decipher the response of tolerant (DT) and sensitive (DS) genotypes to progressive drought based on transcriptome, biochemical and physio-anatomical characterizations. Results indicated that under severe stress, DT relied on a well-functioning taproot while DS displayed a disintegrated root due to collapsed cortical cells. This was attributed to a higher accumulation of osmoprotectants and strong activity of antioxidant enzymes especially peroxidases in DT. From roots, DT could supply water to the aboveground tissues to ensure photosynthetic activities and improve endurance under stress. Temporal transcriptome sequencing under drought further confirmed that DT strongly activated genes related to antioxidant activity, osmoprotection and hormonal signaling pathways including abscisic acid and Ethylene. Furthermore, DT displayed unique differentially expressed genes in root functioning as peroxidases, interleukin receptor-associated kinase, heat shock proteins, APETALA2/ethylene-responsive element-binding protein and mitogen activated protein kinase, to effectively scavenge reactive oxygen species and preserve root cell integrity. Finally, 61 candidate genes conferring higher drought tolerance in DT were discovered and may constitute useful resources for drought tolerance improvement in sesame.

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.

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.

Sesame is an important crop in West and Central Africa playing a role of an alternative cash crop for smallholders. However, sesame productivity is highly impaired by drought. This study aimed at identifying some drought-resistant genotypes and efficient screening traits in large sesame germplasm. Ten genotypes were examined based on 21 biochemical, physiological, agromorphological and seed quality traits under three weeks of water stress. A high variability for drought resistance was observed among the genotypes. The genotypes WC17, WC18 and WC14 were drought resistant, WC12, WC13, WC06 and WC03 were moderately drought resistant while, WC02, WC10 and WC08 were drought sensitive, based on principal component analysis. The resistant genotypes exhibited both avoidance and tolerance features including increase of the root system, reduced water loss, highest activity of antioxidative enzymes and accumulation of proline. They produced higher biomass and had higher ability to maintain seed quality under drought stress compared with the sensitive genotypes. Strong accumulation (~200% ratio stress/control) of biochemical markers including superoxide dismutase, ascorbate peroxidase, catalase and proline could be regarded as an important indicator for selecting drought resistant genotypes. This study represents a reference for future research towards developing new varieties with improved drought resistance in West and Central Africa.

Background: West Africa's Sahel is characterized by a dry and hot climate with limited rainfall that impairs the production of several crops. Sesame is a resilient crop that is well suited to this environment. Unfortunately, there is a lack of data relative to the status of its production in West Africa. We made investigations in four major sesame-growing areas of Senegal and Mali, into the status of the crop's production, its agronomic practices, the challenges farmers face and their preferences concerning the traits that should be improved. Results: A total of 256 sesame producers in 47 villages were interviewed using a semi-structured questionnaire. The results showed that sesame is a multi-ethnic crop and only 20% of the total fields owned by farmers were allocated to its cultivation. The yield and the seasonal production of sesame per farmer was quite weak showing that this crop is still a commodity grown on a small scale. Various cultivars were grown, and the most widely grown ones have considerable levels of oil (53–60.34%) and protein (18–21.89%) contents. In both countries, seed marketing was the main impediment the producers faced on account of a lack of reliable markets and of a considerable fluctuation in prices. Conclusions: Overall, the sesame sector is still traditional but is progressively developing and sesame could become an important cash crop for smallholders in West Africa's Sahel. Research programs should target the release of the varieties with higher yield, a stronger resistance to drought, heat, diseases and pests, a good seed quality and improved plant architecture. This study represents the first insight into the sesame sector in West Africa's Sahel, and our findings may guide researchers and policy-makers to boost this sector for ensuring food security and the improvement of small-scale farmers' livelihood.

The sequencing of the full nuclear genome of sesame (Sesamum indicum L.) provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR) in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78%) were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/), which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.

The MYB gene family constitutes one of the largest transcription factors (TFs) modulating various biological processes in plants. Although genome-wide analysis of this gene family has been carried out in some species, only three MYB members have been functionally characterized heretofore in sesame (Sesamum indicum L.). Here, we identified a relatively high number (287) of sesame MYB genes (SIMYBs) with an uncommon overrepresentation of the 1R-subfamily. A total of 95% of SIMYBs was mapped unevenly onto the 16 linkage groups of the sesame genome with 55 SIMYBs tandemly duplicated. In addition, molecular characterization, gene structure, and evolutionary relationships of SIMYBs were established. Based on the close relationship between sesame and Arabidopsis thaliana, we uncovered that the functions of SIMYBs are highly diverse. A total of 65% of SIMYBs were commonly detected in five tissues, suggesting that they represent key TFs modulating sesame growth and development. Moreover, we found that SIMYBs regulate sesame responses to drought and waterlogging, which highlights the potential of SIMYBs towards improving stress tolerance in sesame. This work presents a comprehensive picture of the MYB gene family in sesame and paves the way for further functional validation of the members of this versatile gene family.

Background. Sesame is an important oilseed crop mainly grown in inclement areas with high temperatures and frequent drought. Thus, drought constitutes one of the major constraints of its production. The AP2/ERF is a large family of transcription factors known to play significant roles in various plant processes including biotic and abiotic stress responses. Despite their importance, little is known about sesame AP2/ERF genes. This constitutes a limitation for drought-tolerance candidate genes discovery and breeding for tolerance to water deficit. Results. One hundred thirty-two AP2/ERF genes were identified in the sesame genome. Based on the number of domains, conserved motifs, genes structure and phylogenetic analysis including 5 relatives species, they were classified into 24 AP2, 41 DREB, 61 ERF, 4 RAV and 2 Soloist. The number of sesame AP2/ERF genes was relatively few compared to that of other relatives, probably due to gene loss in ERF and DREB subfamilies during evolutionary process. In general, the AP2/ERF genes were expressed differently in different tissues but exhibited the highest expression levels in the root. Mostly all DREB genes were responsive to drought stress. Regulation by drought is not specific to one DREB group but depends on the genes and the group A6 and A1 appeared to be more actively expressed to cope with drought. Conclusions. This study provides insights into the classification, evolution and basic functional analysis of AP2/ERF genes in sesame which revealed their putative involvement in multiple tissue-/developmental stages. Out of 20 genes which were significantly up- /down-regulated under drought stress, the gene AP2si16 may be considered as potential candidate gene for further functional validation as well for utilization in sesame improvement programs for drought stress tolerance.

Sesame is an important oil crop widely cultivated in Africa and Asia. Understanding the genetic diversity of accessions from these continents is critical to designing breeding methods and for additional collection of sesame germplasm. To determine the genetic diversity in relation to geographical regions, 96 sesame accessions collected from 22 countries distributed over six geographic regions in Africa and Asia were genotyped using 33 polymorphic SSR markers. Large genetic variability was found within the germplasm collection. The total number of alleles was 137, averaging 4.15 alleles per locus. The accessions from Asia displayed more diversity than those from Africa. Accessions from Southern Asia (SAs), Eastern Asia (EAs), and Western Africa (WAf) were highly diversified, while those from Western Asia (WAs), Northern Africa (NAf), and Southeastern Africa (SAf) had the lowest diversity. The analysis of molecular variance revealed that more than 44% of the genetic variance was due to diversity among geographic regions. Five subpopulations, including three in Asia and two in Africa, were cross-identified through phylogenetic, PCA, and STRUCTURE analyses. Most accessions clustered in the same population based on their geographical origins. Our results provide technical guidance for efficient management of sesame genetic resources in breeding programs and further collection of sesame germplasm from these different regions.

Sesame is a survivor crop cultivated for ages in arid areas under high temperatures and limited water conditions. Since its entire genome has been sequenced, revealing evolution, and functional characterization of its abiotic stress genes became a hot topic. In this study, we performed a whole-genome identification and analysis of Hsf gene family in sesame. Thirty genes encoding Hsf domain were found and classified into 3 major classes A, B, and C. The class A members were the most representative one and Hsf genes were distributed in 12 of the 16 linkage groups (except the LG 8, 9, 13, and 16). Evolutionary analysis revealed that, segmental duplication events which occurred around 67 MYA, were the primary force underlying Hsf genes expansion in sesame. Comparative analysis also suggested that sesame has retained most of its Hsf genes while its relatives viz. tomato and potato underwent extensive gene losses during evolution. Continuous purifying selection has played a key role in the maintenance of Hsf genes in sesame. Expression analysis of the Hsf genes in sesame revealed their putative involvement in multiple tissue-/developmental stages. Time-course expression profiling of Hsf genes in response to drought stress showed that 90% Hsfs are drought responsive. We infer that classes B-Hsfs might be the primary regulators of drought response in sesame by cooperating with some class A genes. This is the first insight into this gene family and the results provide some gene resources for future gene cloning and functional studies toward the improvement in stress tolerance of sesame.