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Abstract Development of high yielding cowpea varieties coupled with good taste and rich in essential minerals can promote consumption and thus nutrition and profitability. The sweet taste of cowpea grain is determined by its sugar content, which comprises mainly sucrose and galacto-oligosaccharides (GOS) including raffinose and stachyose. However, GOS are indigestible and their fermentation in the colon can produce excess intestinal gas, causing undesirable bloating and flatulence. In this study, we aimed to examine variation in grain sugar and mineral concentrations, then map quantitative trait loci (QTLs) and estimate genomic-prediction (GP) accuracies for possible application in breeding. Grain samples were collected from a multi-parent advanced generation intercross (MAGIC) population grown in California during 2016–2017. Grain sugars were assayed using high-performance liquid chromatography. Grain minerals were determined by inductively coupled plasma–optical emission spectrometry and combustion. Considerable variation was observed for sucrose (0.6–6.9%) and stachyose (2.3–8.4%). Major QTLs for sucrose (QSuc.vu-1.1), stachyose (QSta.vu-7.1), copper (QCu.vu-1.1) and manganese (QMn.vu-5.1) were identified. Allelic effects of major sugar QTLs were validated using the MAGIC grain samples grown in West Africa in 2017. GP accuracies for minerals were moderate (0.4–0.58). These findings help guide future breeding efforts to develop mineral-rich cowpea varieties with desirable sugar content.

Improving sorghum adoption rates by developing adapted varieties that meet end-user preferences is a major challenge in West Africa. In this study, a participatory rural appraisal was undertaken to identify the main sorghum production constraints, farmers’ preferred variety traits and their perceptions on sorghum grain mold. The study was conducted in four representative rural communities located in the main sorghum producing area of Senegal. A total of 260 farmers were interviewed and data were collected through focus group discussions and individual questionnaires. Our results indicated that Striga, insects, poor soil fertility and drought are the major sorghum producing constraints in Senegal. Grain mold was identified as the second most important sorghum disease after the damping-off. Discoloration on grain surface was the most important criteria farmers used to recognize the disease. The most important sorghum traits farmers desired in improved varieties are medium to short plant maturity cycle, medium plant height, large open or semi-compact panicle, big and white grain, and adaptation to local growing conditions. The results showed that the sorghum cropping system is dominated by male farmers who mainly grow local landraces. These results will provide updated recommendations for the breeding products profile to meet end-user preferences in Senegal.

Abstract Drought is a major constraint on plant productivity globally. Sorghum [Sorghum bicolor (L.) Moench] landraces have evolved in drought‐prone regions, but the genetics of their adaptation is poorly understood. Here we sought to identify novel drought‐tolerance loci and test hypotheses on the role of known loci including those underlying stay‐green (Stg) postflowering drought tolerance. We phenotyped 590 diverse sorghum accessions from West Africa in 10 environments, under field‐based managed drought stress [preflowering water stress (WS1), postflowering water stress (WS2), and well‐watered (WW)] and rainfed (RF) conditions over 4 yr. Days to 50% flowering (DFLo), aboveground dry biomass (DBM), plant height (PH), and plant grain yield components (including grain weight [GrW], panicle weight [PW] and grain number [GrN] per plant, and 1000‐grain weight [TGrW]) were measured, and genome‐wide association studies (GWAS) was conducted. Broad‐sense heritability for biomass and plant grain yield was high (33–92%) across environments. There was a significant correlation between stress tolerance index (STI) for GrW per plant across WS1 and WS2. Genome‐wide association studies revealed that SbZfl1 and SbCN12, orthologs of maize (Zea mays L.) flowering genes, likely underlie flowering time variation under these conditions. Genome‐wide association studies further identified associations (n = 134; common between two GWAS models) for STI and drought effects on plant yield components including 16 putative pleiotropic associations. Thirty of the associations colocalized with Stg1, Stg2, Stg3, and Stg4 loci and had large effects. Seven lead associations, including some within Stg1, overlapped with positive selection outliers. Our findings reveal previously undescribed natural genetic variation for drought‐tolerance‐related traits and suggest a broad role of Stg loci in drought adaptation of sorghum.

Abstract Background The benefits of leaf stay-green for maintaining grain filling in sorghum under drought was largely demonstrated. However, its role in the stability of a dual production (grain, stem sugar) in tall sweet sorghum remains to be elucidated. This study aimed to analyze the impact of a post-anthesis drought on sugar accumulation along stem internodes in sweet and tall West-African sorghum with variable leaf stay-green and grain yield abilities. Methods Four accessions with similar phenology were studied in two consecutive years in the field at the National Agronomic Research Centre (CNRA) of Bambey (Senegal, West Africa) under two post-anthesis water treatments (irrigated, non-irrigated). Plant morphology, stem sugar related traits, grain production, and plant leaf area (PLA) variation were assessed. Carbohydrate contents (sucrose, hexoses, starch) were determined during grain filling in the whole stem juice and at three internode levels: bottom, median, top. Analysis of variance was performed to test post-anthesis water treatment, accession, organ, year effects and their interactions on the studied traits. Results Panicle dry weight (PDW) was not affected by drought, but strongly varied among years and accessions. The PDW/PLA ratio was negatively correlated with the variation of sucrose and hexoses at the three internodes levels. This carbohydrates reduction was mainly influenced by the PDW. The bigger the panicle the higher the carbohydrates remobilization from the stem to panicle for grain filling. This was mainly shown on accessions G3 and G11 which exhibited low stay green ability. However, G10 with low PDW/PLA ratio and showing higher stay green ability, exhibited a low reduction of total soluble sugars and sucrose and inversely higher increase of hexoses mainly at the median internode. Conclusions This ability to better maintain green leaf area and high hexoses in the stem under post-flowering drought could be an osmoregulation mechanism to adapt to drought. Therefore, stay-green is an important trait to consider for sweet sorghum breeding and particularly in the objective of developing dual purpose varieties in drought prone environments.

Abstract Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolor L. Moench) in western Africa (WA) has diversified across a mosaic of cultures and end uses and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping‐by‐sequencing (GBS) was used to generate 159,101 high‐quality biallelic single nucleotide polymorphisms (SNPs), with 43% in intergenic regions and 13% in genic regions. High genetic diversity was observed within the WASAP (π = .00045), only slightly less than in a global diversity panel (GDP) (π = .00055). Linkage disequilibrium (LD) decayed to background level (r2 < .1) by ∼50 kb in the WASAP. Genome‐wide diversity was structured both by botanical type and by populations within botanical type with eight ancestral populations identified. Most populations were distributed across multiple countries, suggesting several potential common gene pools across the national programs. Genome‐wide association studies (GWAS) of days to flowering (DFLo) and plant height (PH) revealed eight and three significant quantitative trait loci (QTL), respectively, with major height QTL at canonical height loci Dw3 and SbHT7.1. Colocalization of two of eight major flowering time QTL with flowering genes previously described in U.S. germplasm (Ma6 and SbCN8) suggests that photoperiodic flowering in West African sorghum is conditioned by both known and novel genes. This genomic resource provides a foundation for genomics‐enabled breeding of climate‐resilient varieties in WA.

Abstract Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum (Sorghum bicolor L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. To address this issue, we characterized a large panel of 421 georeferenced sorghum landrace accessions from Senegal and adjacent locations at 213,916 single‐nucleotide polymorphisms (SNPs) using genotyping‐by‐sequencing. Seven subpopulations distributed along the north‐south precipitation gradient were identified. Redundancy analysis found that climate variables explained up to 8% of SNP variation, with climate collinear with space explaining most of this variation (6%). Genome scans of nucleotide diversity suggest positive selection on chromosome 2, 4, 5, 7, and 10 in durra sorghums, with successive adaptation during diffusion along the Sahel. Putative selective sweeps were identified, several of which colocalize with stay‐green drought tolerance (Stg) loci, and a priori candidate genes for photoperiodic flowering and inflorescence morphology. Genome‐wide association studies of photoperiod sensitivity and panicle compactness identified 35 and 13 associations that colocalize with a priori candidate genes, respectively. Climate‐associated SNPs colocalize with Stg3a, Stg1, Stg2, and Ma6 and have allelic distribution consistent with adaptation across Sahelian and Soudanian zones. Taken together, the findings suggest an oligogenic basis of adaptation to Sahelian versus Soudanian climates, underpinned by variation in conserved floral regulatory pathways and other systems that are less understood in cereals.

Combining resistance to grain mold with high grain yield in tannin-free white-grained photoperiod-insensitive sorghum is of major interest for farmers in Senegal. In this study, GGE biplot analysis was used to assess the performance, adaptability, and stability of eleven sorghum parental lines and their hybrid combinations for yield and grain mold resistance under Senegalese environments. Eleven inbred lines along with their 22 hybrid combinations and one check were evaluated across three sites during the 2015 and 2016 rainy seasons under natural grain mold infestation. The results of this study showed strong genetic variability among studied genotypes for all measured traits. The highly significant G × E interaction effects for grain yield and panicle grain mold rating score (PGMR) indicated that both traits are influenced by genetics and to some extent by environment. Broad-sense heritability computed was high for all these traits except PGMR, showing a high environmental pressure on this later. The study showed that grain mold pressure in the studied sites decreased following a South-North gradient similar to the rainfall pattern, with the south region wetter, explaining the high disease pressure in Darou and Sinthiou Maleme contrary to Bambey. The GGE biplot analysis performed showed that the first two principal components explained 85.84% of the total variation of GGE sum of squares for grain yield. The which-won-where view of the GGE biplot for grain yield showed that the hybrid HB16 was the most adapted for Bambey area. The ranking of genotypes based on both yield performance and stability showed that HB16, HB5, HB21, HB18, and HB7 were the best hybrids combining high grain yield, high stability performance, and tolerance to grain mold disease across the test environments. These hybrids outperformed the best yielding inbred line P29 (2196.7 kg ha−1) with grain yield advantages ranging 17–60%. Therefore, these hybrids could be recommended to farmers in order to improve sorghum yield in Senegal.

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.

Pearl millet is an important cereal crop for smallholder farmers’ food security in West and Central Africa. However, its production has stagnated due to several factors such as the continuous use of local populations. A set of 17 inbred lines was crossed with Sosat C 88 and Souna 3 following a line × tester mating design. The F1 hybrids, their parents, and a check were evaluated in Bambey and Nioro research stations during the rainy season of 2017. Data on downy mildew incidence, plant height, flowering time, panicle length and diameter, productive tillers, thousand-grain weight, panicle, and grain yield were recorded. GCA and SCA mean squares were significant for most of the traits indicating that both additive and nonadditive gene effects were involved in the control of the inheritance of these traits. However, the contribution of GCA to total mean squares was higher than that of SCA for all the traits, providing that additive gene action was more important in their inheritance. The top-cross hybrid IBL155-2-1 × Sosat C 88 exhibited negative and significant SCA effects for downy mildew incidence, flowering time, and plant height. Lines IBL003-B-1, IBL091-1-1, IBL095-4-1, IBL110-B-1, and IBL 206-1-1 had positive GCA effects for grain yield and negative GCA effects for downy mildew, flowering time, and plant height. These lines can be used as parents to create synthetic varieties or hybrids.

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.

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.

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 towards the improvement in stress tolerance of sesame.

The stay-green phenomenon is a key plant trait with wide usage in managing crop production under limited water conditions. This trait enhances delayed senescence, biomass, and grain yield under drought stress. In this study we sought to identify QTLs in cowpea (Vigna unguiculata) consistent across experiments conducted in Burkina Faso, Nigeria, Senegal, and the United States of America under limited water conditions. A panel of 383 diverse cowpea accessions and a recombinant inbred line population (RIL) were SNP genotyped using an Illumina 1536 GoldenGate assay. Phenotypic data from thirteen experiments conducted across the four countries were used to identify SNP-trait associations based on linkage disequilibrium association mapping, with bi-parental QTL mapping as a complementary strategy. We identified seven loci, five of which exhibited evidence suggesting pleiotropic effects (stay-green) between delayed senescence, biomass, and grain yield. Further, we provide evidence suggesting the existence of positive pleiotropy in cowpea based on positively correlated mean phenotypic values (0.34< r

Abstract Cowpea (Vigna unguiculata) plays a key role in family farming systems in Senegal. It makes an essential contribution to economic, nutritional and food security. Although it is crucial, little is known about how farmers classify the diversity of local varieties or about the social practices associated with them. The aim of this study is to characterize the farming practices associated with growing cowpea in Senegal. Surveys were conducted involving 335 rural farmers living in 37 villages, spread across seven regions that produce cowpea. An average of ten farmers were randomly selected in each village. The results reveal that cowpea is a key feature of cropping systems in the studied area. Our findings highlight the high diversity of local cowpea varieties with 59 local names inventoried. In 75% of cases, the name refers to the seed’s morphology or color. Cowpea production is more diverse in Diourbel and Louga and less diverse in the south. More than half the farmers (57%) acquired their cowpea seeds (early, semi-early and late maturity varieties) outside their village, either from markets, seed suppliers or NGOs. This new understanding of farmers’ expertize in the management of cowpea and its local variability will help to valorize local diversity in breeding programs.

Sesame is an important oilseed crop in Africa and Asia, owing to its high nutritional quality seed and market value. Variation in sesame seed components including oil, oleic acid, linoleic acid, and protein was investigated by near-infrared reflectance spectrometry in 139 samples collected from different countries. Oil and protein contents were between 40.8% and 60.3% (mean 53.0%) and 15.5% to 25.5% (mean 20.4%), respectively. Linoleic acid, ranging from 31.8% to 52.4% (mean 46%) was more abundant than oleic acid (31.8%–50.6%, mean 38.1%). Light-seeded samples displayed higher nutritional quality, as they were richer in oil, protein, and linoleic acid than dark seeds. Samples from Africa had higher oil and linoleic acid contents, while Asian samples had higher oleic content. The analysis revealed West African sesame cultivars containing especially high levels of seed components, which may command high market values. Two clusters of sesame samples grouped by seed composition were obtained, including one cluster with high oil and oleic acid content and the other with high protein and linoleic acid content. This study revealed that sesame samples from Africa and Asia harbor high variation for major seed components and also provided background information for breeding high-nutrition varieties according to the demands of sesame seed markets.

Abstract 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.

Abstract 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 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.

Sorghum [Sorghum bicolor (L.) Moench] is an important staple food crop in northern Benin. In order to assess its diversity in Benin, 142 accessions of landraces collected from Northern Benin were grown in Central Benin and characterised using 10 qualitative and 14 quantitative agromorphological traits. High variability among both qualitative and quantitative traits was observed. Grain yield (0.72–10.57 tons/ha), panicle weight (15–215.95 g), days to 50% flowering (57–200 days), and plant height (153.27–636.5 cm) were among traits that exhibited broader variability. Correlations between quantitative traits were determined. Grain yield for instance exhibited highly positive association with panicle weight (r=0.901, P=0.000) and 100 seed weight (r=0.247, P=0.000). UPGMA cluster analysis classified the 142 accessions into 89 morphotypes. Based on multivariate analysis, twenty promising sorghum genotypes were selected. Among them, AT41, AT14, and AT29 showed early maturity (57 to 66 days to 50% flowering), high grain yields (4.85 to 7.85 tons/ha), and shorter plant height (153.27 to 180.37 cm). The results obtained will help enhancing sorghum production and diversity and developing new varieties that will be better adapted to the current soil and climate conditions in Benin.

Cowpea [ (L.) Walp.] is a major tropical legume crop grown in warm to hot areas throughout the world and especially important to the people of sub-Saharan Africa where the crop was domesticated. To date, relatively little is understood about its domestication origins and patterns of genetic variation. In this study, a worldwide collection of cowpea landraces and African ancestral wild cowpea was genotyped with more than 1200 single nucleotide polymorphism markers. Bayesian inference revealed the presence of two major gene pools in cultivated cowpea in Africa. Landraces from gene pool 1 are mostly distributed in western Africa while the majority of gene pool 2 are located in eastern Africa. Each gene pool is most closely related to wild cowpea in the same geographic region, indicating divergent domestication processes leading to the formation of two gene pools. The total genetic variation within landraces from countries outside Africa was slightly greater than within African landraces. Accessions from Asia and Europe were more related to those from western Africa while accessions from the Americas appeared more closely related to those from eastern Africa. This delineation of cowpea germplasm into groups of genetic relatedness will be valuable for guiding introgression efforts in breeding programs and for improving the efficiency of germplasm management.

Highlights • We studied the role of DNA methylation in sesame response to two abiotic stresses. • Opposite DNA methylation patterns are induced by drought and waterlogging. • Drought and waterlogging trigger contrasting transcript level regulations in sesame. • High correlation between transcript level regulations and DNA methylation patterns. Abstract 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. [ABSTRACT FROM AUTHOR]