Dynamic transcriptome landscape of sesame (Sesamum indicum L.) under progressive drought and after rewatering.
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SUBMITTER: Dossa K
PROVIDER: S-EPMC5288455 | biostudies-literature | 2017 Mar
REPOSITORIES: biostudies-literature
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Dynamic transcriptome landscape of sesame (<i>Sesamum indicum</i> L.) under progressive drought and after rewatering.
Dossa Komivi K Li Donghua D Wang Linhai L Zheng Xiaomin X Yu Jingyin J Wei Xin X Fonceka Daniel D Diouf Diaga D Liao Boshou B Cisse Ndiaga N Zhang Xiurong X
Genomics data 20170127
Drought is one of the most important abiotic stresses that impair sesame (<i>Sesamum indicum</i> 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 ...[more]
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Project description:Sesame is predominantly cultivated in rainfed and low fertile lands and is frequently exposed to terminal drought. Sesamum species inhabiting dryland ecosystems adaptively diverge from those inhabiting rainfed habitats, and drought-specific traits have a genetic basis. In sesame, traits associated with drought conditions have not been explored to date, yet studies of these traits are needed given that drought is predicted to become more frequent and severe in many parts of the world because of climate change. Here, 76 accessions from the available Indian core set were used to quantify variation in several traits under irrigated (WW) and terminal drought stress (WS) conditions as well as their association with seed yield over two consecutive years. The range of trait variation among the studied genotypes under WW and WS was significant. Furthermore, the traits associated with seed yield under WW and WS differed. The per se performance of the accessions indicated that the expression of most traits was reduced under WS. The correlation analysis revealed that the number of branches, leaf area (LA), leaves dry weight (LDW), number of capsules plant-1, and harvest index (HI) were positively correlated with seed yield under WW and WS, and total dry matter (TDM), plant stem weight, and canopy temperature (CT) were negatively correlated with seed yield under WW and WS, indicating that smaller and cooler canopy genotypes had higher yields. The genotypes IC-131936, IC-204045, IC-204861, IC-205363, IC-205311, and IC-73576 with the highest seed yields were characterized by low canopy temperature, high relative water content, and high harvest index under WS. Phenotypic and molecular diversity analysis was conducted on genotypes along with checks. Phenotypic diversity was assessed using multivariate analysis, whereas molecular diversity was estimated using simple sequence repeat (SSR) loci to facilitate the use of sesame in breeding and genetic mapping. SSRs showed low allelic variation, as indicated by a low average number of alleles (2.31) per locus, gene diversity (0.25), and polymorphism information content (0.22). Cluster analysis (CA) [neighbor-joining (NJ) tree] revealed three major genotypic groups and structure analysis showed 4 populations. The diverse genotypes identified with promising morpho-physiological traits can be used in breeding programs to develop new varieties.
| S-EPMC8709571 | biostudies-literature
Project description:Sesame (Sesamum indicum L.) is an important cash crop cultivated under rain-fed conditions where it contributes a significant proportion of Ethiopia's foreign exchange earnings. However, its productivity is constrained by drought stress. The present study aimed to evaluate the agromorphological and yield performance of sesame varieties and to identify drought tolerant varieties using drought tolerance indices. The sesame varieties were evaluated under well-watered (WW) and water-stressed (WS) field conditions with a factorial design laid down in randomized complete block design in three replications. The results revealed the presence of a significant variation in agromorphological traits and drought tolerance indices due to water levels, varieties and their interactive effect. On average, a 21.8, 49.6, 48.4, 47.9 and 21.7% reduction was recorded in plant height, number of leaves per plant, leaf length, leaf width and relative growth rate (RGR), respectively under WS condition. Similarly, a significant reduction was found in shoot biomass, root biomass, biological yield, number of pods per plant and seed yield under WS condition. These traits showed an average reduction of 52.2, 72.5, 54.0, 51.9 and 52.8%, respectively compared to WW condition. The highest yield reduction was recorded from wollega under WS condition, while the lowest was from abasena. Wollega variety produced the highest seed yield (kg/ha) under WW condition, while gondar-1 and humera-1 had the highest yield in kg/ha under WS condition. Under both water levels, abasena produced the lowest yield (kg/ha). Moreover, gondar-1 and humera-1 varieties had a comparatively higher values of stress tolerance index (STI), yield stress score index (YSSI), yield potential score index (YPSI), geometric mean productivity (GMP) and mean productivity (MP) that are significantly and positively correlated with yield under WS, indicating higher yield performance under water stress. The biplot analysis clustered the varieties as low yielding (abasena) and relatively above average performing varieties (humera-1, gondar-1 and wollega). According to the rank sum of all indices, humera-1 was identified as drought tolerant, while abasena as the most susceptible and low yielding varieties. Thus, humera-1 followed by gondar-1 were found to be drought tolerant and high yielding varieties. However, further studies focusing on drought tolerance mechanisms of the varieties are recommended.
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Project description:Major lignans of sesame sesamin and sesamolin are benzodioxol--substituted furofurans. Sesamol, sesaminol, its epimers, and episesamin are transformation products found in processed products. Synthetic routes to all lignans are known but only sesamol is synthesized industrially. Biosynthesis of furofuran lignans begins with the dimerization of coniferyl alcohol, followed by the formation of dioxoles, oxidation, and glycosylation. Most genes of the lignan pathway in sesame have been identified but the inheritance of lignan content is poorly understood. Health-promoting properties make lignans attractive components of functional food. Lignans enhance the efficiency of insecticides and possess antifeedant activity, but their biological function in plants remains hypothetical. In this work, extensive literature including historical texts is reviewed, controversial issues are critically examined, and errors perpetuated in literature are corrected. The following aspects are covered: chemical properties and transformations of lignans; analysis, purification, and total synthesis; occurrence in Seseamum indicum and related plants; biosynthesis and genetics; biological activities; health-promoting properties; and biological functions. Finally, the improvement of lignan content in sesame seeds by breeding and biotechnology and the potential of hairy roots for manufacturing lignans in vitro are outlined.
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Project description:Sesamum indicum is an ancient oil crop grown in tropical and subtropical areas of the world. We have analyzed 23,538 coding sequences (CDS) of S. indicum to understand the factors shaping codon usage in this important oil crop plant. We identified eleven highly preferred codons in S. indicum that have AT-endings. The slope of a neutrality plot was less than one while effective number of codons (ENC) plot showed distribution above and below the standard curve. There is a significant relationship between protein length and relative synonymous codon usage (RSCU) at the primary axis while there is a weak correlation between protein length and Nc values. Correspondence analysis conducted on RSCU values differentiated CDS based on their GC content and their characteristic feature and showed a discrete distribution. Moreover, by determining codon usage, we found out that majority of the lignan biosynthesis related genes showed a weaker codon usage bias. These results provide insights into understanding codon evolution in sesame.
| S-EPMC8789531 | biostudies-literature
Project description:Simple Summary Sesame (Sesamum indicum L.) is an important oilseed crop that is well known for its highly nutritious oil content. Due to its high oil content and nutritional properties, sesame is also known as the ‘queen of oilseeds’. Phytoplasma-associated diseases such as phyllody and little leaf are critical threats to sesame cultivation worldwide. Sesame phyllody is the leading biotic constraint drastically affecting sesame productivity and resulting in yield losses of up to 80% in major sesame-producing countries in the world. In this study, we explored the role of DNA methylation in phytoplasma infection. Whole Genome Bisulfite Sequencing and a Quantitative analysis of DNA methylation using real-time PCR (qAMP) revealed an alteration of methylation pattern upon phytoplasma infection. Few selected development and defense-related loci were either hypo- or hypermethylated. We hereby report the first methylome study in healthy and phytoplasma-infected sesame. Our study provides fundamental insights into the role of DNA methylation in the symptom development of phytoplasma infection in sesame plants. Abstract Phytoplasma-associated diseases such as phyllody and little leaf are critical threats to sesame cultivation worldwide. The mechanism of the dramatic conversion of flowers to leafy structures leading to yield losses and the drastic reduction in leaf size due to Phytoplasma infection remains yet to be identified. Cytosine methylation profiles of healthy and infected sesame plants studied using Whole Genome Bisulfite Sequencing (WGBS) and Quantitative analysis of DNA methylation with the real-time PCR (qAMP) technique revealed altered DNA methylation patterns upon infection. Phyllody was associated with global cytosine hypomethylation, though predominantly in the CHH (where H = A, T or C) context. Interestingly, comparable cytosine methylation levels were observed between healthy and little leaf-affected plant samples in CG, CHG and CHH contexts. Among the different genomic fractions, the highest number of differentially methylated Cytosines was found in the intergenic regions, followed by promoter, exonic and intronic regions in decreasing order. Further, most of the differentially methylated genes were hypomethylated and were mainly associated with development and defense-related processes. Loci for STOREKEEPER protein-like, a DNA-binding protein and PP2-B15, an F-Box protein, responsible for plugging sieve plates to maintain turgor pressure within the sieve tubes were found to be hypomethylated by WGBS, which was confirmed by methylation-dependent restriction digestion and qPCR. Likewise, serine/threonine-protein phosphatase-7 homolog, a positive regulator of cryptochrome signaling involved in hypocotyl and cotyledon growth and probable O-methyltransferase 3 locus were determined to be hypermethylated. Phytoplasma infection-associated global differential methylation as well as the defense and development-related loci reported here for the first time significantly elucidate the mechanism of phytoplasma-associated disease development.
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Project description:The development and validation of different types of molecular markers is crucial to conducting marker-assisted sesame breeding. Insertion-deletion (InDel) markers are highly polymorphic and suitable for low-cost gel-based genotyping. From this perspective, this study aimed to discover and develop InDel markers through bioinformatic analysis of double digest restriction site-associated DNA sequencing (ddRADSeq) data from 95 accessions belonging to the Mediterranean sesame core collection. Bioinformatic analysis indicated the presence of 7477 InDel positions genome wide. Deletions accounted for 61% of the InDels and short deletions (1-2 bp) were the most abundant type (94.9%). On average, InDels of at least 2 bp in length had a frequency of 2.99 InDels/Mb. The 86 InDel sites having length ≥8 bp were detected in genome-wide analysis. These regions can be used for the development of InDel markers considering low-cost genotyping with agarose gels. In order to validate these InDels, a total of 38 InDel regions were selected and primers were successfully amplified. About 13% of these InDels were in the coding sequences (CDSs) and in the 3'- and 5'- untranslated regions (UTRs). Furthermore, the efficiencies of these 16 InDel markers were assessed on 32 sesame accessions. The polymorphic information content (PIC) of these 16 markers ranged from 0.06 to 0.62 (average: 0.33). These results demonstrated the success of InDel identification and marker development for sesame with the use of ddRADSeq data. These agarose-resolvable InDel markers are expected to be useful for sesame breeders.
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Project description:Sesame (Sesamum indicum L.) is an important and ancient oilseed crop. Sesame seed coat color is related to biochemical functions involved in protein and oil metabolism, and antioxidant content. Because of its complication, the genetic basis of sesame seed coat color remains poorly understood. To elucidate the factors affecting the genetic architecture of seed coat color, 366 sesame germplasm lines were evaluated for seed coat color in 12 environments. The genome-wide association studies (GWAS) for three seed coat color space values, best linear unbiased prediction (BLUP) values from a multi-environment trial analysis and principal component scores (PCs) of three seed coat color space values were conducted. GWAS for three seed coat color space values identified a total of 224 significant single nucleotide polymorphisms (SNPs, P < 2.34×10-7), with phenotypic variation explained (PVE) ranging from 1.01% to 22.10%, and 35 significant SNPs were detected in more than 6 environments. Based on BLUP values, 119 significant SNPs were identified, with PVE ranging from 8.83 to 31.98%. Comparing the results of the GWAS using phenotypic data from different environments and the BLUP values, all significant SNPs detected in more than 6 environments were also detected using the BLUP values. GWAS for PCs identified 197 significant SNPs, and 30 were detected in more than 6 environments. GWAS results for PCs were consistent with those for three color space values. Out of 224 significant SNPs, 22 were located in the confidence intervals of previous reported quantitative trait loci (QTLs). Finally, 92 candidate genes were identified in the vicinity of the 4 SNPs that were most significantly associated with sesame seed coat color. The results in this paper will provide new insights into the genetic basis of sesame seed coat color, and should be useful for molecular breeding in sesame.
| S-EPMC8139513 | biostudies-literature
Project description:The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has been widely utilized for targeted genome modification in a wide range of species. It is a powerful genome editing technology, providing significant benefits for gene functional research and molecular breeding. However, to date, no study has applied this genome editing tool to sesame (Sesamum indicum L.), one of the most ancient and important oil crops used widely in diverse industries such as food and medicine. Herein, the CRISPR/Cas9 system along with hairy root transformation was used to induce targeted mutagenesis in sesame. Two single guide RNAs (sgRNAs) were designed to target two sesame cytochrome P450 genes (CYP81Q1 and CYP92B14), which are the key biosynthetic gene of sesamin and sesamolin, respectively. Sequencing data illustrated the expected InDel mutations at the target sites, with 90.63 and 93.33% mutation frequency in CYP81Q1 and CYP92B14, respectively. The most common editing event was single nucleotide deletion and insertion. Sequencing of potential off-target sites of CYP92B14-sgRNA showed no off-target events in cases of three mismatches. High-performance liquid chromatography analysis showed that sesamin and sesamolin biosynthesis was effectively disrupted in the mutated hairy roots, confirming the crucial role of CYP81Q1 and CYP92B14 in sesame lignan biosynthesis. These results demonstrated that targeted mutagenesis was efficiently created by the CRISPR/Cas9 system, and CRISPR/Cas9 coupled with hairy root transformation is an effective tool for assessing gene functions in sesame.
| S-EPMC9309882 | biostudies-literature
Project description:BackgroundSesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In addition, a shortage of sesame molecular markers limits the efficiency and accuracy of genetic breeding. High-throughput transcriptomic sequencing is essential to generate a large transcriptome sequence dataset for gene discovery and molecular marker development.ResultsSesame transcriptomes from five tissues were sequenced using Illumina paired-end sequencing technology. The cleaned raw reads were assembled into a total of 86,222 unigenes with an average length of 629 bp. Of the unigenes, 46,584 (54.03%) had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value < 10-5). Of these annotated unigenes, 10,805 and 27,588 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In total, 22,003 (25.52%) unigenes were mapped onto 119 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Furthermore, 44,750 unigenes showed homology to 15,460 Arabidopsis genes based on BLASTx analysis against The Arabidopsis Information Resource (TAIR, Version 10) and revealed relatively high gene coverage. In total, 7,702 unigenes were converted into SSR markers (EST-SSR). Dinucleotide SSRs were the dominant repeat motif (67.07%, 5,166), followed by trinucleotide (24.89%, 1,917), tetranucleotide (4.31%, 332), hexanucleotide (2.62%, 202), and pentanucleotide (1.10%, 85) SSRs. AG/CT (46.29%) was the dominant repeat motif, followed by AC/GT (16.07%), AT/AT (10.53%), AAG/CTT (6.23%), and AGG/CCT (3.39%). Fifty EST-SSRs were randomly selected to validate amplification and to determine the degree of polymorphism in the genomic DNA pools. Forty primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 24 sesame accessions.ConclusionsThis study demonstrates that Illumina paired-end sequencing is a fast and cost-effective approach to gene discovery and molecular marker development in non-model organisms. Our results provide a comprehensive sequence resource for sesame research.
| S-EPMC3184296 | biostudies-literature