The genetic basis of drought tolerance in the high oil crop Sesamum indicum

Fine Mapping of the QTL qRLP12 That Controls Root Length Under Polyethylene glycol-Induced Drought Stress During the Early Seedling Stage of Sesame

A deeper root system can improve the efficiency of water and nutrient absorption from soil; therefore, genetic improvements to the root length of crops are essential for yield stability under drought stress. We previously identified a stable quantitative trait locus (QTL) qRLP12 for root length under polyethylene glycol (PEG)-induced drought stress in a Jinhuangma (JHM, sensitive)/Zhushanbai (ZSB, tolerant) recombinant inbred line (RIL) population. To validate and fine map this QTL, in this study, a secondary F2 population was constructed, and the genetic effect of the target QTL was validated by comparing the phenotype data of different genotypes. Using newly developed markers, 14 genotypes of recombinant F2 individuals were obtained. A phenotypic analysis of homozygous recombinant progeny lines narrowed qRLP12 to a 91 kb region. Seven putative predicted genes were identified in the target region, among which LOC105165547, a callose synthase gene, was the only one containing nonsynonymous variations in the coding region between two parents. Quantitative real-time PCR analysis revealed that LOC105165547 was significantly induced by PEG stress in the qRLP12+ line. These indicated that LOC105165547 might be the candidate gene for qRLP12, which is responsible for root length subjected to PEG stress. Our results provide a favored gene resource for improving root length under drought stress in sesame.

Assessing the drought tolerance of some sesame genotypes using agro-morphological, physiological, and drought tolerance indices

BACKGROUND

One significant abiotic stressor that harms sesame productivity globally is drought. This investigation used six sesame genotypes to measure variance in many variables under irrigated and terminal drought stress environments. Growth characteristics (plant height, fruiting zone length, branches' number), yield-related parameters (capsules' number per plant, capsule's length, 1000 seeds' weight, seed yield per plant, and seed yield per feddan) and physiological characters (relative water content, chlorophyll A content, chlorophyll B content, chlorophyll A + B content, and proline concentration) of sesame were measured. Six drought indices (geometric mean productivity (GMP), mean productivity (MP), stress tolerance index (STI), tolerance index (TOL), stress susceptibility index (SSI) and, yield stability index (YSI)) were derived using seed yield per feddan. This study was aimed to investigate the effects of drought stress on the physiological and yield-related characteristics of the sesame genotypes and to find the qualities that were most helpful in selecting drought-resistant genotypes.

RESULTS

The analysis of variance revealed significant differences in genotypes and water depletion ratios, as well as their interactions, for all growth variables, except the interaction between genotypes and water depletion ratios for plant height and relative water content. Line 13 (H. 102) had the highest branches' number (6.85), capsules' number per plant (239.33) and capsule's length (3.35 cm) attributes under normal circumstances. Line 31 (H. 68) produced the maximum yield per plant (33.45 g) and feddan (679.83) and had the highest weight of 1000 seeds (3.9 g) under normal circumstances. Under the level (80% water depletion ratio), H. 68 had the highest amounts of chlorophyll A (5.73) and chlorophyll A + B (17.37) whereas H. 102 exhibited the highest concentration of chlorophyll B (5.73). The genotype H. 68 of sesame was found to have the greatest MP (650.35), GMP (649.32) and YI (1.16) indices followed by genotype H. 102. The Shandaweell 3 genotype resulted in the lowest SSI (36.92) and TOL (0.55) indices. Line 26 (H132) exhibited the highest average YSI values.

CONCLUSIONS

These data revealed that genotypes H. 102, H. 68 and Shandaweell 3 are the most drought-tolerant among the genotypes utilized in this study. These results may contribute to developing effective breeding techniques for drought-stressed sesame in the future.

Genome-wide identification and expression analysis of the lipoxygenase gene family in sesame reveals regulatory networks in response to abiotic stress

BACKGROUND

Plant lipoxygenase (Lox) genes, catalyze polyunsaturated fatty acids and play essential roles in plant growth, development, and stress responses. It is extensively studied under various stresses, their role in abiotic stress responses remains unexplored in sesame.

METHODS AND RESULTS

This study identified seven Lox genes in sesame divided into two subfamilies: 9-Lox (Silox1, Silox2 and Silox3) are likely involved in pathogen defence and signalling and 13-Lox (Type-I: Silox4 and Type-II: Silox5, Silox6 and Silox7) play crucial roles in jasmonic acid biosynthesis and abiotic stress responses. Silox genes have undergone purifying selection, promoting the stability of gene function and prefer codons with A or T in the third position. The chromosomal distribution, sequence similarity, and subcellular localization, with conserved lipoxygenase domains and motifs were analysed. Promoter regions contained 34 cis-acting regulatory elements (e.g. WRKY, ERF, and bHLH) and 35 transcription factors binding sites (TFBS) linked to light, stress (e.g. MYC, W-box, ERE and STRE), phytohormones, and growth. Differential Gene Expression (DGE) analysis showed Lox1 was upregulated in Drought sensitive (DS) and in Drought tolerant (DT) the Lox1 & Lox3 were upregulated when compared to control. In addition, weighted gene co-expression network analysis (WGCNA) of Lox, showed that blue module is positively correlated with drought tolerance. Fourteen hub genes related to stress were identified, which closely associated with Lox1. Gene ontology and KEGG pathway analyses showed that these genes were linked to linoleic acid metabolism, lipid metabolism, and stress response. Quantitative Real-Time PCR (qRT-PCR) analysis confirmed that Silox genes showed time-varying differential expression under drought, salt and a combined drought-salt stress treatments.

CONCLUSION

This research lays the groundwork for future studies on the role of Lox genes in sesame's growth and stress adaptation.

Leveraging genomics and temporal high-throughput phenotyping to enhance association mapping and yield prediction in sesame

Sesame (Sesamum indicum) is an important oilseed crop with rising demand owing to its nutritional and health benefits. There is an urgent need to develop and integrate new genomic-based breeding strategies to meet these future demands. While genomic resources have advanced genetic research in sesame, the implementation of high-throughput phenotyping and genetic analysis of longitudinal traits remains limited. Here, we combined high-throughput phenotyping and random regression models to investigate the dynamics of plant height, leaf area index, and five spectral vegetation indices throughout the sesame growing seasons in a diversity panel. Modeling the temporal phenotypic and additive genetic trajectories revealed distinct patterns corresponding to the sesame growth cycle. We also conducted longitudinal genomic prediction and association mapping of plant height using various models and cross-validation schemes. Moderate prediction accuracy was obtained when predicting new genotypes at each time point, and moderate to high values were obtained when forecasting future phenotypes. Association mapping revealed three genomic regions in linkage groups 6, 8, and 11, conferring trait variation over time and growth rate. Furthermore, we leveraged correlations between the temporal trait and seed-yield and applied multi-trait genomic prediction. We obtained an improvement over single-trait analysis, especially when phenotypes from earlier time points were used, highlighting the potential of using a high-throughput phenotyping platform as a selection tool. Our results shed light on the genetic control of longitudinal traits in sesame and underscore the potential of high-throughput phenotyping to detect a wide range of traits and genotypes that can inform sesame breeding efforts to enhance yield.

Combined GWAS and eGWAS reveals the genetic basis underlying drought tolerance in emmer wheat (Triticum turgidum L.)

Drought is one of the major environmental constraints for wheat production world-wide. As the progenitor and genetic reservoir of common wheat, emmer wheat is considered as an invaluable gene pool for breeding drought-tolerant wheat. Combining GWAS and eGWAS analysis of 107 accessions, we identified 86 QTLs, 105 462 eQTLs as well as 68 eQTL hotspots associating with drought tolerance (DT) in emmer wheat. A complex regulatory network composed of 185 upstream regulator and 2432 downstream drought-responsive candidates was developed, of which TtOTS1 was found to play a negative effect in determining DT through affecting root development. This study sheds light on revealing the genetic basis underlying DT, which will provide the indispensable genes and germplasm resources for elite drought tolerance wheat improvement and breeding.

QTL mapping in sesame (Sesamum indicum L.): A review

Sesame (Sesamum indicum L.) is an important oilseed crop used for food, feed, medicinal, and industrial applications. Inherently low genetic yield potential and susceptibility to biotic and abiotic stresses contribute to low productivity in sesame. Development of stress resistant varieties coupled with high yield is a viable option to raise the genetic potential of sesame. Conventional phenotype-based breeding methods have made an important role in the last couple of decades by developing several sesame varieties with improved quality, yield, and tolerance to biotic and abiotic stresses. However, due to adverse environmental effects, time consuming to develop new variety, and low genetic gain, conventional phenotype-based approach is not adequate to satisfy the rising population growth. In this context, advanced method of genotype selection via modern techniques of biotechnology plays essential roles in reducing the constraints and boosting sesame production to satisfy the huge demand. In line to this, quantitative trait loci (QTL) mapping is considered as a promising method to address the problems of sesame breeding. Previously, huge data have been generated in the practical use of QTL for sesame improvement. Therefore, this paper aims to review recent advances in the area of QTL mapping for yield and yield related traits in sesame for enhancing and sustaining sesame production. In this section, we present an intensive review on the identification and mapping of the most desirable potential candidate genes/QTLs associated with desirable traits. Moreover, this review focuses on the major QTL regions and/or potential candidate genes and associated molecular markers that could provide potential genetic resources for molecular marker-assisted selection and further cloning of functional genes for yield and yield-related traits as well as various biotic and abiotic stress tolerances. Finally, the summarized QTL mapping data shed light on future directions for enhanced sesame breeding programs.

Omics technologies towards sesame improvement: a review

Genetic improvement of sesame (Sesamum indicum L.), one of the most important oilseed crops providing edible oil, proteins, minerals, and vitamins, is important to ensure a balanced diet for the growing world population. Increasing yield, seed protein, oil, minerals, and vitamins is urgently needed to meet the global demand. The production and productivity of sesame is very low due to various biotic and abiotic stresses. Therefore, various efforts have been made to combat these constraints and increase the production and productivity of sesame through conventional breeding. However, less attention has been paid to the genetic improvement of the crop through modern biotechnological methods, leaving it lagging behind other oilseed crops. Recently, however, the scenario has changed as sesame research has entered the era of "omics" and has made significant progress. Therefore, the purpose of this paper is to provide an overview of the progress made by omics research in improving sesame. This review presents a number of efforts that have been made over past decade using omics technologies to improve various traits of sesame, including seed composition, yield, and biotic and abiotic resistant varieties. It summarizes the advances in genetic improvement of sesame using omics technologies, such as germplasm development (web-based functional databases and germplasm resources), gene discovery (molecular markers and genetic linkage map construction), proteomics, transcriptomics, and metabolomics that have been carried out in the last decade. In conclusion, this review highlights future directions that may be important for omics-assisted breeding in sesame genetic improvement.

Molecular Advances to Combat Different Biotic and Abiotic Stresses in Linseed (Linum usitatissimum L.): A Comprehensive Review

Flax, or linseed, is considered a "superfood", which means that it is a food with diverse health benefits and potentially useful bioactive ingredients. It is a multi-purpose crop that is prized for its seed oil, fibre, nutraceutical, and probiotic qualities. It is suited to various habitats and agro-ecological conditions. Numerous abiotic and biotic stressors that can either have a direct or indirect impact on plant health are experienced by flax plants as a result of changing environmental circumstances. Research on the impact of various stresses and their possible ameliorators is prompted by such expectations. By inducing the loss of specific alleles and using a limited number of selected varieties, modern breeding techniques have decreased the overall genetic variability required for climate-smart agriculture. However, gene banks have well-managed collectionns of landraces, wild linseed accessions, and auxiliary Linum species that serve as an important source of novel alleles. In the past, flax-breeding techniques were prioritised, preserving high yield with other essential traits. Applications of molecular markers in modern breeding have made it easy to identify quantitative trait loci (QTLs) for various agronomic characteristics. The genetic diversity of linseed species and the evaluation of their tolerance to abiotic stresses, including drought, salinity, heavy metal tolerance, and temperature, as well as resistance to biotic stress factors, viz., rust, wilt, powdery mildew, and alternaria blight, despite addressing various morphotypes and the value of linseed as a supplement, are the primary topics of this review.

Plant Tolerance to Drought Stress with Emphasis on Wheat

Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.

Insights into chloroplast genome structure and phylogenetic relationships within the Sesamum species complex (Pedaliaceae)

Background: In the Sesamum species complex, the lack of wild species genomic resources hinders the evolutionary comprehension of phylogenetic relationships. Results: In the present study, we generated complete chloroplast genomes of six wild relatives (Sesamum alatum, Sesamum angolense, Sesamum pedaloides, Ceratotheca sesamoides (syn. Sesamum sesamoides), Ceratotheca triloba (syn. Sesamum trilobum), and Sesamum radiatum) and a Korean cultivar, Sesamum indicum cv. Goenbaek. A typical quadripartite chloroplast structure, including two inverted repeats (IR), a large single copy (LSC), and a small single copy (SSC), was observed. A total of 114 unique genes encompassing 80 coding genes, four ribosomal RNAs, and 30 transfer RNAs were counted. The chloroplast genomes (152, 863-153, 338 bp) exhibited the IR contraction/expansion phenomenon and were quite conserved in both coding and non-coding regions. However, high values of the nucleotide diversity index were found in several genes, including ndhA, ndhE, ndhF, ycf1, and psaC-ndhD. Concordant tree topologies suggest ndhF as a useful marker for taxon discrimination. The phylogenetic inference and time divergence dating indicate that S. radiatum (2n = 64) occurred concomitantly with the sister species C. sesamoides (2n = 32) approximately 0.05 million years ago (Mya). In addition, S. alatum was clearly discriminated by forming a single clade, showing its long genetic distance and potential early speciation event in regards to the others. Conclusion: Altogether, we propose to rename C. sesamoides and C. triloba as S. sesamoides and S. trilobum, respectively, as suggested previously based on the morphological description. This study provides the first insight into the phylogenetic relationships among the cultivated and wild African native relatives. The chloroplast genome data lay a foundation for speciation genomics in the Sesamum species complex.

Multi-environment analysis enhances genomic prediction accuracy of agronomic traits in sesame

Introduction: Sesame is an ancient oilseed crop containing many valuable nutritional components. The demand for sesame seeds and their products has recently increased worldwide, making it necessary to enhance the development of high-yielding cultivars. One approach to enhance genetic gain in breeding programs is genomic selection. However, studies on genomic selection and genomic prediction in sesame have yet to be conducted.

Methods: In this study, we performed genomic prediction for agronomic traits using the phenotypes and genotypes of a sesame diversity panel grown under Mediterranean climatic conditions over two growing seasons. We aimed to assess prediction accuracy for nine important agronomic traits in sesame using single- and multi-environment analyses.

Results: In single-environment analysis, genomic best linear unbiased prediction, BayesB, BayesC, and reproducing kernel Hilbert spaces models showed no substantial differences. The average prediction accuracy of the nine traits across these models ranged from 0.39 to 0.79 for both growing seasons. In the multi-environment analysis, the marker-by-environment interaction model, which decomposed the marker effects into components shared across environments and environment-specific deviations, improved the prediction accuracies for all traits by 15%–58% compared to the single-environment model, particularly when borrowing information from other environments was made possible.

Discussion: Our results showed that single-environment analysis produced moderate-to-high genomic prediction accuracy for agronomic traits in sesame. The multi-environment analysis further enhanced this accuracy by exploiting marker-by-environment interaction. We concluded that genomic prediction using multi-environmental trial data could improve efforts for breeding cultivars adapted to the semi-arid Mediterranean climate.

Genome-wise association study identified genomic regions associated with drought tolerance in mungbean (Vigna radiata (L.) R. Wilczek)

A total of 282 mungbean accessions were resequenced to identify genome-wide variants and construct a highly precise variant map, and drought tolerance-related loci and superior alleles were identified by GWAS. Mungbean (Vigna radiata (L.) R. Wilczek) is an important food legume crop that is highly adapted to drought environments, but severe drought significantly curtails mungbean production. Here, we resequenced 282 mungbean accessions to identify genome-wide variants and constructed a highly precise map of mungbean variants. A genome-wide association study was performed to identify genomic regions for 14 drought tolerance-related traits in plants grown under stress and well-watered conditions over three years. One hundred forty-six SNPs associated with drought tolerance were detected, and 26 candidate loci associated with more than two traits were subsequently selected. Two hundred fifteen candidate genes were identified at these loci, including eleven transcription factor genes, seven protein kinase genes and other protein coding genes that may respond to drought stress. Furthermore, we identified superior alleles that were associated with drought tolerance and positively selected during the breeding process. These results provide valuable genomic resources for molecular breeding and will accelerate future efforts aimed at mungbean improvement.

Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement

Sesame is one of the important traditional oil crops in the world, and has high economic and nutritional value. Recently, due to the novel high throughput sequencing techniques and bioinformatical methods, the study of the genomics, methylomics, transcriptomics, proteomics and metabonomics of sesame has developed rapidly. Thus far, the genomes of five sesame accessions have been released, including white and black seed sesame. The genome studies reveal the function and structure of the sesame genome, and facilitate the exploitation of molecular markers, the construction of genetic maps and the study of pan-genomes. Methylomics focus on the study of the molecular level changes under different environmental conditions. Transcriptomics provide a powerful tool to study abiotic/biotic stress, organ development, and noncoding RNAs, and proteomics and metabonomics also provide some support in studying abiotic stress and important traits. In addition, the opportunities and challenges of multi-omics in sesame genetics breeding were also described. This review summarizes the current research status of sesame from the perspectives of multi-omics and hopes to provide help for further in-depth research on sesame.

Genome-wide association analysis for drought tolerance and associated traits in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is an important high protein legume adapted to diverse climatic conditions with multiple benefits for the overall sustainability of the cropping systems. Plant-based protein demand is being expanded and faba bean is a good candidate to cover this need. However, the crop is very sensitive to abiotic stresses, especially drought, which severely affects faba bean yield and development worldwide. Therefore, identifying genes associated with drought stress tolerance is a major challenge in faba bean breeding. Although the faba bean response to drought stress has been widely studied, the molecular approaches to improve drought tolerance in this crop are still limited. Here we built on recent genomic advances such as the development of the first high-density SNP genotyping array, to conduct a genome-wide association study (GWAS) using thousands of genetic polymorphisms throughout the entire faba bean genome. A worldwide collection of 100 faba bean accessions was grown under control and drought conditions and 10 morphological, phenological and physiological traits were evaluated to identify single nucleotide polymorphism (SNP) markers associated with drought tolerance. We identified 29 SNP markers significantly correlated with these traits under drought stress conditions. The flanking sequences were blasted to the Medicago truncatula reference genomes in order to annotate potential candidate genes underlying the causal variants. Three of the SNPs for chlorophyll content after the stress, correspond to uncharacterized proteins indicating the presence of novel genes associated with drought tolerance in faba bean. The significance of stress-inducible signal transducers provides valuable information on the possible mechanisms underlying the faba bean response to drought stress, thus providing a foundation for future marker-assisted breeding in the crop.

Targeted and untargeted metabolomics reveals deep analysis of drought stress responses in needles and roots of Pinus taeda seedlings

Drought stress is one of major environmental stresses affecting plant growth and yield. Although Pinus taeda trees are planted in rainy southern China, local drought sometime occurs and can last several months, further affecting their growth and resin production. In this study, P. taeda seedlings were treated with long-term drought (42 d), and then targeted and untargeted metabolomics analysis were carried out to evaluate drought tolerance of P. taeda. Targeted metabolomics analysis showed that levels of some sugars, phytohormones, and amino acids significantly increased in the roots and needles of water-stressed (WS) P. taeda seedlings, compared with well-watered (WW) pine seedlings. These metabolites included sucrose in pine roots, the phytohormones abscisic acid and sacylic acid in pine needles, the phytohormone gibberellin (GA4) and the two amino acids, glycine and asparagine, in WS pine roots. Compared with WW pine seedlings, the neurotransmitter acetylcholine significantly increased in needles of WS pine seedlings, but significantly reduced in their roots. The neurotransmitters L-glutamine and hydroxytyramine significantly increased in roots and needles of WS pine seedlings, respectively, compared with WW pine seedlings, but the neurotransmitter noradrenaline significantly reduced in needles of WS pine seedlings. Levels of some unsaturated fatty acids significantly reduced in roots or needles of WS pine seedlings, compared with WW pine seedlings, such as linoleic acid, oleic acid, myristelaidic acid, myristoleic acid in WS pine roots, and palmitelaidic acid, erucic acid, and alpha-linolenic acid in WS pine needles. However, three saturated fatty acids significantly increased in WS pine seedlings, i.e., dodecanoic acid in WS pine needles, tricosanoic acid and heptadecanoic acid in WS pine roots. Untargeted metabolomics analysis showed that levels of some metabolites increased in WS pine seedlings, especially sugars, long-chain lipids, flavonoids, and terpenoids. A few of specific metabolites increased greatly, such as androsin, piceatanol, and panaxatriol in roots and needles of WS pine seedlings. Comparing with WW pine seedlings, it was found that the most enriched pathways in WS pine needles included flavone and flavonol biosynthesis, ABC transporters, diterpenoid biosynthesis, plant hormone signal transduction, and flavonoid biosynthesis; in WS pine roots, the most enriched pathways included tryptophan metabolism, caffeine metabolism, sesquiterpenoid and triterpenoid biosynthesis, plant hormone signal transduction, biosynthesis of phenylalanine, tyrosine, and tryptophan. Under long-term drought stress, P. taeda seedlings showed their own metabolomics characteristics, and some new metabolites and biosynthesis pathways were found, providing a guideline for breeding drought-tolerant cultivars of P. taeda.

Applications of Molecular Markers for Developing Abiotic-Stress-Resilient Oilseed Crops

Globally, abiotic stresses, such as temperature (heat or cold), water (drought and flooding), and salinity, cause significant losses in crop production and have adverse effects on plant growth and development. A variety of DNA-based molecular markers, such as SSRs, RFLPs, AFLPs, SNPs, etc., have been used to screen germplasms for stress tolerance and the QTL mapping of stress-related genes. Such molecular-marker-assisted selection strategies can quicken the development of tolerant/resistant cultivars to withstand abiotic stresses. Oilseeds such as rapeseed, mustard, peanuts, soybeans, sunflower, safflower, sesame, flaxseed, and castor are the most important source of edible oil worldwide. Although oilseed crops are known for their capacity to withstand abiotic challenges, there is a significant difference between actual and potential yields due to the adaptation and tolerance to severe abiotic pressures. This review summarizes the applications of molecular markers to date to achieve abiotic stress tolerance in major oilseed crops. The molecular markers that have been reported for genetic diversity studies and the mapping and tagging of genes/QTLs for drought, heavy metal stress, salinity, flooding, cold and heat stress, and their application in the MAS are presented.

Molecular Breeding and Drought Tolerance in Chickpea

Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).

Discovering favorable genes, QTLs, and genotypes as a genetic resource for sesame (Sesamum indicum L.) improvement

Sesame (Sesamum indicum L.) is an ancient diploid oilseed crop with high oil content, quality protein, and antioxidant characteristics that is produced in many countries worldwide. The genes, QTLs, and genetic resources of sesame are utilized by sesame researchers and growers. Researchers have identified the many useful traits of this crop, which are available on different platforms. The genes, genotypes, QTLs, and other genetic diversity data of sesame have been collected and stored in more than nine genomic resources, and five sesame crop marker databases are available online. However, data on phenotypic and genotypic variability, which would contribute to sesame improvements, are limited and not yet accessible. The present study comprehensively reviewed more than 110 original published research papers and scientifically incorporated the results. The candidate genes, genotypes, and QTLs of significantly important traits of sesame were identified. Genetic resources related to grain yield and yield component traits, oil content and quality, drought tolerance, salt tolerance, waterlogging resistance, disease resistance, mineral nutrient, capsule shattering resistance, and other agronomic important traits of sesame were studied. Numerous candidate genotypes, genes, QTLs, and alleles associated with those traits were summarized and discovered. The chromosome regions and linkage groups, maps associated with the best traits, and candidate genes were also included. The variability presented in this paper combined with sesame genetic information will help inform further sesame improvement.

Sesame (Sesamum indicum L.): A Comprehensive Review of Nutritional Value, Phytochemical Composition, Health Benefits, Development of Food, and Industrial Applications

Sesame (Sesamum indicum L.), of the Pedaliaceae family, is one of the first oil crops used in humans. It is widely grown and has a mellow flavor and high nutritional value, making it very popular in the diet. Sesame seeds are rich in protein and lipids and have many health benefits. A number of in vitro and in vivo studies and clinical trials have found sesame seeds to be rich in lignan-like active ingredients. They have antioxidant, cholesterol reduction, blood lipid regulation, liver and kidney protection, cardiovascular system protection, anti-inflammatory, anti-tumor, and other effects, which have great benefits to human health. In addition, the aqueous extract of sesame has been shown to be safe for animals. As an important medicinal and edible homologous food, sesame is used in various aspects of daily life such as food, feed, and cosmetics. The health food applications of sesame are increasing. This paper reviews the progress of research on the nutritional value, chemical composition, pharmacological effects, and processing uses of sesame to support the further development of more functionalities of sesame.

Food and nutraceutical functions of sesame oil: An underutilized crop for nutritional and health benefits

Sesame is the oldest oilseed crop known to humanity, though it contributes a small share in the global vegetable oil production. Sesame oil contains nutrients, including lignans, tocopherols, phytosterols, natural antioxidants, and bioactive compounds. It provides various health benefits such as anti-lipogenic, hypo-cholesterolemic, anti-degenerative, and neural health-promoting properties. Being an under-utilized minor crop, it has not received enough research attention for its food and nutraceutical potential. The sesame crop is a potential candidate to maintain the diversity of food oils and harness its benefits for improving human health. The present review will provide detailed research on sesame oil contents, health effects, nutraceuticals, oil quality, and value addition strategies. Also, the sesame oil nutritional quality was compared with other vegetable oils, highlighting the potential health and nutrition-related benefits. The way forward for further sesame improvement through value addition traits was also discussed.

Identification of Quantitative Trait Locus and Candidate Genes for Drought Tolerance in a Soybean Recombinant Inbred Line Population

With global warming and regional decreases in precipitation, drought has become a problem worldwide. As the number of arid regions in the world is increasing, drought has become a major factor leading to significant crop yield reductions and food crises. Soybean is a crop that is relatively sensitive to drought. It is also a crop that requires more water during growth and development. The aim of this study was to identify the quantitative trait locus (QTL) that affects drought tolerance in soybean by using a recombinant inbred line (RIL) population from a cross between the drought-tolerant cultivar 'Jindou21' and the drought-sensitive cultivar 'Zhongdou33'. Nine agronomic and physiological traits were identified under drought and well-watered conditions. Genetic maps were constructed with 923,420 polymorphic single nucleotide polymorphism (SNP) markers distributed on 20 chromosomes at an average genetic distance of 0.57 centimorgan (cM) between markers. A total of five QTLs with a logarithm of odds (LOD) value of 4.035-8.681 were identified on five chromosomes. Under well-watered conditions and drought-stress conditions, one QTL related to the main stem node number was located on chromosome 16, accounting for 17.177% of the phenotypic variation. Nine candidate genes for drought resistance were screened from this QTL, namely Glyma.16G036700, Glyma.16G036400, Glyma.16G036600, Glyma.16G036800, Glyma.13G312700, Glyma.13G312800, Glyma.16G042900, Glyma.16G043200, and Glyma.15G100700. These genes were annotated as NAC transport factor, GATA transport factor, and BTB/POZ-MATH proteins. This result can be used for molecular marker-assisted selection and provide a reference for breeding for drought tolerance in soybean.

Genome-wide association analysis and transcriptome reveal novel loci and a candidate regulatory gene of fatty acid biosynthesis in sesame (Sesamum indicum L.)

The regulatory mechanisms of fatty acid (FA) biosynthesis and triacylglycerols (TAGs) assembly remain largely misunderstood in sesame. Gas chromatography was used to analyze the natural variation in FA compositions and oil content (OC) in 400 sesame accessions grown in three different environments. The phenotypic data was associated with the newly released SNP data from whole-genome resequencing, and 43 significant loci for FA and OC were identified. Comparative transcriptomics analysis of high-OC and low-OC materials was performed, and 515 differentially expressed genes (DEGs) were identified across three seed developmental stages. By integrating the genome-wide association study (GWAS) and DEGs analysis, twenty candidate genes were identified, of which SiTPS1 (trehalose-6-phosphate synthase 1) has emerged as a key regulatory gene of FAs and TAGs metabolism in sesame. Overexpression of SiTPS1 in transgenic Arabidopsis influenced FA composition and significantly increased OC. Our study provides resources for the markers-based improvement of OC and quality in sesame and other crops.

Integrated omics approaches for flax improvement under abiotic and biotic stress: Current status and future prospects

Flax (Linum usitatissimum L.) or linseed is one of the important industrial crops grown all over the world for seed oil and fiber. Besides oil and fiber, flax offers a wide range of nutritional and therapeutic applications as a feed and food source owing to high amount of α-linolenic acid (omega-3 fatty acid), lignans, protein, minerals, and vitamins. Periodic losses caused by unpredictable environmental stresses such as drought, heat, salinity-alkalinity, and diseases pose a threat to meet the rising market demand. Furthermore, these abiotic and biotic stressors have a negative impact on biological diversity and quality of oil/fiber. Therefore, understanding the interaction of genetic and environmental factors in stress tolerance mechanism and identification of underlying genes for economically important traits is critical for flax improvement and sustainability. In recent technological era, numerous omics techniques such as genomics, transcriptomics, metabolomics, proteomics, phenomics, and ionomics have evolved. The advancements in sequencing technologies accelerated development of genomic resources which facilitated finer genetic mapping, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection in major cereal and oilseed crops including flax. Extensive studies in the area of genomics and transcriptomics have been conducted post flax genome sequencing. Interestingly, research has been focused more for abiotic stresses tolerance compared to disease resistance in flax through transcriptomics, while the other areas of omics such as metabolomics, proteomics, ionomics, and phenomics are in the initial stages in flax and several key questions remain unanswered. Little has been explored in the integration of omic-scale data to explain complex genetic, physiological and biochemical basis of stress tolerance in flax. In this review, the current status of various omics approaches for elucidation of molecular pathways underlying abiotic and biotic stress tolerance in flax have been presented and the importance of integrated omics technologies in future research and breeding have been emphasized to ensure sustainable yield in challenging environments.

Transgenic Forsythia plants expressing sesame cytochrome P450 produce beneficial lignans

Lignans are widely distributed plant secondary metabolites that have received attention for their benefits to human health. Sesamin is a furofran lignan that is conventionally extracted from Sesamum seeds and shows anti-oxidant and anti-inflammatory activities in the human liver. Sesamin is biosynthesized by the Sesamum-specific enzyme CYP81Q1, and the natural sources of sesamin are annual plants that are at risk from climate change. In contrast, Forsythia species are widely distributed perennial woody plants that highly accumulate the precursor lignan pinoresinol. To sustainably supply sesamin, we developed a transformation method for Forsythia leaf explants and generated transgenic Forsythia plants that heterologously expressed the CYP81Q1 gene. High-performance liquid chromatography (HPLC) and LC-mass spectrometry analyses detected sesamin and its intermediate piperitol in the leaves of two independent transgenic lines of F. intermedia and F. koreana. We also detected the accumulation of sesamin and piperitol in their vegetatively propagated descendants, demonstrating the stable and efficient production of these lignans. These results indicate that CYP81Q1-transgenic Forsythia plants are promising prototypes to produce diverse lignans and provide an important strategy for the cost-effective and scalable production of lignans.

Current Research Trends and Prospects for Yield and Quality Improvement in Sesame, an Important Oilseed Crop

Climate change is shifting agricultural production, which could impact the economic and cultural contexts of the oilseed industry, including sesame. Environmental threats (biotic and abiotic stresses) affect sesame production and thus yield (especially oil content). However, few studies have investigated the genetic enhancement, quality improvement, or the underlying mechanisms of stress tolerance in sesame. This study reveals the challenges faced by farmers/researchers growing sesame crops and the potential genetic and genomic resources for addressing the threats, including: (1) developing sesame varieties that tolerate phyllody, root rot disease, and waterlogging; (2) investigating beneficial agro-morphological traits, such as determinate growth, prostrate habit, and delayed response to seed shattering; (3) using wild relatives of sesame for wide hybridization; and (4) advancing existing strategies to maintain sesame production under changing climatic conditions. Future research programs need to add technologies and develop the best research strategies for economic and sustainable development.

Systematic analysis of HD-ZIP transcription factors in sesame genome and gene expression profiling of SiHD-ZIP class I entailing drought stress responses at early seedling stage

BACKGROUND

Sesame is an ancient oilseed crop, known for its high oil content and quality. Its sensitivity to drought at early seedling stage is one of the limiting factors affecting its world-wide growth and productivity. Among plant specific transcription factors, the association of HD-ZIPs with sesame drought responses at early seedling stage is not well-established yet and is very important to develop our molecular understanding on sesame drought tolerance.

METHODS AND RESULTS

In this study, total 61 sesame HD-ZIP proteins were identified, based on their protein sequence homology with Arabidopsis and protein domain(s) architecture prediction, followed by their phylogenetic, conserved domain(s) motifs and gene structure analyses to classify them into four classes (HD-ZIP Class I-IV). HD-ZIP Class I was also subdivided into four subgroups: α (SiHZ25, SiHZ43, SiHZ9 and SiHZ16), β1 (SiHZ10, SiHZ30, SiHZ32 and SiHZ26), β2 (SiHZ42 and SiHZ45) and γ (SiHZ17, SiHZ7 and SiHZ35) by a comparative phylogenetic analysis of sesame with Arabidopsis and maize. Afterwards, twenty-one days old sesame seedlings were exposed to drought stress by withholding water for 7 days (when soil moisture content reduced to ~16%) and gene expression of HD-ZIP Class I (13 members) was performed in well- watered (control) and drought stressed seedlings. The gene expression analysis showed that the expressions of SiHZ7 (6.8 fold) and SiHZ35 (2.6 fold) from γ subgroup were significantly high in drought seedlings.

CONCLUSIONS

This study is useful in demonstrating the role of SiHD-ZIP Class I in sesame drought responses at early seedling stage and to develop its novel drought tolerant varieties.

Identifying Traits Associated With Terminal Drought Tolerance in Sesame (Sesamum indicum L.) Genotypes

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.

Comprehensive Analysis of SRO Gene Family in Sesamum indicum (L.) Reveals Its Association with Abiotic Stress Responses

SIMILAR TO RCD-ONEs (SROs) comprise a small plant-specific gene family which play important roles in regulating numerous growth and developmental processes and responses to environmental stresses. However, knowledge of SROs in sesame (Sesamum indicum L.) is limited. In this study, four SRO genes were identified in the sesame genome. Phylogenetic analysis showed that 64 SROs from 10 plant species were divided into two groups (Group I and II). Transcriptome data revealed different expression patterns of SiSROs over various tissues. Expression analysis showed that Group II SROs, especially SiSRO2b, exhibited a stronger response to various abiotic stresses and phytohormones than those in Group I, implying their crucial roles in response to environmental stimulus and hormone signals. In addition, the co-expression network and protein-protein interaction network indicated that SiSROs are associated with a wide range of stress responses. Moreover, transgenic yeast harboring SiSRO2b showed improved tolerance to salt, osmotic and oxidative stress, indicating SiSRO2b could confer multiple tolerances to transgenic yeast. Taken together, this study not only lays a foundation for further functional dissection of the SiSRO gene family, but also provides valuable gene candidates for genetic improvement of abiotic stress tolerance in sesame.

Genome-wide association analysis uncovers the genetic architecture of tradeoff between flowering date and yield components in sesame

BACKGROUND

Unrevealing the genetic makeup of crop morpho-agronomic traits is essential for improving yield quality and sustainability. Sesame (Sesamum indicum L.) is one of the oldest oil-crops in the world. Despite its economic and agricultural importance, it is an 'orphan crop-plant' that has undergone limited modern selection, and, as a consequence preserved wide genetic diversity. Here we established a new sesame panel (SCHUJI) that contains 184 genotypes representing wide phenotypic variation and is geographically distributed. We harnessed the natural variation of this panel to perform genome-wide association studies for morpho-agronomic traits under the Mediterranean climate conditions.

RESULTS

Field-based phenotyping of the SCHUJI panel across two seasons exposed wide phenotypic variation for all traits. Using 20,294 single-nucleotide polymorphism markers, we detected 50 genomic signals associated with these traits. Major genomic region on LG2 was associated with flowering date and yield-related traits, exemplified the key role of the flowering date on productivity.

CONCLUSIONS

Our results shed light on the genetic architecture of flowering date and its interaction with yield components in sesame and may serve as a basis for future sesame breeding programs in the Mediterranean basin.

Leaf size modulation by cytokinins in sesame plants

Phytohormones play important roles in controlling leaf size and in the modulation of various stress responses, including drought. In this study, hormone profiling analyses by ultra high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry (UHPLC-MS/MS) was performed in leaves collected at three stages of active leaf growth to unravel which phytohormones modulate leaf size in sesame (Sesamum indicum L.) plants, an important oil-rich crop. Furthermore, endogenous contents of phytohormones were measured in parallel to various stress markers in sesame plants exposed to mild water deficit conditions by withholding water in potted plants for one week. Results revealed a major role of cytokinins and auxin in the modulation of leaf growth in sesame plants (which increased by 21.5 and 2.1-fold, respectively, with leaf growth), as well as a putative antagonistic response between jasmonic acid and salicylic acid during leaf development. Furthermore, growth arrest during water deficit stress appeared to be modulated by cytokinins, the endogenous contents of which decreased (by 48%) in parallel with ABA increases (by 59%). Reductions in the contents of the active cytokinin trans-zeatin occurred in parallel with increases in isopentenyladenine contents under drought, which suggests a partial metabolic limitation in cytokinin biosynthesis in leaves upon water deficit stress. These results provide useful information for the hormonal modulation of leaf size and the improvement of leaf growth and production in sesame plants through manipulation of the levels of key regulatory phytohormones.

QTL mapping of yield-related traits in sesame

Improving yield is one of the most important targets of sesame breeding. Identifying quantitative trait loci (QTLs) of yield-related traits is a prerequisite for marker-assisted selection (MAS) and QTL/gene cloning. In this study, a BC1 population was developed and genotyped with the specific-locus amplified fragment (SLAF) sequencing technology, and a high-density genetic map was constructed. The map consisted of 13 linkage groups, contained 3528 SLAF markers, and covered a total of 1312.52 cM genetic distance, with an average distance of 0.37 cM between adjacent markers. Based on the map, 46 significant QTLs were identified for seven yield-related traits across three environments. These QTLs distributed on 11 linkage groups, each explaining 2.34-71.41% of the phenotypic variation. Of the QTLs, 23 were stable QTLs that were detected in more than one environment, and 20 were major QTLs that explained more than 10% of the corresponding phenotypic variation in at least one environment. Favorable alleles of 38 QTLs originated from the locally adapted variety, Yuzhi 4; the exotic germplasm line, BS, contributed favorable alleles to only 8 QTLs. The results should provide useful information for future molecular breeding and functional gene cloning.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01236-x.

Genome-wide association study and its applications in the non-model crop Sesamum indicum

BACKGROUND

Sesame is a rare example of non-model and minor crop for which numerous genetic loci and candidate genes underlying features of interest have been disclosed at relatively high resolution. These progresses have been achieved thanks to the applications of the genome-wide association study (GWAS) approach. GWAS has benefited from the availability of high-quality genomes, re-sequencing data from thousands of genotypes, extensive transcriptome sequencing, development of haplotype map and web-based functional databases in sesame.

RESULTS

In this paper, we reviewed the GWAS methods, the underlying statistical models and the applications for genetic discovery of important traits in sesame. A novel online database SiGeDiD ( http://sigedid.ucad.sn/ ) has been developed to provide access to all genetic and genomic discoveries through GWAS in sesame. We also tested for the first time, applications of various new GWAS multi-locus models in sesame.

CONCLUSIONS

Collectively, this work portrays steps and provides guidelines for efficient GWAS implementation in sesame, a non-model crop.

Genome-wide association study of seed coat color in sesame (Sesamum indicum L.)

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.

A novel motif in the 5'-UTR of an orphan gene 'Big Root Biomass' modulates root biomass in sesame

Developing crops with improved root system is crucial in current global warming scenario. Underexploited crops are valuable reservoirs of unique genes that can be harnessed for the improvement of major crops. In this study, we performed genome-wide association studies on seven root traits in sesame (Sesamum indicum L.) and uncovered 409 significant signals, 19 quantitative trait loci containing 32 candidate genes. A peak SNP significantly associated with root number and root dry weight traits was located in the promoter of the gene named 'Big Root Biomass' (BRB), which was subsequently validated in a bi-parental population. BRB has no functional annotation and is restricted to the Lamiales order. We detected the presence of a novel motif 'AACACACAC' located in the 5'-UTR of BRB in single and duplicated copy in accessions with high and small root biomass, respectively. A strong expression level of BRB was negatively correlated with high root biomass, and this was attributed to the gene SiMYB181 which represses the activity of BRB by binding specifically to the single motif but not to the duplicated one. Curiously, the allele that enhanced BRB expression has been intensively selected by modern breeding. Overexpression of BRB in Arabidopsis modulates auxin pathway leading to reduced root biomass, improved yield parameters under normal growth conditions and increased drought stress sensitivity. Overall, BRB represents a solid gene model for improving the performance of sesame and other crops.

QTL mapping of PEG-induced drought tolerance at the early seedling stage in sesame using whole genome re-sequencing

Improvement in sesame drought tolerance at seedling stage is important for yield stability. Genetic approaches combing with conventional breeding is the most effective way to develop drought-tolerant cultivars. In this study, three traits and their relative values, including seedling weight (SW), shoot length (SL) and root length (RL), were evaluated under control and osmotic conditions in a recombinant inbred line (RIL) population derived from cross of Zhushanbai and Jinhuangma. Significant variation and high broad sense heritability were observed for all traits except SW under stress condition in the population. With this population, a high-density linkage map with 1354 bin markers was constructed through whole genome re-sequencing (WGS) strategy. Quantitative trait loci (QTL) mapping was performed for all the traits. A total of 34 QTLs were detected on 10 chromosomes. Among them, 13 stable QTLs were revealed in two independent experiments, eight of them were associated with traits under water stress condition. One region on chromosome 12 related to RL under osmotic condition and relative RL had the highest LOD value and explained the largest phenotypic variation among all the QTLs detected under water stress condition. These findings will provide new genetic resources for molecular improvement of drought tolerance and candidate gene identification in sesame.

Lignans of Sesame (Sesamum indicum L.): A Comprehensive Review

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.

Loci harboring genes with important role in drought and related abiotic stress responses in flax revealed by multiple GWAS models

QTNs associated with drought tolerance traits and indices were identified in a flax mini-core collection through multiple GWAS models and phenotyping at multiple locations under irrigated and non-irrigated field conditions. Drought is a critical phenomenon challenging today's agricultural sector. Crop varieties adapted to moisture deficit are becoming vital. Flax can be greatly affected by limiting moisture conditions, especially during the early development and reproductive stages. Here, a mini-core collection comprising genotypes from more than 20 major growing countries was evaluated for 11 drought-related traits in irrigated and non-irrigated fields for 3 years. Heritability of the traits ranged from 44.7 to 86%. Six of the 11 traits showed significant phenotypic difference between irrigated and non-irrigated conditions. A genome-wide association study (GWAS) was performed for these six traits and their corresponding stress indices based on 106 genotypes and 12,316 single nucleotide polymorphisms (SNPs) using six multi-locus and one single-locus models. The SNPs were then assigned to 8050 linkage disequilibrium (LD) blocks to which a restricted two-stage multi-locus multi-allele GWAS was applied. A total of 144 quantitative trait nucleotides (QTNs) and 13 LD blocks were associated with at least one trait or stress index. Of these, 16 explained more than 15% of the genetic variance. Most large-effect QTN loci harbored gene(s) previously predicted to play role(s) in the associated traits. Genes mediating responses to abiotic stresses resided at loci associated with stress indices. Flax genes Lus10009480 and Lus10030150 that are predicted to encode WAX INDUCER1 and STRESS-ASSOCIATED PROTEIN (SAP), respectively, are among the important candidates detected. Accessions with multiple favorable alleles outperformed others for grain yield, thousand seed weight and fiber/biomass in non-irrigated conditions, suggesting their potential usefulness in breeding and genomic selection.

Male Sterility is linked to the Flavonoid Biosynthesis Pathways in Prunus mira

Sterility plays an important role in plant adaptation and evolution and has contributed to the development of high yielding crop hybrids. We used the widely targeted metabolomics profiling to survey the metabolites and biological pathways associated with male sterility in Prunus mira by comparing flowers from fertile and sterile trees. Male sterile flowers displayed abnormal stamen, uncolored anthers, and distorted and shrunken pollen grains with an apparent lack of turgidity. We report 566 metabolites in six flower samples and 140 differentially accumulated metabolites (DAMs) between both flower types. Most of the DAMs belong to the phenyl propanoid biosynthesis pathway, particularly flavonoid, flavone and flavonol biosynthesis pathways, implying that alterations in these key pathways link to male sterility in P. mira. The known link between low levels of flavonoid metabolites, weak expression levels of several structural genes from the phenyl propanoid biosynthesis pathway and hyper accumulation of reactive oxygen species were highlighted for understanding the underlying mechanism leading to the abnormal or aborted pollen grains observed in the sterile flowers. Data on the molecular mechanism of male sterility in Prunus mira will facilitate further in-depth investigations on this important agronomic and ecological trait.

Ectopic expression of the sesame MYB transcription factor SiMYB305 promotes root growth and modulates ABA-mediated tolerance to drought and salt stresses in Arabidopsis

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.

Molecular Analysis of UV-C Induced Resveratrol Accumulation in Polygonum cuspidatum Leaves

Resveratrol is one of the most studied plant secondary metabolites owing to its numerous health benefits. It is accumulated in some plants following biotic and abiotic stress pressures, including UV-C irradiation. Polygonum cuspidatum represents the major natural source of concentrated resveratrol but the underlying mechanisms as well as the effects of UV-C irradiation on resveratrol content have not yet been documented. Herein, we found that UV-C irradiation significantly increased by 2.6-fold and 1.6-fold the resveratrol content in irradiated leaf samples followed by a dark incubation for 6 h and 12 h, respectively, compared to the untreated samples. De novo transcriptome sequencing and assembly resulted into 165,013 unigenes with 98 unigenes mapped to the resveratrol biosynthetic pathway. Differential expression analysis showed that P.cuspidatum strongly induced the genes directly involved in the resveratrol synthesis, including phenylalanine ammonia-lyase, cinnamic acid 4-hydroxylase, 4-coumarate-CoA ligase and stilbene synthase (STS) genes, while strongly decreased the chalcone synthase (CHS) genes after exposure to UV-C. Since CHS and STS share the same substrate, P. cuspidatum tends to preferentially divert the substrate to the resveratrol synthesis pathway under UV-C treatment. We identified several members of the MYB, bHLH and ERF families as potential regulators of the resveratrol biosynthesis genes.

Root diversity in sesame (Sesamum indicum L.): insights into the morphological, anatomical and gene expression profiles

Sesame harbors a large diversity in root morphological and anatomical traits and a high root biomass improves the plant aboveground biomass as well as the seed yield. Sesame provides one of the most nutritious and healthy vegetable oils, sparking an increasing demand of its seeds. However, with the low yield and productivity of sesame, there is still a huge gap between the seed demand and supply. Improving the root system has a high potential to increase crop productivity, but information on the diversity of the sesame root systems is still lacking. In this study, 40 diverse sesame varieties were grown in soil and hydroponics systems and the diversity of the root system was investigated. The results showed that sesame holds a large root morphological and anatomical diversity, which can be harnessed in breeding programmes. Based on the clustering of the genotypes in hydroponics and soil culture systems, we found that similar genotypes were commonly clustered either in the small-root or in the big-root group, indicating that the hydroponics system can be employed for a large-scale root phenotyping. Our results further revealed that the root biomass positively contributes to increased seed yield in sesame, based on multi-environmental trials. By comparing the root transcriptome of two contrasting genotypes, 2897 differentially expressed genes were detected and they were enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, stilbenoid, diarylheptanoid and gingerol biosynthesis, flavonoid biosynthesis, suggesting that these pathways are crucial for sesame root growth and development. Overall, this study sheds light on the diversity of sesame root system and offers the basis for improving root traits and increasing sesame seed yield.

Protective Role of Leaf Variegation in Pittosporum tobira under Low Temperature: Insights into the Physio-Biochemical and Molecular Mechanisms

Leaf variegation has been demonstrated to have adaptive functions such as cold tolerance. Pittosporum tobira is an ornamental plant with natural leaf variegated cultivars grown in temperate regions. Herein, we investigated the role of leaf variegation in low temperature responses by comparing variegated “Variegatum” and non-variegated “Green Pittosporum” cultivars. We found that leaf variegation is associated with impaired chloroplast development in the yellow sector, reduced chlorophyll content, strong accumulation of carotenoids and high levels of ROS. However, the photosynthetic efficiency was not obviously impaired in the variegated leaves. Also, leaf variegation plays low temperature protective function since “Variegatum” displayed strong and efficient ROS-scavenging enzymatic systems to buffer cold (10 °C)-induced damages. Transcriptome analysis under cold conditions revealed 309 differentially expressed genes between both cultivars. Distinctly, the strong cold response observed in “Variegatum” was essentially attributed to the up-regulation of HSP70/90 genes involved in cellular homeostasis; up-regulation of POD genes responsible for cell detoxification and up-regulation of FAD2 genes and subsequent down-regulation of GDSL genes leading to high accumulation of polyunsaturated fatty acids for cell membrane fluidity. Overall, our results indicated that leaf variegation is associated with changes in physiological, biochemical and molecular components playing low temperature protective function in P. tobira.

Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame (Sesamum indicum L.)

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.