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Manhattan plots representing association mapping for the 112 fenugreek genotypes using 38,142 SNPs of seed length (a), width (b), and color (c) arranged in random order (x-axis). The green horizontal solid line represents Bonferroni correction threshold at 6.5. The dashed gray line represents false discovery rate at 5.9.
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Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs u...
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The perennial grass Thinopyrum intermedium (intermediate wheatgrass [IWG]) is being domesticated as a food crop. With a deep root system and high biomass, IWG can help reduce soil and water erosion and limit nutrient runoff. As a novel grain crop undergoing domestication, IWG lags in yield, seed size, and other agronomic traits compared to annual g...
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... Special attention has been given to symbiotic nitrogen fixation, with studies focusing on dynamic processes in root nodules using plant and bacterial mutants [16]. Tools like the Gene Expression Atlas published by Benedito et al. [17,18] have shed light on gene expression patterns in root nodules and seeds, which revealed key regulatory genes and transcription factors that govern genetic reprogramming during development and differentiation. ...
... Special attention has been given to symbiotic nitrogen fixation, with studies focusing on dynamic processes in root nodules using plant and bacterial mutants [16]. Tools like the Gene Expression Atlas published by Benedito et al. [17,18] have shed light on gene expression Many legume-specific genes are predominantly expressed in nitrogen-fixing nodules, indicating their evolutionary specialization [17]. In M. truncatula, transcriptomic studies have further characterized gene expression responses to environmental cues and developmental stages. ...
Members of the Leguminosae family are important crops that provide food, animal feed and vegetable oils. Legumes make a substantial contribution to sustainable agriculture and the nitrogen cycle through their unique ability to fix atmospheric nitrogen in agricultural ecosystems. Over the past three decades, Medicago truncatula and Lotus japonicus have emerged as model plants for genomic and physiological research in legumes. The advancement of innovative molecular and genetic tools, particularly insertional mutagenesis using the retrotransposon Tnt1, has facilitated the development of extensive mutant collections and enabled precise gene tagging in plants for the identification of key symbiotic and developmental genes. Building on these resources, twelve years ago, our research team initiated the establishment of a platform for functional genomic studies of legumes in Bulgaria. In the framework of this initiative, we conducted systematic sequencing of selected mutant lines and identified genes involved in plant growth and development for detailed functional characterization. This review summarizes our findings on the functions of selected genes involved in the growth and development of the model species, discusses the molecular mechanisms underlying important developmental processes and examines the potential for the translation of this fundamental knowledge to improve commercially important legume crops in Bulgaria and globally.
... Estimating broad-sense heritability revealed that most traits were moderately or highly heritable, indicating that the observed variation has a genetic foundation rather than being caused by environmental influences. Therefore, our study has enough power to map significant SNPs associated with the measured traits using the fenugreek population, previously genotyped with 38,142 polymorphic SNPs using ddRAD-seq technology [29]. ...
... The fenugreek population comprising 111 Fenugreek genotypes [29] were grown in pots under open field conditions at the Faculty of Agriculture, Cairo University, Giza, Egypt, in the 2022-2023 growing season. Temperature and humidity ranged between 18 and 30 • C and between 65 and 75%, respectively. ...
... The double-digest restriction site-associated DNA sequencing (ddRAD-seq) technique [54] was used for genotyping the 111 fenugreek genotypes. Briefly, 38,142 bi-allelic SNPs with a minimum quality score of 30, a maximum of 0.2% missing data per SNP, a minimum mean coverage depth of 20, and a minimum minor allele frequency (MAF) of 0.05 were used for our mapping analysis [29]. The mixed linear model (MLM), kinship matrix, and principal component implemented in the TASSEL software, version 5.0 [55], assisted in identifying SNP markers associated with the raw data of the measured traits. ...
Salinity is a significant factor restricting plant growth and production. The effect of salinity stress on different growth parameters of 111 fenugreek genotypes was examined in an experiment with three salinity levels (0, 3000, 6000 mgL−1). A completely randomized block design with two replicated pots per treatment was used. Non-significant treatment effects were observed on fresh weight (FW); however, all traits showed significant genotype-by-treatment (GxT) interactions. This GxT was reflected in substantial SNP x environment interactions. Of 492 significant SNPs associated with the measured traits, 212 SNPs were linked to the correlated traits using an arbitrary threshold of three. Several SNPs were associated with FW and dry weight, measured under the same salinity treatment. The correlation between both traits was 0.98 under the three salinity treatments. In addition, 280 SNPs with conditional neutrality effects were mapped. The identified SNPs can be used in future marker-assisted breeding programs to select salt-tolerant genotypes. The results of this research shed light on the salt-tolerant properties of fenugreek.
... We used 112 fenugreek genotypes collected directly from local farmers in several Egyptian governorates. For example, seven, 20, 17, and 15 genotypes were collected from Qalyubia, Qena, Beni-Suef, and Minya governorates, Egypt [20]. We used a complete randomized block design with three replications. ...
... The 112 fenugreek genotypes were genotyped using the double digest restriction site-associated DNA sequencing (ddRAD-seq) technique [21]. Briefly, 38,142 bi-allelic SNPs with a minimum quality score of 30, a maximum of 0.2% missing data per SNP, a minimum mean coverage depth of 20, and a minimum minor allele frequency (MAF) of 0.05 were retained for association analysis [20]. ...
... Therefore, the UPOV approved the application of molecular markers on the DUS test under three models. However, the potential application of the first UPOV model in fenugreek requires the development of molecular markers associated with genes underlying various agronomic and non-agronomical traits [27], which is impractical due to the limited information on the fenugreek genome [20]. Regarding the third UPOV model, there is also a big argument because the determination of distinctness at three SNPs differences can lead to an inaccurate conclusion of the uniformity and stability results [27]. ...
Distinctness, uniformity, and stability (DUS) test is the legal requirement in crop breeding to grant the intellectual property right for new varieties by evaluating their morphological characteristics across environments. On the other hand, molecular markers accurately identify genetic variations and validate the purity of the cultivars. Therefore, genomic DUS can improve the efficiency of traditional DUS testing. In this study, 112 Egyptian fenugreek genotypes were grown in Egypt at two locations: Wadi El-Natrun (Wadi), El-Beheira Governorate, with salty and sandy soil, and Giza, Giza governorate, with loamy clay soil. Twelve traits were measured, of which four showed a high correlation above 0.94 over the two locations. We observed significant genotype-by-location interactions (GxL) for seed yield, as it was superior in Wadi, with few overlapping genotypes with Giza. We attribute this superiority in Wadi to the maternal habitat, as most genotypes grew in governorates with newly reclaimed salty and sandy soil. As a first step toward genomic DUS, we performed an association study, and out of 38,142 SNPs, we identified 39 SNPs demonstrating conditional neutrality and four showing pleiotropic effects. Forty additional SNPs overlapped between both locations, each showing a similar impact on the associated trait. Our findings highlight the importance of GxL in validating the effect of each SNP to make better decisions about its suitability in the marker-assisted breeding program and demonstrate its potential use in registering new plant varieties.
... 101 Using double digest restriction site-associated DNA sequencing a number of 112 genotypes with 153,881 single nucleotide polymorphisms (SNPs) were genotyped toinvestigate the genetic diversity. Seed length, width and colour were selected as traits to prove the suitability of this population for association mapping studies and we found three trait-associated SNPs.102 Therefore, it could be assumed that quality control of standardised herbal extracts could be implemented via a synergetic approach using both metabolic profiling and DNA-based techniques, to overcome problems from DNA degradation. ...
Introduction:
Fenugreek has been used in traditional remedies since ancient times. It has a long history of use against medical ailments as an antidiabetic, anticarcinogenic, hypocholesterolemic, antioxidant, antibacterial, hypoglycemic, gastric stimulant, and anti-anorexia agent. The major active constituents include alkaloids, fibres, saponins, proteins, and amino acids.
Objectives:
To provide a comprehensive overview of the application of chromatographic and spectroscopic methods, in addition to DNA-profiling methods to assess the quality of fenugreek. Also, to highlight the recent application of chemometrics combined with quality control methods during the last two decades.
Methodology:
A literature search conducted from January 2000 up to December 2020 using various scientific databases (e.g., Scopus, Medline, PubMed, EBSCO, JSTOR, ScienceDirect, Google Scholar, Web of Science and Egyptian Knowledge Bank, Academic Journals, and Springer Link); general web searches were also undertaken using Google applying some related search terms. Studies involving the application of quality control analyses were classified into three categories according to the conducted analysis method including chromatographic [high-performance liquid chromatography (HPLC), high-performance thin-layer chromatography (HPTLC), and gas chromatography (GC)], spectroscopic [ultraviolet (UV), infrared (IR), and nuclear magnetic resonance (NMR)], and DNA-based markers.
Results:
This review shed the light on relevant studies covering the past two decades, presenting the application of spectroscopic and chromatographic methods and DNA profiling in the quality control of fenugreek.
Conclusion:
The reviewed chromatographic and spectroscopic methods combined with chemometrics provide a powerful tool that could be applied widely for the quality control of fenugreek.
... A recent report identified genes with direct or indirect influence on plant reproduction in water yam (Dioscorea alata l.), among which was the Mt-Zn-CCHC gene [27]. Additionally, high-density SNP-based association mapping of seed treat in Fenugreek identified dDocent_Contig_466_145, which indicates an association between the Znf-C2HC domain (corresponding to the domain in Mt-Zn-CCHC) and its role in gene transcription and effect on seed size [28]. Fusaro et al. [23] demonstrated that AtCSP2 knockdown plants had a reduced number of stamens and high rates of abnormal development of seeds/embryos. ...
Zinc finger proteins bind nucleic acids or act in transcriptional or translational regulation. The present study aimed to explore the effect of heterologous expression of the Medicago truncatula gene (Mt-Zn-CCHC), which encodes a Zinc finger CCHC type protein, in Arabidopsis thaliana. The Mt-Zn-CCHC gene, which affects seed size in M. truncatula, was used for construction of transgenic A. thaliana transcriptional reporter plants expressing pMt-Zn-CCHC::GUS::GFP, as well as lines with modified expression – overexpressed (OE) and knockdown (RNAi). In silico analysis of the promoter cis-elements of pAt-Zn-CCHC and pMt-Zn-CCHC suggested regulation during meristem activity, seed development, as well as cold stress. The expression of pMt-Zn-CCHC was localized in shoot apical meristem and in the base of the siliques. In the RNAi lines, successfully repressed endogenous At-Zn-CCHC expression resulted in shortened stem and reduction in silique number, silique size, seed number per silique, and decreased expression of the meristem marker AtSWP. In the gain-of-function lines, overexpression of Mt-Zn-CCHC acted as a positive regulator in silique and seed parameters, as well as increased AtSWP expression. Cold treatment of WT plants demonstrated upregulation of the endogenous At-Zn-CCHC and the RD29A cold marker gene. In the OE line, RD29A transcription was induced by cold faster but in the RNAi line, slower. The overall data support the roles of the studied Zn-CCHC gene in the development of shoot meristem, seeds and cold response, which highlights this protein as a conserved regulator in plant reproduction and stress signal transduction.
Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.2006786 .
Trigonella corniculata (L) L. or Nagauri pan /Kasuri methi, is an important spice crop with high nutraceutical potential. We report the de novo chromosome-scale assembly of T. corniculata genome using high coverage PacBio, Illumina and Hi-C reads. The assembly spans 798 Mb (Megabases) in 282 scaffolds with a scaffold N50 of 99.6 Mb. More than 98% of the sequence length is captured in eight different pseudomolecules with an average length of 98 Mb. A BUSCO score of over 97% is suggestive of the high degree of completeness and contiguity of the genome. A total of 64,801 protein-coding genes are predicted. Genome-wide Simple Sequence Repeats (99,149) have been identified and wet lab validated at forty-eight loci. The chromosome-scale genome assembly of T. corniculata and the SSR markers identified in this study will provide a strong foundation for future structural and functional genomics studies in T. corniculata and other fenugreek species.
Fenugreek, a key medicinal-aromatic plant, offers rich bioactive compounds and nutritional value. Its diverse applications in cuisine and pharmaceuticals, coupled with health benefits like anti-diabetic and antioxidant properties, underscore its significance. Assessing genetic diversity becomes crucial for effective conservation and utilization. In this study, we examined the molecular diversity and population structure of 34 fenugreek genotypes collected from 18 countries worldwide using 24 inter-primer binding site (iPBS) markers. The iPBS primers produced 499 bands, with the total number of bands per primer ranging from 15 (iPBS-2224) to 26 (iPBS-2077), averaging 20.79. Polymorphism information content (PIC) ranged from 0.03 (iPBS-2374) to 0.34 (iPBS-2237), averaging 0.23. In the molecular analysis, the G1 genotype (Isfahan/Iran) exhibited the maximum effective number of alleles (Ne), Nie’s gene diversity (He), and Shannon’s information index (I) at 1.946, 0.486, and 0.679, respectively. Conversely, the G34 genotype (India/B) displayed the lowest values at 1.539, 0.350, and 0.535, respectively. Utilizing the unweighted pair-group means average (UPGMA) method, the iPBS-based tree revealed three distinct groups corresponding to the genomic constitution of fenugreek genotypes, a pattern partially corroborated by principal component analysis (PCA). Further model-based cluster analysis classified the 34 genotypes into four subpopulations, with expected heterozygosity (He) values of 0.428, 0.390, 0.426, and 0.007, respectively. The F-statistic (Fst) values for these subpopulations were 0.197, 0.210, 0.187, and 0.356, respectively. These findings underscored significant genetic variation among the tested fenugreek genotypes, thereby demonstrating the efficacy of iPBS markers in accurately assessing genetic diversity and phylogenetic relationships within fenugreek populations.
In the scenario of increasing global population and changing climatic conditions, breeding approaches in crops need to be integrated with novel technologies for enhancing yield, quality, and resistance to biotic/abiotic stresses. The international trade demands quality clean spices without any pesticide residues. With the advent of next-generation sequencing, whole-genome sequence information and RNA-seq-based transcriptome data are available in major spice crops. Furthermore, proteome profiling and metabolome fingerprinting of spices have been reported to understand major peptides, amino acids, phenolic compounds, fatty acids, and other metabolites linked to quality and stress tolerance. This chapter gives an account of the research in omics for spice crop improvements and the future perspective of spice research in the light of genomics, transcriptomics, proteomics, and metabolomics.
Fenugreek (Trigonella foenum-graecum), known as methi in much of South Asia, is a widely used spice and vegetable crop. Fenugreek is a multiuse legume crop grown in dry and semiarid regions of the developing world. It is an annual, dicotyledonous, self-pollinated plant belonging to the family Fabaceae. It is a diploid with 2n = 16 and is estimated to have 685 Mbp of genome size. The genus Trigonella L. includes about 135 species worldwide and is native to South-Eastern Europe and West Asia. Most widely known as a spice in Europe, it is also widely used medicinally and as a green vegetable or sprout and as a forage crop. Surprisingly it does not yet have a published genome, and refocusing attention on its uses may stimulate much-needed research on this underutilized crop. Key questions a genome will help address are trade-offs in performance among the various uses of fenugreek and improved understanding of its unique secondary metabolite profile.KeywordsSpice domesticationForage cropFood securityNutrition
