Genome-wide association analysis and transgenic characterization for amylose content regulating gene in tuber of Dioscorea zingiberensis.

BACKGROUND: Amylose, a prebiotic found in yams is known to be beneficial for the gut microflora and is particularly advantageous for diabetic patients' diet. However, the genetic machinery underlying amylose production remains elusive. A comprehensive characterization of the genetic basis of amylose content in yam tubers is a prerequisite for accelerating the genetic engineering of yams with respect to amylose content variation. RESULTS: To uncover the genetic variants underlying variation in amylose content, we evaluated amylose content in freshly harvested tubers from 150 accessions of Dioscorea zingibensis. With 30,000 high-quality single nucleotide polymorphisms (SNP), we performed a genome-wide association analysis (GWAS). The population structure analysis classified the D. zingiberensis accessions into three groups. A total of 115 significant loci were detected on four chromosomes. Of these, 112 significant SNPs (log10(p) = 5, q-value < 0.004) were clustered in a narrow window on the chromosome 6 (chr6). The peak SNP at the position 75,609,202 on chr6 could explain 63.15% of amylose variation in the population and fell into the first exon of the ADP-glucose pyrophosphorylase (AGPase) small subunit gene, causing a non-synonymous modification of the resulting protein sequence. Allele segregation analysis showed that accessions with the rare G allele had a higher amylose content than those harboring the common A allele. However, AGPase, a key enzyme precursor of amylose biosynthesis, was not expressed differentially between accessions with A and G alleles. Overexpression of the two variants of AGPase in Arabidopsis thaliana resulted in a significantly higher amylose content in lines transformed with the AGPase-G allele. CONCLUSIONS: Overall, this study showed that a major genetic variant in AGPase probably enhances the enzyme activity leading to high amylose content in D. zingiberensis tuber. The results provide valuable insights for the development of amylose-enriched genotypes.

White yam (Dioscorea rotundata) plants exhibiting virus-like symptoms are co-infected with a new potyvirus and a new crinivirus in Ethiopia.

White yam (Dioscorea rotundata) plants collected from farmers' fields and planted at the Areka Agricultural Research Center, Southern Ethiopia, displayed mosaic, mottling, and chlorosis symptoms. To determine the presence of viral pathogens, an investigation for virome characterization was conducted by Illumina high-throughput sequencing. The bioinformatics analysis allowed the assembly of five viral genomes, which according to the ICTV criteria were assigned to a novel potyvirus (3 genome sequences) and a novel crinivirus (2 genome sequences). The potyvirus showed ~ 66% nucleotide (nt) identity in the polyprotein sequence to yam mosaic virus (NC004752), clearly below the demarcation criteria of 76% identity. For the crinivirus, the RNA 1 and RNA 2 shared the highest sequence identity to lettuce chlorosis virus, and alignment of the aa sequence of the RdRp, CP and HSP70h (~ 49%, 45% and 76% identity), considered for the demarcation criteria, revealed the finding of a novel virus species. The names Ethiopian yam virus (EYV) and Yam virus 1 (YV-1) are proposed for the two tentative new virus species.

Identification of genetic variants controlling diosgenin content in Dioscorea zingiberensis tuber by genome-wide association study.

BACKGROUND: Diosgenin is an important steroidal precursor renowned for its diverse medicinal uses. It is predominantly sourced from Dioscorea species, particularly Dioscorea zingiberensis. Dioscorea zingiberensis has an ability to accumulate 2-16% diosgenin in its rhizomes. In this study, a diverse population of 180 D. zingiberensis accessions was used to evaluate the genomic regions associated with diosgenin biosynthesis by the genome wide association study approach (GWAS). RESULTS: The whole population was characterized for diosgenin contents from tubers by gas chromatography mass spectrometry. The individuals were genotyped by the genotyping-by-sequencing approach and 10,000 high-quality SNP markers were extracted for the GWAS. The highest significant marker-trait-association was observed as an SNP transversion (G to T) on chromosome 10, with 64% phenotypic variance explained. The SNP was located in the promoter region of CYP94D144 which is a member of P450 gene family involved in the independent biosynthesis of diosgenin from cholesterol. The transcription factor (TF) binding site enrichment analysis of the promoter region of CYP94D144 revealed NAC TF as a potential regulator. The results were further validated through expression profiling by qRT-PCR, and the comparison of high and low diosgenin producing hybrids obtained from a bi-parental population. CONCLUSIONS: This study not only enhanced the understanding of the genetic basis of diosgenin biosynthesis but also serves as a valuable reference for future genomic investigations on CYP94D144, with the aim of augmenting diosgenin production in yam tubers.

Pseudomonas fortuita sp. nov., isolated from the endosphere of a wild yam.

A Gram-negative, strictly aerobic bacterial strain was isolated from asymptomatic leaf tissue of a wild yam plant. Optimal growth was observed at 28 °C and pH 7, and catalase and oxidase activities were detected. Polyphasic taxonomic and comparative genomics revealed that strain LMG 33091T represents a novel species of Pseudomonas. The nearest phylogenetic neighbours of strain LMG 33091T were Pseudomonas putida NBRC 14164T (with 99.79 % 16S rRNA sequence identity), Pseudomonas alkylphenolica KL28T (99.28 %) and Pseudomonas asplenii (99.07 %) ATCC 23835T. MALDI-TOF MS analysis yielded distinct profiles for strain LMG 33091T and the nearest phylogenetic neighbours. Average nucleotide identity analyses between the whole genome sequence of strain LMG 33091T and of the type strains of its nearest-neighbour taxa yielded values below the species delineation threshold and thus confirmed that the strain represented a novel Pseudomonas species, for which we propose the name Pseudomonas fortuita sp. nov., with strain LMG 33091T (=GMI12077T= CFBP 9143T) as the type strain.

Resistant starch from yam: Preparation, nutrition, properties and applications in the food sector.

Yam is a significant staple food and starch source, particularly in tropical and subtropical regions, holding the fourth position among the world's top ten tuber crops. Yam tubers are rich in essential nutrients and a diverse range of beneficial plant compounds, which contribute to their multifaceted beneficial functions. Furthermore, the abundant starch and resistant starch (RS) content in yam can fulfil the market demand for RS. The inherent and modified properties of yam starch and RS make them versatile ingredients for a wide range of food products, with the potential to become one of the most cost-effective raw materials in the food industry. In recent years, research on yam RS has experienced progressive expansion. This article provides a comprehensive summary of the latest research findings on yam starch and its RS, elucidating the feasibility of commercial RS production and the technology's impact on the physical and chemical properties of starch. Yam has emerged as a promising reservoir of tuber starch for sustainable RS production, with thermal, chemical, enzymatic and combination treatments proving to be effective manufacturing procedures for RS. The adaptability of yam RS allows for a wide range of food applications.

Protection effect of Dioscoreae Rhizoma against ethanol-induced gastric injury in vitro and in vivo: A phytochemical and pharmacological study.

ETHNOPHARMACOLOGICAL RELEVANCE: Dioscoreae Rhizoma, a kind of Chinese yam, is a medicinal and edible plant used in China for strengthening the spleen and stomach. However, there is a lack of modern pharmacology studies regarding its anti-gastric injury activity. AIM OF THE STUDY: This study aimed to investigate the phytochemical composition of Chinese yam aqueous extract (CYW) and evaluate its gastroprotective effects against ethanol-induced gastric injury in vitro and in vivo. MATERIALS AND METHODS: The active components of CYW were identified using HPLC-QTOF-MS/MS in combination with the GNPS molecular networking and network pharmacology. In vitro studies were performed in the RAW264.7/GES-1 cell coculture system. In vivo study, mice were treated with CYW (0.31, 0.63, and 3.14 g/kg BW, orally) for 14 days, followed by a single oral dose of ethanol (10 mL/kg BW) to induce gastric injury. The biochemical, inflammation and oxidative stress markers were analyzed using commercial kits. Histopathology was used to assess the degree of gastric injury. Gene and protein expressions were studied using RT-qPCR and western blotting, respectively. RESULTS: CYW significantly restored the levels of SOD, GPx and CAT, and reduced the MDA content. Further analyses showed that CYW significantly alleviated the gastric oxidative stress by inhibiting the inflammation via decreasing p-NF-κB and p-IκB-α expression levels and inhibiting the generation of IL-6, TNF-α, and IL-1ß. At the same time, the fraction remarkably upregulated Bcl-2, downregulated Bax and increased growth factor secretion, thereby prevented gastric mucous cell. Besides, The combination of HPLC-QTOF-MS/MS, GNPS molecular networking analysis, and network pharmacology demonstrated that linoleic acid, 3-acetyl-11-keto-beta-boswellic acid, adenosine, aminocaproic acid, tyramine, DL-tryptophan, cycloleucine, lactulose, melibiose, alpha-beta-trehalose, and sucrose would be the main active compounds of CYW against ethanol-induced gastric injury. CONCLUSION: This study showed that CYW is potentially rich source of anti-oxidant and anti-inflammatory bioactive compounds. It showed efficacy against ethanol-induced gastric injury by inhibiting inflammation, oxidative stress, and apoptosis in the stomach. The results of the current work indicate that Dioscoreae Rhizoma could be utilized as a type of natural resource for production of new medicine and functional foods to prevent and/or ameliorate ethanol-induced gastric injury.

Antibacterial activity of Dioscorea bulbifera Linn. extract and its active component flavanthrinin against skin-associated bacteria.

BACKGROUND: Dioscorea bulbifera Linn. has been used for wound care in Thailand. However, a comprehensive evaluation of its antibacterial activity is required. This study aimed to investigate the antibacterial efficacy of D. bulbifera extract against skin-associated bacteria and isolate and characterize its active antibacterial agent, flavanthrinin. METHODS: Air-dried bulbils of D. bulbifera were pulverised and extracted with hexane, dichloromethane, ethyl acetate, methanol, ethanol, and distilled water; vacuum filtered; concentrated; freeze-dried; and stored at -20 ºC. Antibacterial activity of the extracts was assessed using microdilution techniques against several skin-associated bacteria. Thin-layer chromatography (TLC) bioautography was used to identify the active compounds in the extract, which were fractionated by column chromatography and purified by preparative TLC. The chemical structures of the purified compounds were analysed using nuclear magnetic resonance (NMR). The cytotoxicity of the extract and its active compounds was evaluated in Vero cells. RESULTS: The ethyl acetate extract exhibited distinct inhibition zones against bacteria compared to other extracts. Therefore, the ethyl acetate extract of D. bulbifera in the ethyl acetate layer was used for subsequent analyses. D. bulbifera extract exhibited antibacterial activity, with minimum inhibitory concentrations (MICs) of 0.78-1.56 mg/mL. An active compound, identified through TLC-bioautography, demonstrated enhanced antibacterial activity, with MICs of 0.02-0.78 mg/mL. NMR analysis identified this bioactive compound as flavanthrinin. Both D. bulbifera extract and flavanthrinin-containing fraction demonstrated potent antibacterial activity against Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), and S. epidermidis. The flavanthrinin containing fraction demonstrated low cytotoxicity against Vero cells, showing CC50 values of 0.41 ± 0.03 mg/mL. These values are lower than the MIC value, indicating that this fraction is safer than the initial ethyl acetate extract. CONCLUSIONS: Dioscorea bulbifera extract and its bioactive component flavanthrinin demonstrated significant antibacterial activity against the skin-associated bacteria Staphylococci, including MRSA. Flavanthrinin has potential as a complementary therapeutic agent for managing skin infections owing to its potent antibacterial effects and low cytotoxicity.

[Study on mechanism of Chinese Yam polysaccharide synergizing nucleoside analogues against hepatitis B virus through p38 MAPK signaling pathway].

This study explore the molecular mechanism of the synergistic effect of Chinese Yam polysaccharides and nucleoside analogues(NAs) on hepatitis B virus(HBV) resistance. Different concentrations of Chinese Yam polysaccharide and entecavir were ad-ded to HepG2.2.15 cells. After the cytotoxicity was detected by cell counting kit-8(CCK-8), the optimal concentration and time of the two drugs to inhibit HepG2.2.15 cells were screened out. They were divided into control group, Chinese Yam polysaccharide group, entecavir group and combination drug group(Chinese Yam polysaccharide + entecavir). The drugs were added to HepG2.2.15 cells, ELISA was used to detect the effects of each group of drugs on the secretion of hepatitis B virus surface antigen(HBsAg) and hepatitis B virus e antigen(HBeAg) in cell supernatant, probe quantitative real-time PCR(probe qRT-PCR) was used to detect the effects of drugs on HBV-DNA in HepG2.2.15 cells, and Western blot was used to detect the effects of each group of drugs on the expression of p38 MAPK, p-p38 MAPK, NTCP proteins in HepG2.2.15 cells. The qRT-PCR was used to detect the effect of drugs on the expression of p38 MAPK and NTCP mRNA in HepG2.2.15 cells. The results showed that compared with control group, the concentrations of HBeAg and HBsAg in Chinese Yam polysaccharide group, entecavir group and combination group decreased(P<0.01 or P<0.001), and both of them inhibited HBV-DNA in HepG2.2.15 cells(P<0.01), and the HBV-DNA inhibition of HepG2.2.15 cells in the combination group was more obvious(P<0.001), and the protein expression levels of p-p38 MAPK and NTCP were significantly decreased(P<0.05 or P<0.01), the mRNA expression level of p38 MAPK increased, and the mRNA expression level of NTCP decreased(P<0.05 or P<0.01). To sum up, Chinese Yam polysaccharide can reduce the expression of NTCP protein and mRNA through p38 MAPK signaling pathway and cooperate with entecavir in anti-HBV.

The anti-non-small cell lung cancer effect of Diosbulbin B: Targeting YY1 induced cell cycle arrest and apoptosis.

BACKGROUND: Toxic components frequently exhibit unique characteristics and activities, offering ample opportunities for the advancement of anti-cancer medications. As the main hepatotoxic component of Dioscorea bulbifera L. (DB), Diosbulbin B (DIOB) has been widely studied for its anti-tumor activity at nontoxic doses. However, the effectiveness and mechanism of DIOB against non-small cell lung cancer (NSCLC) remains unclear. PURPOSE: To evaluate the anti-NSCLC activity of DIOB and to elucidate the specific mechanism of action. METHOD: The effect of DIOB on NSCLCL in vitro was evaluated through CCK8, colony formation, and flow cytometry. The in vivo efficacy and safety of DIOB in treating NSCLC were assessed using various techniques, including HE staining, tunel staining, immunohistochemistry, and biochemical index detection. To understand the underlying mechanism, cell transfection, western blotting, molecular docking, cellular thermal shift assay (CESTA), and surface plasmon resonance (SPR) were employed for investigation. RESULTS: DIOB effectively hindered the progression of NSCLC both in vitro and in vivo settings at a no-observed-adverse-effect concentration (NOAEC) and a safe dosage. Specifically, DIOB induced significant G0/G1 phase arrest and apoptosis in A549, PC-9, and H1299 cells, while also notably inhibiting the growth of subcutaneous tumors in nude mice. Mechanistically, DIOB could directly interact with oncogene Yin Yang 1 (YY1) and inhibit its expression. The reduction in YY1 resulted in the triggering of the tumor suppressor P53, which induced cell cycle arrest and apoptosis in NSCLC cells by inhibiting the expression of Cyclin A2, B2, CDK1, CDK2, CDK4, BCL-2, and inducing the expression of BAX. In NSCLC cells, the induction of G0/G1 phase arrest and apoptosis by DIOB was effectively reversed when YY1 was overexpressed or P53 was knocked down. Importantly, we observed that DIOB exerted the same effect by directly influencing the expression of YY1-regulated c-Myc and BIM, particularly in the absence of P53. CONCLUSION: For the inaugural investigation, this research unveiled the anti-NSCLC impact of DIOB, alongside its fundamental mechanism. DIOB has demonstrated potential as a treatment agent for NSCLC due to its impressive efficacy in countering NSCLC.

Molecular mechanism for the influence of yam starch multiscale structure on the sensory texture of cooked yam.

Yam is a dual-purpose crop as both medicine and food. However, the mechanism controlling the eating quality of yam remains to be elucidated. This study explored the influence of starch multiscale structure on the texture of yam. The results indicated that FS and RC yam have higher hardness and chewiness, while BZ, XM, and PL yam possess waxiness, Fineness, and Stickiness. Statistically, high amylose (AM) can increase hardness, chewiness, and compactness; and average molecular size (Rh) is positively correlated with stickiness, fineness, and waxiness. Specifically, medium- and long-chain amylose (1000 < X ≤ 10,000) and amylopectin (24 < X ≤ 100), particularly medium-chain amylose (1000 < X ≤ 5000) and long-chain amylopectin (24 < X ≤ 36), primarily affect sensory and rheological stickiness. The long chains of amylose form a straight chain interspersed in the crystalline and amorphous regions to support the entire lamellar structure. Higher proportion of amylose long chains, promoting the starch's structural rigidity, which in turn enhanced its hardness-related attributes. Moreover, a higher ratio of long chains within amylopectin results in tightly intertwined adjacent outer chains, forming double helix crystalline zones. This consequently augmenting the texture quality linked to stickiness-related attributes.

Investigating the impact of ultrasound on the structural, physicochemical, and emulsifying characteristics of Dioscorin: Insights from experimental data and molecular dynamics simulation.

This study investigated the impact of ultrasound treatment on dioscorin, the primary storage protein found in yam tubers. Three key factors, namely ultrasound power, duration, and frequency, were focused on. The research revealed that ultrasound-induced cavitation effects disrupted non-covalent bonds, resulting in a reduction in α-helix and ß-sheet contents, decreased thermal stability, and a decrease in the apparent hydrodynamic diameter (Dh) of dioscorin. Additionally, previously hidden amino acid groups within the molecule became exposed on its surface, resulting in increased surface hydrophobicity (Ho) and zeta-potential. Under specific ultrasound conditions (200 W, 25 kHz, 30 min), Dh decreased while Ho increased, facilitating the adsorption of dioscorin molecules onto the oil-water interface. Molecular dynamics (MD) simulations showed that at lower frequencies and pressures, the structural flexibility of dioscorin's main chain atoms increased, leading to more significant fluctuations between amino acid residues. This transformation improved dioscorin's emulsifying properties and its oil-water interface affinity.

Partial substitution of chemical fertilizer by organic fertilizer increases yield, quality and nitrogen utilization of Dioscorea polystachya.

This field experiment aimed to investigate the effects of different ratios of organic and inorganic fertilizers with maintaining equal nitrogen application rates on the yield, quality, and nitrogen uptake efficiency of Dioscorea polystachya (yam). Six treatments were set, including a control without fertilizer (CK), sole application of chemical fertilizer (CF), sole application of organic fertilizer (OM), 25% organic fertilizer + 75% chemical fertilizer (25%OM + 75%CF), 50% organic fertilizer + 50% chemical fertilizer (50%OM + 50%CF), and 75% organic fertilizer + 25% chemical fertilizer (75%OM + 25%CF). The experiment followed a randomized complete block design with three replications. Various yield parameters, morphology, quality indicators, and nitrogen utilization were analyzed to assess the differences among treatments. The results indicated that all fertilizer treatments significantly increased the yield, morphology, quality indicators, and nitrogen utilization efficiency compared to the control. Specifically, 25%OM + 75%CF achieved the highest yield of 31.96 t hm-2, which was not significantly different from CF (30.18 t hm-2). 25%OM + 75%CF exhibited the highest values at 69.23 cm in tuber length and 75.86% in commodity rate, 3.14% and 1.57% higher than CF respectively. Tuber thickness and fresh weight of 25%OM + 75%CF showed no significant differences from CF, while OM and 50%OM+50%CF exhibited varying degrees of reduction compared to CF. Applying fertilizer significantly enhanced total sugar, starch, crude protein, total amino acid, and ash contents of D. polystachya (except ash content between CK and OM). Applying organic fertilizer increased the total sugar, starch, crude protein, total amino acid, and ash contents in varying degrees when compared with CF. The treatment with 25%OM+75%CF exhibited the highest increases of 6.31%, 3.78%, 18.40%, 29.70%, and 10%, respectively. Nitrogen content in different plant parts followed the sequence of tuber > leaves > stems > aerial stem, with the highest nitrogen accumulation observed in 25%OM + 75%CF treatment. Nitrogen harvest index did not show significant differences among treatments, fluctuating between 0.69 and 0.74. The nitrogen apparent utilization efficiency was highest in 25%OM + 75%CF (9.89%), followed by CF (9.09%), both significantly higher than OM (5.32%) and 50%OM + 50%CF (6.69%). The nitrogen agronomic efficiency varied significantly among treatments, with 25%OM + 75%CF (33.93 kg kg-1) being the highest, followed by CF (29.68 kg kg-1), 50%OM + 50%CF (21.82 kg kg-1), and OM (11.85 kg kg-1). Nitrogen partial factor productivity was highest in 25%OM + 75%CF treatment (76.37 kg kg-1), followed by CF (72.11 kg kg-1), both significantly higher than 50%OM + 50%CF (64.25 kg kg-1) and OM (54.29 kg kg-1), with OM exhibiting significantly lower values compared to other treatments. In conclusion, the combined application of organic and inorganic fertilizers can effectively enhance the yield, quality, and nitrogen utilization efficiency of D. polystachya. Particularly, the treatment with 25% organic fertilizer and 75% chemical fertilizer showed the most promising results.

Identification of WRKY gene family in Dioscorea opposita Thunb. reveals that DoWRKY71 enhanced the tolerance to cold and ABA stress.

WRKY transcription factors constitute one of the largest plant-specific gene families, regulating various aspects of plant growth, development, physiological processes, and responses to abiotic stresses. This study aimed to comprehensively analyze the WRKY gene family of yam (Dioscorea opposita Thunb.), to understand their expression patterns during the growth and development process and their response to different treatments of yam and analyze the function of DoWRKY71 in detail. A total of 25 DoWRKY genes were identified from the transcriptome of yam, which were divided into six clades (I, IIa, IIc, IId, IIe, III) based on phylogenetic analysis. The analysis of conserved motifs revealed 10 motifs, varying in length from 16 to 50 amino acids. Based on real-time quantitative PCR (qRT-PCR) analysis, DoWRKY genes were expressed at different stages of growth and development and responded differentially to various abiotic stresses. The expression level of DoWRKY71 genes was up-regulated in the early stage and then down-regulated in tuber enlargement. This gene showed responsiveness to cold and abiotic stresses, such as abscisic acid (ABA) and methyl jasmonate (MeJA). Therefore, further study was conducted on this gene. Subcellular localization analysis revealed that the DoWRKY71 protein was localized in the nucleus. Moreover, the overexpression of DoWRKY71 enhanced the cold tolerance of transgenic tobacco and promoted ABA mediated stomatal closure. This study presents the first systematic analysis of the WRKY gene family in yam, offering new insights for studying WRKY transcription factors in yam. The functional study of DoWRKY71 lays theoretical foundation for further exploring the regulatory function of the DoWRKY71 gene in the growth and development related signaling pathway of yam.

A Comparative Analysis between Whole Chinese Yam and Peeled Chinese Yam: Their Hypolipidemic Effects via Modulation of Gut Microbiome in High-Fat Diet-Fed Mice.

Chinese yam is a "medicine food homology" food with medical properties, but little is known about its health benefits on hyperlipidemia. Furthermore, the effect of peeling processing on the efficacy of Chinese yam is still unclear. In this study, the improvement effects of whole Chinese yam (WY) and peeled Chinese yam (PY) on high-fat-diet (HFD)-induced hyperlipidemic mice were explored by evaluating the changes in physiological, biochemical, and histological parameters, and their modulatory effects on gut microbiota were further illustrated. The results show that both WY and PY could significantly attenuate the HFD-induced obesity phenotype, accompanied by the mitigative effect on epididymis adipose damage and hepatic tissue injury. Except for the ameliorative effect on TG, PY retained the beneficial effects of WY on hyperlipemia. Furthermore, 16S rRNA sequencing revealed that WY and PY reshaped the gut microbiota composition, especially the bloom of several beneficial bacterial strains (Akkermansia, Bifidobacterium, and Faecalibaculum) and the reduction in some HFD-dependent taxa (Mucispirillum, Coriobacteriaceae_UCG-002, and Candidatus_Saccharimonas). PICRUSt analysis showed that WY and PY could significantly regulate lipid transport and metabolism-related pathways. These findings suggest that Chinese yam can alleviate hyperlipidemia via the modulation of the gut microbiome, and peeling treatment had less of an effect on the lipid-lowering efficacy of yam.

The association between Dioscorea sansibarensis and Orrella dioscoreae as a model for hereditary leaf symbiosis.

Hereditary, or vertically-transmitted, symbioses affect a large number of animal species and some plants. The precise mechanisms underlying transmission of functions of these associations are often difficult to describe, due to the difficulty in separating the symbiotic partners. This is especially the case for plant-bacteria hereditary symbioses, which lack experimentally tractable model systems. Here, we demonstrate the potential of the leaf symbiosis between the wild yam Dioscorea sansibarensis and the bacterium Orrella dioscoreae (O. dioscoreae) as a model system for hereditary symbiosis. O. dioscoreae is easy to grow and genetically manipulate, which is unusual for hereditary symbionts. These properties allowed us to design an effective antimicrobial treatment to rid plants of bacteria and generate whole aposymbiotic plants, which can later be re-inoculated with bacterial cultures. Aposymbiotic plants did not differ morphologically from symbiotic plants and the leaf forerunner tip containing the symbiotic glands formed normally even in the absence of bacteria, but microscopic differences between symbiotic and aposymbiotic glands highlight the influence of bacteria on the development of trichomes and secretion of mucilage. This is to our knowledge the first leaf symbiosis where both host and symbiont can be grown separately and where the symbiont can be genetically altered and reintroduced to the host.

Effects of cooking methods on the physical properties and in vitro digestibility of starch isolated from Chinese yam.

The objective of this study was to compare the structural and functional attributes of Chinese yam starches obtained via different domestic cooking methods. Cooking changed the crystalline type from the C type to the CB type, and disrupted the short- and long-range molecular order of Chinese yam starch. The average chain length of amylopectin in BOS (boiling starch) was the smallest at 22.78, while RWS had the longest average chain length, reaching 24.24. These alterations in molecular structure resulted in variations in functional properties such as solubility, swelling power (SP), pasting characteristics, and rheological properties. Among these alterations, boiling was the most effective method for increasing the water-binding capacity and SP of starch. Specifically, its water holding capacity was 2.12 times that of RWS. In vitro digestion experiments indicated that BOS has a higher digestion rate (k = 0.0272 min-1) and lower RDS (rapidly digestible starch), which may be related to its amylopectin chain length distribution. This study can guide us to utilize yam starch through suitable cooking methods, which is relevant for the processing and application of Chinese yam starch.

Whole-genome sequencing and comparative genomics reveal candidate genes associated with quality traits in Dioscorea alata.

BACKGROUND: Quality traits are essential determinants of consumer preferences. Dioscorea alata (Greater Yam), is a starchy tuber crop in tropical regions. However, a comprehensive understanding of the genetic basis underlying yam tuber quality remains elusive. To address this knowledge gap, we employed population genomics and candidate gene association approaches to unravel the genetic factors influencing the quality attributes of boiled yam. METHODS AND RESULTS: Comparative genomics analysis of 45 plant species revealed numerous novel genes absent in the existing D. alata gene annotation. This approach, adding 48% more genes, significantly enhanced the functional annotation of three crucial metabolic pathways associated with boiled yam quality traits: pentose and glucuronate interconversions, starch and sucrose metabolism, and flavonoid biosynthesis. In addition, the whole-genome sequencing of 127 genotypes identified 27 genes under selection and 22 genes linked to texture, starch content, and color through a candidate gene association analysis. Notably, five genes involved in starch content and cell wall composition, including 1,3-beta Glucan synthase, ß-amylase, and Pectin methyl esterase, were common to both approaches and their expression levels were assessed by transcriptomic data. CONCLUSIONS: The analysis of the whole-genome of 127 genotypes of D. alata and the study of three specific pathways allowed the identification of important genes for tuber quality. Our findings provide insights into the genetic basis of yam quality traits and will help the enhancement of yam tuber quality through breeding programs.

Prospects of yam (Dioscorea) polysaccharides: Structural features, bioactivities and applications.

Yam (Dioscorea) is a tuber crop cultivated for food security, revenue, and medicinal purposes. It has been used to treat diabetes, asthma, diarrhea, and other diseases. The main active ingredients in yam, polysaccharides, are regarded to be the important reason for its widespread applications. Now, a comprehensive review of research developments of yam polysaccharides (YPs) was presented to explore their prospects. We outlined the structural characteristics, biological activities, structure-activity relationships, and potential applications. Around 13 neutral components and 17 acidic components were separated. They exhibited various bioactivities, including immunomodulatory, hypoglycemic, hypolipidemic, antioxidant, gastrointestinal protective, anti-fatigue, and senile disease treatment activities, as well as prebiotic effect. Structure-activity relationships illustrated that unique structural properties, chemical modifications, and carried biopolymers could influence the bioactivities of YPs. The potential applications in medicine, food, and other fields have also been summarized.

Identification of breadfruit (Artocarpus altilis) and South American crops introduced during early settlement of Rapa Nui (Easter Island), as revealed through starch analysis.

Starch residue analysis was carried out on stone tools recovered from the bottom layer of the Anakena site on Rapa Nui (Easter Island). These deposits have been dated to AD 1000-1300 AD and so far, represent the earliest evidence of human settlement on this island. Twenty obsidian tools were analyzed. Analysis of 46 starch grains recovered from 20 obsidian tools from the earliest dated level of the Anakena site on Rapa Nui provides direct evidence for translocation of traditional crop plants at initial stages of the colonization of this island. The analysis of starch grains was based mainly on statistical methods for species identification but was complemented by visual inspection in some cases. Our results identify taxons previously unknown to have been cultivated on the island, such as breadfruit (Artocarpus altilis), Zingiber officinale (ginger), and starch grains of the Spondias dulcis and Inocarpus fagifer tropical trees. Additionally, starch grains of Colocasia esculenta (taro) and Dioscorea sp. (yam), both common species in Pacific agriculture, were identified. Furthermore, the presence of four American taxa Ipomoea batatas (sweet potato), Canna sp. (achira), Manihot esculenta (manioc), and Xanthosoma sp., was detected. The occurrence of Canna sp., M. esculenta, and Xanthosoma sp. starch grains suggests the translocation of previously not described South American cultivars into the Pacific. The detection of I. batatas from this site in Rapa Nui constitutes the earliest record of this cultigen in the Pacific. Our study provides direct evidence for translocation of a set of traditional Polynesian and South American crop plants at the initial stages of colonization in Rapa Nui.

The genus Dioscorea L. (Dioscoreaceae), a review of traditional uses, phytochemistry, pharmacology, and toxicity.

ETHNOPHARMACOLOGICAL RELEVANCE: The genus Dioscorea, a member of the Dioscoreaceae family, comprises approximately 600 species and is widely distributed across temperate and tropical regions such as Asia, South Africa, and North America. The traditional medicinal uses of Dioscorea have been documented in Asian and African pharmacological systems. In Asia, this genus is traditionally used to treat respiratory illnesses, rheumatism, diabetes, diarrhea, dysentery, and other conditions. In Africa, this genus has been used to treat human immunodeficiency virus and ring worms. However, the traditional medicinal practices in North America rarely mention the use of this genus. AIM OF THE STUDY: The aim of this review is to comprehensively review the genus Dioscorea, focusing on its traditional uses, phytochemical constituents, pharmacological activities, and potential toxicities. The research also aims to highlight the valuable bioactive compounds within Dioscorea and emphasize the need for further investigations into acute and chronic toxicity, activity mechanisms, molecular markers, and other relevant factors to contribute to the discovery of novel pharmaceuticals. MATERIALS AND METHODS: A search for available information on Dioscorea was conducted using scientific databases, including PubMed, ISI-WOS, Scopus, and Google Scholar, as well as recent academic publications from reputable publishers and other literature sources. The search was not limited by language and spanned the literature published between 1950 and 2022. RESULTS: This article provides a comprehensive review of the Dioscorea genus, focusing on its traditional uses, phytochemical constituents, pharmacological activities, and potential toxicities. Extensive research has been conducted on this genus, resulting in the isolation and examination of over 1000 compounds, including steroids, terpenoids, and flavonoids, to determine their biological activities. These activities include anti-tumor, anti-inflammatory, immunomodulatory, neuroprotective, hypoglycemic, and hypolipidemic effects. However, some studies have indicated the potential toxicity of high doses of Dioscorea, highlighting the need for further investigations to assess the safety of this genus. Additionally, this review explores potential avenues for future research and discusses the challenges associated with a comprehensive understanding of the Dioscorea genus. CONCLUSIONS: Based on the existing literature, it can be concluded that Dioscorea is a valuable source of bioactive compounds that have the potential to treat various disorders. Future research should prioritize the investigation of acute and chronic toxicity, activity mechanisms, molecular markers, and other relevant factors. This review provides a comprehensive analysis of the Dioscorea genus, emphasizing its potential to enable a deeper exploration of the biological activity mechanisms of these plants and contribute to the discovery of novel pharmaceuticals.