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Background Dioscorea polystachya and its closely related species are original plants of the tuber crop “yam”, which had been intensively use for medicinal and food purposes and widely cultivated in northern China and its surrounding areas with a long history. Many cultivars of these species are often confused with one another because of similar tuber morphology, however, conventional DNA barcoding faces practical limitations restricting the method to effectively identify closely related species. In addition, phylogenetic relationships among various cultivar groups of Chinese yam ( D. polystachya ) remains unclear. To solve these problems, genomic DNAs of 15 Dioscorea samples were sequenced to assemble and annotate chloroplast genomes, which were used for analyzing their structural characteristics and identifying phylogenetic relationships at the inter- and intraspecific levels. Results The size of chloroplast genomes of the tested samples is about 153 kb, and 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes are annotated. Phylogenetic analysis showed that D. polystachya were sister to Dioscorea japonica , and for Huaishan yams, Dioscorea persimilis did not cluster with Dioscorea alata and Dioscorea fordii . Four cultivar groups of Chinese yam were determined, namely Tiegun group, Anping group, Foshou group and Taihang complex group. Among these cultivar groups, Foshou and Taihang complex are clustered with different wild yams, respectively. Amino acid preferences are similar at the inter- and intraspecific levels, while synonymous codon usage reflects distinct patterns in the majority of cultivars of D. polystachya . There are distinct SSR variations among species, as well as four cultivar groups. Collinearity and SNP analyses show that nucleotide hypervariable regions among Dioscorea species are mainly concentrated in trnK–atpA , rps16–trnQ , atpA–atpH , rpoB–psbD , atpH–atpI , trnV–ndhC in the LSC region, and ccsA–ndhF in the SSC region, while intraspecific variation of Chinese yam is enriched in the intergenic spacers of rpoB–psbC , ndhD–ndhF , and trnQ-trnS , as well as the gene ycf1 . Conclusion Phylogenetic analysis supports that Huaishan yams are not of monophyletic origin and the cultivated Chinese yam has at least two wild origins of domestication, which is consistent with the historical records of these wild yams from Mt. Dabie and Mt. Taihang. The identification efficiency of the newly developed barcodes for cultivar groups based on chloroplast genome SNP screening is significantly better than those of conventional barcodes. This approach to generate viable candidate markers based on the comparison from interspecific and intraspecific hypervariable regions of chloroplast genomes can be applied to conduct phylogenetic relationships of more important crop species and their close relatives, which are difficult to identify, as well as their wild origins of domestication.

Background Vine cutting propagation in yams offers a transformative approach to conventional tuber-dependent cultivation, with enhanced tuber yield and quality. Adventitious root (AR) formation is a critical prerequisite for vine cutting survival, with substantial variability among yam varieties. However, relatively little is known about the regulatory mechanisms that restrict the application of cutting propagation in recalcitrant varieties. In this study, we integrated rooting rate comparisons, anatomical observations, phytohormone content determination, and transcriptomic profiling to elucidate the developmental mechanisms influencing AR formation. Results The adventitious rooting capacity of Dioscorea polystachya was significantly different from that of Dioscorea alata . Six D. alata cultivars showed rooting efficiencies exceeding 70%. In contrast, D. polystachya variety RuiChang Shan Yao (RCSY) exhibited a recalcitrant phenotype with a rooting rate of less than 5%. Phenotypic evaluation identified the AR formation phase from 0 to 12 days after cutting (DAC). Anatomical observations indicated AR initiation within the phloem tissues by two DAC, followed by complete penetration of the cortical and epidermal layers by four DAC in D. alata . Temporal phytohormone profiling showed higher auxin levels in Gan Bai Yu (GBY) and Gan Zi Yun (GZY) than in RCSY during AR formation. Transcriptomic profiling analysis of GBY and GZY at 0, 2, 4, and 8 DAC identified 9,680 differentially expressed genes (DEGs). Integrated with hormonal and rooting data, weighted gene co-expression network analysis delineated AR-associated modules (saddlebrown, magenta, orange). Kyoto Encyclopedia of Genes and Genomes enrichment underscored starch and sucrose metabolism (31 DEGs) and hormone signal transduction (18 DEGs) as central pathways. Exogenous application of 1-naphthaleneacetic acid enhanced the rooting rate. Sucrose and starch accumulation were positively associated with AR competence in GBY, GZY, and the recalcitrant RCSY. Cross-species analysis identified 39 conserved DEGs in RCSY, including six auxin-responsive genes (one IAA16 , one ARF9 , two ARR11 , one SAUR50, one SAUR32 ), two cytokinin-responsive genes (two RR9 ), a GA-related gene (one GID1C ), six ABA-related genes (two PYL10 , one AHG1 , two ABF ), and 24 starch and sucrose metabolism-related genes ( SUS7 , HXK1, FRK2 , SS2 , TPPs , DPEP , GLUs , and BGLUs ), which implied their roles in AR regulation. Conclusions These findings identify the key molecular drivers of AR formation in yams, offering new insights into rooting recalcitrance and strategies for optimizing clonal propagation in agricultural species.

The traditional crop calendar for yam ( Dioscorea spp.) in South-Kivu, eastern Democratic Republic of Congo (DRC), is becoming increasingly inadequate given the significant climatic variability observed over the last three decades. This study aimed at: (i) assessing trends in weather data across time and space to ascertain climate change, and (ii) optimizing the yam crop calendar for various South-Kivu agro-ecological zones (AEZs) to adapt to the changing climate. The 1990–2022 weather data series were downloaded from the NASA-MERRA platform, bias correction was carried out using local weather stations’ records, and analyses were performed using RClimDex 1.9. Local knowledge and CROPWAT 8.0 were used to define planting dates for yam in different AEZs. Results showed the existence of four AEZs in the South-Kivu province, with contrasting altitudes, temperatures, and rainfall patterns. Climate change is real in all these South-Kivu’s AEZs, resulting either in rainfall deficits in some areas, or extreme rainfall events in others, with significant temperature increases across all AEZs. Suitable yam planting dates varied with AEZs, September 15 th and 20 th were recommended for the AEZ 2 while October 15 th was optimal for AEZ 1, AEZ 3, and AEZ 4. However, none of the planting date scenarios could meet the yam water requirements in AEZ1, AEZ3, and AEZ4, since the effective rainfall (Pmm) was always inferior to the plant water demand (ETc), meaning that soil water conservation practices are needed for optimum plant growth and yield in these AEZs. This study does not recommend planting yam during the short rainy season owing to prolonged droughts coinciding with critical growth phases of yam, unless supplemental irrigation is envisaged. This study provided insights on the nature of climate change across the past three decades and suggested a yam crop calendar that suits the changing climate of eastern DRC.

Dioscorea zingiberensis is a perennial herb native to China. The rhizome of D. zingiberensis has long been used as a traditional Chinese medicine to treat rheumatic arthritis. Dioscin is the major bioactive ingredient conferring the medicinal property described in Chinese pharmacopoeia. Several previous studies have suggested cholesterol as the intermediate to the biosynthesis of dioscin, however, the biosynthetic steps to dioscin after cholesterol remain unknown. In this study, a comprehensive D. zingiberensis transcriptome derived from its leaf and rhizome was constructed. Based on the annotation using various public databases, all possible enzymes in the biosynthetic steps to cholesterol were identified. In the late steps beyond cholesterol, cholesterol undergoes site-specific oxidation by cytochrome P450s (CYPs) and glycosylation by UDP-glycosyltransferases (UGTs) to yield dioscin. From the D. zingiberensis transcriptome, a total of 485 unigenes were annotated as CYPs and 195 unigenes with a sequence length above 1000 bp were annotated as UGTs. Transcriptomic comparison revealed 165 CYP annotated unigenes correlating to dioscin biosynthesis in the plant. Further phylogenetic analysis suggested that among those CYP candidates four of them would be the most likely candidates involved in the biosynthetic steps from cholesterol to dioscin. Additionally, from the UGT annotated unigenes, six of them were annotated as 3-O-UGTs and two of them were annotated as rhamnosyltransferases, which consisted of potential UGT candidates involved in dioscin biosynthesis. To further explore the function of the UGT candidates, two 3-O-UGT candidates, named Dz3GT1 and Dz3GT2, were cloned and functionally characterized. Both Dz3GT1 and Dz3GT2 were able to catalyze a C3-glucosylation activity on diosgenin. In conclusion, this study will facilitate our understanding of dioscin biosynthesis pathway and provides a basis for further mining the genes involved in dioscin biosynthesis.

Yam ( Dioscorea spp.) is a tuber-producing crop and an important staple in the tropics and subtropics, valued for its nutritional, health and sociocultural relevance. However, there is limited awareness of its nutritional and health benefits among local communities in eastern Democratic Republic of Congo (DRC), prompting its underutilization. This study aimed to (a) document the diversity of cultivated and semi-domesticated yam species in eastern DRC; (b) explore indigenous knowledge on their nutritional and health benefits; and (c) assess the nutrient composition and antioxidant activity of major yam species consumed in the region. Data collection involved ethno-botanical surveys, plant specimen collections, interviews with 123 community members, and physicochemical profiling using standard analytical methods. Ten yam species were documented in eastern DRC, including two domesticated species, with distribution patterns shaped by biophysical conditions and cultural factors. Species richness was higher in highland forest zones compared to lowland savannas. Local communities use yam to treat more than 15 health conditions, including stomach pains, food intoxications, skin wounds and infections, reproductive abnormalities, immune system deficiency, respiratory challenges, diabetics, etc. Physicochemical composition analysis revealed interspecific variations potentially contributing to their nutritional and therapeutic relevance by local communities. Notably, Dioscorea dumetorum tubers exhibited the highest protein content (8.7 g/100 g) and potassium concentration (240.2 mg/100 g), D. praehensilis was rich in carbohydrates (80.9 g/100 g), and D. bulbifera had highest calcium concentration (40.1 mg/100 g), underscoring the yam nutritional significance in the local diet. All yam species encompassed saponins, terpenoids, and alkaloids, though D. praehensilis and purple D. alata had the highest antioxidant activity that exceeded 90% inhibition level. These findings provide valuable insights on yam diversity and their potential to sustain nutritious healthy diets in eastern DRC.

Yams ( Dioscorea spp.) host a diverse range of badnaviruses (genus Badnavirus , family Caulimoviridae ). The first complete genome sequence of Dioscorea bacilliform RT virus 3 (DBRTV3), which belongs to the monophyletic species group K5, is described. This virus is most closely related to Dioscorea bacilliform SN virus (DBSNV, group K4) based on a comparison of genome sequences. Recombination analysis identified a unique recombination event in DBRTV3, with DBSNV likely to be the major parent and Dioscorea bacilliform AL virus (DBALV) the minor parent, providing the first evidence for recombination in yam badnaviruses. This has important implications for yam breeding programmes globally.

Yams are the edible subterranean rhizomes, or tubers, of plants from the genus Dioscorea. There are approximately 600 species of yam plants in the world, with more than 90 of these growing in East Asia. One particular species, Dioscorea opposita Thunb., is highly praised as “the Chinese yam”. This distinction arises from millennia of storied history, both as a nutritional food source and as a principal ingredient in traditional Chinese medicine. Among the many cultivars of Dioscorea opposita Thunb., Huai Shanyao has been widely regarded as the best. This review surveyed the historical background, physiochemical composition, applications as food and medicine, and research prospects for the Chinese yam. Modern science is finally beginning to confirm the remarkable health benefits of this yam plant, long-known to the Chinese people. Chinese yam promises anti-diabetic, anti-oxidative, anti-inflammatory, immunomodulatory, anti-hyperlipidemic, anti-hypertensive, anti-cancer, and combination treatment applications, both as a functional food and as medicine.

Dioscorea zingiberensis is a medicinal herb containing a large amount of steroidal saponins, which are the major bioactive compounds and the primary storage form of diosgenin. The CYP72A gene family, belonging to cytochromes P450, exerts indispensable effects on the biosynthesis of numerous bioactive compounds. In this work, a total of 25 CYP72A genes were identified in D. zingiberensis and categorized into two groups according to the homology of protein sequences. The characteristics of their phylogenetic relationship, intron–exon organization, conserved motifs and cis-regulatory elements were performed by bioinformatics methods. The transcriptome data demonstrated that expression patterns of DzCYP72As varied by tissues. Moreover, qRT-PCR results displayed diverse expression profiles of DzCYP72As under different concentrations of jasmonic acid (JA). Likewise, eight metabolites in the biosynthesis pathway of steroidal saponins (four phytosterols, diosgenin, parvifloside, protodeltonin and dioscin) exhibited different contents under different concentrations of JA, and the content of total steroidal saponin was largest at the dose of 100 μmol/L of JA. The redundant analysis showed that 12 DzCYP72As had a strong correlation with specialized metabolites. Those genes were negatively correlated with stigmasterol and cholesterol but positively correlated with six other specialized metabolites. Among all DzCYP72As evaluated, DzCYP72A6, DzCYP72A16 and DzCYP72A17 contributed the most to the variation of specialized metabolites in the biosynthesis pathway of steroidal saponins. This study provides valuable information for further research on the biological functions related to steroidal saponin biosynthesis.

Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.

Development of core collection representing the diversity in the entire germplasm creates a better access and enhanced utilization of the main collection thus allowing rapid evaluation in crop improvement programs. Core collections are dynamic in nature and needs revisiting when additional germplasm and information becomes available. In the current study, an attempt was made to re-define the previously developed yam (Dioscorea spp) core collection using 56 morphological traits. Information on additional acquired germplasm and presence of duplicates or mislabelled accessions in the entire collection was also used. The re-defined core collection consisted of 843 accessions and represented about 20% of the entire collection. It included six Dioscorea species, of which accessions of Dioscorea rotundata are in the majority (73.54%) followed by Dioscorea alata (21.35%), Dioscorea bulbifera (1.66%), Dioscorea cayenensis (1.42%), Dioscorea dumetorum (1.42%) and Dioscorea esculenta (0.59%). The Shannon weaver diversity index and principal component analysis revealed the maximum diversity captured in the core from the base collection. This re-defined core collection is more valuable than the original core since it represents true-to-type accessions ensuring reliability for enhanced utilization of germplasm in yam improvement programs.