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A better understanding of the structure and extent of genetic variability in a breeding population of a crop is essential for translating genetic diversity to genetic gain. We assessed the nature and pattern of genetic variability and differentiation in a panel of 100 winged-yam ( Dioscorea alata ) accessions using 24 phenotypic traits and 6,918 single nucleotide polymorphism (SNP) markers. Multivariate analysis for phenotypic variability indicated that all phenotypic traits assessed were useful in discriminating the yam clones and cultivars. Cluster analysis based on phenotypic data distinguished two significant groups, while a corresponding analysis with SNP markers indicated three genetic groups. However, joint analysis for the phenotypic and genotypic data provided three clusters that could be useful for the identification of heterotic groups in the D. alata breeding program. Our analysis for phenotypic and molecular level diversity provided valuable information about overall diversity and variation in economically important traits useful for establishing crossing panels with contrasting traits of interest. The selection and hybridization of parental lines from the different heterotic groups identified would facilitate maximizing diversity and exploiting population heterosis in the D. alata breeding program.

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.

Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome resequencing platform. Various diversity matrices and clustering methods were evaluated for a comprehensive characterization of genetic diversity in white Guinea yam from West Africa at phenotypic and molecular levels. The translation of the different diversity matrices from the phenotypic and genomic information into distinct groups varied with the hierarchal clustering methods used. Gower distance matrix based on phenotypic data and identity by state (IBS) distance matrix based on SNP data with the UPGMA clustering method found the best fit to dissect the genetic relationship in current set materials. However, the grouping pattern was inconsistent (r = − 0.05) between the morphological and molecular distance matrices due to the non-overlapping information between the two data types. Joint analysis for the phenotypic and molecular information maximized a comprehensive estimate of the actual diversity in the evaluated materials. The results from our study provide valuable insights for measuring quantitative genetic variability for breeding and genetic studies in yam and other root and tuber crops.

White Guinea yam (Dioscorea rotundata) is an important staple tuber crop in West Africa. However, its origin remains unclear. In this study, we resequenced 336 accessions of white Guinea yam and compared them with the sequences of wild Dioscorea species using an improved reference genome sequence of D. rotundata. In contrast to a previous study suggesting that D. rotundata originated from a subgroup of Dioscorea praehensilis, our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species D. praehensilis and the savannah-adapted species Dioscorea abyssinica. We identified a greater genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improving this crop through molecular breeding.

Background Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop. Results To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam ( Dioscorea rotundata ) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage. Conclusions Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture.

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.

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.

Water yam ( Dioscorea alata L.) or greater yam, is an essential species of the Dioscoreceae family in tropical and subtropical regions. The wide geographical distribution is owing to its higher tuber yield, storability, and better nutritional and health benefits compared to many other species. Despite these promising characteristics, water yam remains less preferred by consumers for traditional food products, particularly boiled and pounded yam preparations. Fast and efficient development of superior genotypes that meet farmers and end-users needs have been challenging through classical breeding methods. The objective of the study was to use genome-wide associations to assess the genetics of post-harvest tuber quality, mainly targeting the consumer-preferred traits. A panel of 404 water yam genotypes were assessed to decipher the genomic regions associated with traits such as tuber oxidative browning, dry matter content, and boiled and pounded tuber quality. The Multiple Random Mixed Linear Model was employed for marker-trait association analysis using the naive, Q, and Q + K models, followed by gene annotation and marker or allele substitution effects. Fourteen SNP markers were significantly linked with the assessed tuber quality traits and r 2 values ranged from 0.62 to 10.02%. The gene annotation analysis revealed presence of 32 putative candidate genes playing crucial roles in enzymatic browning and carbohydrate biosynthesis pathways for dry matter accumulation. The molecular information generated in the present study can be deployed for water yam improvement.

Background Dehydration responsive element-binding protein ( DREB ) serves as a core transcriptional regulator of abiotic stress responses, yet a systematic DREB gene locus map has not been established for Chinese yam ( Dioscorea opposita ). Given Chinese yam’s dual role as a staple food crop and medicinal tuber, elucidating DREB gene function is of considerable importance. It remains unclear whether, and how, the Chinese yam DREB family coordinates responses to drought, high salinity, or low temperature. Therefore, a genome-wide survey of DREB members, coupled with functional validation of the key drought-tolerance regulator DoDREB28 , may reveal the molecular framework underlying this food-medicine crop’s adaptation to adverse environments. Results We identified 32 DoDREB members that clustered into six subgroups (A1-A6), a number markedly lower than that of Arabidopsis (56) and rice (57); the closely related species greater yam also harbors only 47 loci, indicating a contractive pattern of the family within Dioscorea . All paralogues retain an intact AP2 domain, and 84.62% of duplicate pairs originated from segmental duplication under strong purifying selection (Ka/Ks < 0.35), underscoring the functional conservation. Transcriptome profiling integrating drought, salt, and cold stress revealed that the DoDREB family exhibits distinct expression patterns. Specifically, DoDREB28 showed sustained upregulation within 24 h under 20% (w/v) PEG-simulated drought stress, whereas its expression remained suppressed throughout 24 h of 200 mM NaCl salt stress. Overexpression of DoDREB28 in Arabidopsis enhanced primary-root elongation, proline content, and SOD activity, while reducing MDA and H₂O₂ accumulation under 300 mM mannitol, confirming that improved osmotic adjustment and antioxidant capacity confer greater drought tolerance. Population-genomic analysis of 101 landraces uncovered two haplotypes: Haplotype 1 (Hap1) displayed significantly higher drought-induced expression than Haplotype 2 (Hap2), which predominates in humid regions (Shandong and Hunan provinces, China), implying relaxed selection during domestication. Conclusions Our study systematically analyzed the Chinese yam DREB family based on the current dataset, revealing that DoDREB28 exhibits significant upregulation in drought-stressed transcriptomes. It can be tentatively classified as a candidate positive regulator involved in drought response. This gene and its variant sites serve only as preliminary molecular marker resources.