Yam Germplasm Research Articles

Genetic Diversity Research of Yam Germplasm Resources

Yam (Dioscorea spp.), a versatile economic crop used both as food and medicine, is widely distributed globally, particularly in tropical and subtropical regions. Its abundant germplasm resources provide a crucial foundation for genetic diversity research. This paper reviews the latest advances in the genetic diversity study of yam germplasm resources, focusing on research methods and outcomes based on morphological traits, cytological markers, and molecular markers. By analyzing the application and effectiveness of these research methods, this paper summarizes key findings in yam genetic diversity research and proposes future research directions, aiming to provide theoretical support and technical guidance for yam genetic improvement and germplasm resource conservation.

An Improved Phenotyping Method for Evaluation of Yam (Dioscorea spp.) Resistance to Nematodes Belonging to the Genera Meloidogyne and Scutellonema.

Phenotyping yam (Dioscorea spp.) germplasm for resistance to parasitic nematodes is hampered by the lack of an efficient screening method. In this study, we developed a new method using rooted yam vine cuttings and yam plantlets generated from semi-autotrophic hydroponics (SAHs) propagation for phenotyping yam genotypes for nematode resistance. The method was evaluated using 26 genotypes of D. rotundata for their reaction to Scutellonema bradys and four root-knot nematode species, Meloidogyne arenaria, M. enterolobii, M. incognita, and M. javanica. Yam plantlets established in nursery bags filled with steam-sterilized soil were used for screening against single nematode species. Plants were inoculated four weeks after planting and assessed for nematode damage eight weeks later. A severity rating scale was used to classify genotypes as resistant, tolerant, or susceptible determine based on the nematode feeding damage on tubers and the rate of nematode multiplication in the roots of inoculated plants. The results demonstrated putative resistance and tolerance against S. bradys in 58% of the genotypes and 88%, 65%, 65%, and 58% against M. arenaria, M. javanica, M. incognita, and M. enterolobii, respectively. The method is rapid, flexible, and seasonally independent, permitting year-round screening under controlled conditions. This method increases the throughput and speed of phenotyping and improves the selection process.

Identification and pathogenicity of Colletotrichum truncatum causing yam anthracnose – A new record in China

Yam (Dioscorea spp.) is a significant tuber crop. In October 2022, yam (Dioscorea opposita Thunb.) leaves exhibiting typical anthracnose symptoms were observed at the Yam Germplasm Resource Nursery of Wen County, Jiaozuo City, Henan Province, China. The disease incidence was recorded at 92.05%. The symptoms manifested as brown to dark brown circular or irregular large spots on the leaves, some of which displayed noticeable irregular concentric rings. A total of 23 isolates were obtained, with JCHN023-1 and JCHN003 isolates being the representative. The pathogen was successfully re-isolated from lesions of inoculated leaves, fulfilling Koch's postulates. Morphologically, the conidia appeared colorless, crescent-shaped, circular blunt at both ends, and measured (15.2-) 18.2–30 (−34.1) × (2.1-) 2.3–3.9 (−4.2) μm in length (average = 24.1 × 3.1 μm) without septa. The setae were black-brown and exhibited 1-4 septa. Subsequently, a multigene phylogenetic analysis, involving internal transcribed spacer (ITS), partial actin (ACT), chitin synthase 1 (CHS-1) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), identified the fungus as Colletotrichum truncatum. Inoculation of detached leaves from 10 varieties of D. opposita confirmed their broad-spectrum pathogenicity to yam. This represents the first report of yam anthracnose caused by C. truncatum in China and provides a theoretical foundation for yam anthracnose prevention and control.

Analysis of Genetic Diversity and Population Structure in Yam (Dioscorea Species) Germplasm Using Start Codon Targeted (SCoT) Molecular Markers

Yam (Dioscorea spp.) is an important food security crop with economic, nutritional, and medicinal value. It is a source of carbohydrates for millions of people in tropical and sub-tropical regions of Africa, Asia, South America, the Caribbean, and the South Pacific Islands. Determining the appropriate parents for breeding programs is the most important decision that plant breeders must make to maximize genetic variability and produce excellent recombinant varieties. However, adequate genetic diversity and the population structure of yam accessions in Kenya are not available to guide accurate selection of parents for breeding. In the present study, 25 start-codon-targeted (SCoT) molecular markers were used to determine the genetic diversity and population structure among 20 yam accessions grown in Kenya. A total of 294 fragments were amplified, of which 95% were polymorphic with an average of 11.16 polymorphic fragments per primer. The polymorphic information content (PIC) value and primer resolving power (Rp) of 0.58 and 5.91, respectively, revealed high genetic diversity among the accessions. A dendrogram based on the unweighted pair group method of arithmetic means (UPGMA) grouped the 20 yam accessions into two clusters at 0.61 genetic similarity coefficients. Bayesian structure analysis revealed the existence of three subpopulations and some admixed accessions. Analysis of molecular variance (AMOVA) revealed a variance of 60% within the subpopulations and 40% among the subpopulations. The high degree of genetic diversity in the yam accessions successfully exhibited by SCoT molecular markers may serve as a valuable aid to widen the genetic base in yam breeding programs. The selection and hybridization of parental lines from the different clusters and sub-clusters identified could provide a foundation and could be exploited for yam breeding and variety development.

Genetic diversity and population structure of Uganda's yam (Dioscorea spp.) genetic resource based on DArTseq.

Assessing the genetic diversity of yam germplasm from different geographical origins for cultivation and breeding purposes is an essential step for crop genetic resource conservation and genetic improvement, especially where the crop faces minimal attention. This study aimed to classify the population structure, and assess the extent of genetic diversity in 207 Dioscorea rotundata genotypes sourced from three different geographical origins. A total of 4,957 (16.2%) single nucleotide polymorphism markers were used to assess genetic diversity. The SNP markers were informative, with polymorphic information content ranging from 0.238 to 0.288 and a mean of 0.260 across all the genotypes. The observed and expected heterozygosity was 0.12 and 0.23, respectively while the minor allele frequency ranged from 0.093 to 0.124 with a mean of 0.109. The principal coordinate analysis, model-based structure and discriminant analysis of principal components, and the Euclidean distance matrix method grouped 207 yam genotypes into three main clusters. Genotypes from West Africa (Ghana and Nigeria) had significant similarities with those from Uganda. Analysis of molecular variance revealed that within-population variation across three different geographical origins accounted for 93% of the observed variation. This study, therefore, showed that yam improvement in Uganda is possible, and the outcome will constitute a foundation for the genetic improvement of yams in Uganda.

Phenotypic Diversity within Ugandan Yam (Dioscorea species) Germplasm Collection

A proper understanding of the diversity of the available germplasm is an initial step for the genetic improvement of a crop through breeding. However, there is limited information on the diversity of Uganda’s yam germplasm. The study sought to characterize the diversity of yam germplasm utilized for decades in Uganda together with germplasm recently introduced from West Africa using phenotypic traits. A germplasm collection of 291 genotypes was characterized using 28 phenotypic traits. Data were subjected to multivariate analysis using principal component analysis and cluster analysis. The traits assessed were informative and discriminating, with 62% of the total variation explained among the first six principal components. Results showed that the important phenotypic traits contributing to most of the variability among the genotypes were leaves, flowering, and tuber traits. Ugandan genotypes were identified with amorphous tuber shapes compared to West African genotypes. The study has shown that there is ample phenotypic variability within the major yam genotypes in Uganda yam germplasm that can be used for genetic improvement. More in-depth molecular and biochemical studies to further understand the diversity are recommended. The preprint was made available by research square in the following link: “https://www.researchsquare.com/article/rs-1518551/v1.”

Development of Simple Sequence REPEAT Markers for Genetic Diversity Analysis Based on the cDNA Sequences of Chinese Yam (Dioscorea spp.)

Chinese yam, with its rich taste and high nutritive value, has remained an essential part of Chinese cuisine. As China is rich in yam germplasm resources, understanding the genetic diversity of local varieties, which is important for the proper management, conservation, variety improvement, and sustainable utilization of yam germplasms, is crucial. In this study, an Illumina Hi-seq 2500 sequencing (Illumina, San Diego, CA, USA) system was used to sequence cDNA libraries of root, stem, and leaf tissues of Chinese yam; 14,450 unigenes containing SSR sites were identified from the transcriptome dataset. About half of the SSRs were mononucleotides and approximately 23% were dinucleotides and trinucleotides. In addition, 100 SSR primers were randomly designed for PCR and polymorphism verification. A total of 32 yam materials used in the study were identified by 24 primer pairs. Based on the Qinling-Huaihe River line, the northern and southern germplasms were divided into different taxa, but no clear geographical pattern was observed in the southern germplasms. The 32 germplasms were also divided into three categories using a clustering analysis, with samples in the same group possessing similar morphological characters. These 24 newly identified SSR markers can provide the basis for the genetic identification, diversity analysis, and marker-assisted selection breeding of Dioscoreaceae.

Viruses of Yams (Dioscorea spp.): Current Gaps in Knowledge and Future Research Directions to Improve Disease Management.

Viruses are a major constraint for yam production worldwide. They hamper the conservation, movement, and exchange of yam germplasm and are a threat to food security in tropical and subtropical areas of Africa and the Pacific where yam is a staple food and a source of income. However, the biology and impact of yam viruses remains largely unknown. This review summarizes current knowledge on yam viruses and emphasizes gaps that exist in the knowledge of the biology of these viruses, their diagnosis, and their impact on production. It provides essential information to inform the implementation of more effective virus control strategies.

Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm.

Viruses of the genus Badnavirus (family Caulimoviridae) are double-stranded DNA-reverse transcribing (dsDNA-RT) plant viruses and have emerged as serious pathogens of tropical and temperate crops globally. Endogenous badnaviral sequences are found integrated in the genomes of several economically important plant species. Infection due to activation of replication-competent integrated copies of the genera Badnavirus, Petuvirus and Cavemovirus has been described. Such endogenous badnaviral elements pose challenges to the development of nucleic acid-based diagnostic methods for episomal virus infections and decisions on health certification for international movement of germplasm and seed. One major food security crop affected is yam (Dioscorea spp.). A diverse range of Dioscorea bacilliform viruses (DBVs), and endogenous DBV (eDBV) sequences have been found to be widespread in yams cultivated in West Africa and other parts of the world. This study outlines the development of multiplex PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE) to assist in the detection and analysis of eDBVs, through the example of analysing yam germplasm from Nigeria and Ghana. Primers targeting the three most prevalent DBV monophyletic species groups in West Africa were designed to improve DGGE resolution of complex eDBV sequence fingerprints. Multiplex PCR-DGGE with the addition of a tailor-made DGGE sequence marker enables rapid comparison of endogenous badnaviral sequence diversity across germplasm, as illustrated in this study for eDBV diversity in yam.

Characterizing diversity based on phenotypes and molecular marker analyses of purple yam (Dioscorea alata L.) germplasm in southern China

Characterizing diversity based on phenotypes and molecular marker analyses of purple yam (Dioscorea alata L.) germplasm in southern China

Diversity, trait preferences, management and utilization of yams landraces (Dioscorea species): an orphan crop in DR Congo

Yam (Dioscorea spp.) is cultivated in many villages of DR Congo as a means to sustain food security and alleviate poverty. However, the extent of the existing diversity has not been studied in details thus, considered as an orphan. A survey covering 540 farmers in 54 villages was conducted in six major yam growing territories covering three provinces in DR Congo to investigate the diversity, management and utilization of yam landraces using pre-elaborate questionnaires. Subject to synonymy, a total of 67 landraces from five different species were recorded. Farmers’ challenges limiting yam production were poor tuber qualities (69%), harvest pest attack (7%), difficulty in harvesting (6%), poor soil status (6%). The overall diversity was moderate among the recorded yam germplasm maintained at the household level (1.32) and variability exist in diversity amongst the territories and provinces. Farmers’ in territories of Tshopo and Mongala provinces maintained higher level of germplasm diversity (2.79 and 2.77) compared to the farmers in territories of Bas-Uélé (1.67). Some yam landraces had limited abundance and distribution due to loss of production interest in many villages attributable to poisons contained hence, resulting in possible extinction. Farmers’ most preferred seed source for cultivation were backyard (43%) and exchange with neighboring farmers (31%) with the objective of meeting food security and generating income. In villages where yam production is expanding, farmers are relying on landraces with good tuber qualities and high yield even though they are late maturing. This study revealed the knowledge of yam landrace diversity, constraints to production and farmers’ preferences criteria as a guide for collection and conservation of yam germplasm for yam improvement intervention.

Diversity Assessment in the In Vitro Conservation Response of Philippine Yam (Dioscorea Species) Accessions

The National Plant Genetic Resources Laboratory maintains the largest in vitro germplasm collection of Dioscorea in the Philippines and has remained steadfast in its aim to safeguard accessions with potential use. Due to costly and time-consuming operations, most gene banks operate with the guidance of diversity assessments to measure the genetic integrity of one’s collection and design appropriate protocols for conservation. Diversity assessment under in vitro conditions remains unexplored even with the advantages of increased security and functionality in limited spaces. This study aimed to assess the genetic diversity of the in vitro conservation response of yam germplasm collection of the country. Four Dioscorea species totaling 217 accessions were subjected to in vitro culture conditions. Parameters such as % surviving cultures, % shoot regeneration, and degree of tissue browning were analyzed using the Shannon-Weaver diversity index and cluster analysis. Assessment of initial culture establishment and regeneration responses revealed a high degree of variability. D. alata had the highest response in % surviving cultures and % shoot regeneration. Diversity analysis using the Shannon-Weaver index revealed high diversity among the species and differences in diversity within species. This high level of diversity can be attributed to the distribution of responses observed in the accessions of each species. This high genetic diversity observed in the in vitro cultured Dioscorea indicates the necessity for the development of several in vitro culture protocols to obtain optimum responses for regeneration, conservation, and other in vitro applications.

Physico-chemical characterization of fresh tuber of water yam (Dioscorea alata) germplasm

Information of the physical and chemical characteristics in water yam tuber (Dioscorea alata) is needed to complete the database of germplasm, support the breeding activities and utilization for both food and industry purposes. This study was conducted at the Food Chemistry Laboratory of Iletri to observe the physical and chemical characteristics of the water yam fresh tuber derived from 22 Iletri’s germplasm accessions. The fleshed of water yam color were varied, namely white, yellow, mixture of white and purple, white and yellow, yellow and purple. The trial was arranged using a completely randomized design with three replications. The moisture content ranged from 56.08-80.03%, dry matter 18.82-43.02%, ash 2.56-4.97% dw, starch 61.81-75.87% dw, amylose 28.40-43.15% dw, and reducing sugar 0.27-1.49% dw. The fiber content varied widely from 4.33% to 13.99% dw. The water yam also had a wide range of texture, ranging from soft to hard with a hardness level of 6.78-57.78 N. Based on the starch and fiber contents of the fresh tuber, MLGAR 0071, MLGAR 0183, MLGAR 0003 and MLGAR 0006 accessions were potential to be used as parent materials in breeding program to obtain superior varieties of water yam with high starch and fiber contents.

Physico-chemical characteristics of elephant foot yam (Amorphophallus campanulatus) germplasm

The diversity of elephant food yam (Amorphophallus campanulatus) in Indonesia is essential to be explored concerning its potential use for food and benefit for health. Breeding for release new varieties with spesific characters needs a various of genetic materials, particularly from germplasm collection. Therefore, this study was performed to identify the physicochemical characteristics of 14 elephant food yam germplasm collected by Indonesian Legumes and Tuber Crops Research Institute (ILETRI). The physical observations showed that the colour of the flesh varied from yellow to orange with the lightness values (L*) ranging from 70.53 to 81.63. The moisture, ash, reducing sugar, and amylose contents also varied from 66.58 – 88.36 %, 2.49-4.91 % (dm), 1.42-7.89 % (dm), 23.84-31,37 % (dm), respectively. These elephant food yam genotypes particularly contained high dietary fiber with the highest value observed in MLGAR 0101 (54.29 % dm) and MLGAR 0016 (53.15 % dm). The hardness levels of the boiled tubers ranged from 11.90-38.1 N with the highest value observed in MLGAR 0131, suggesting that this genotype had the most firm texture when used for direct consumption. Based on the results of chemical properties, MLGAR 0034, MLGAR 0111, MLGAR 030, MLGAR 0150, MLGAR 0312, and MLGAR 0131 are classified into one cluster.

Molecular Viral Diagnosis and Sanitation of Yam Genetic Resources: Implications for Safe Yam Germplasm Exchange.

Yam (Dioscorea spp.) is an important crop in tropical and subtropical regions. Many viruses have been recently identified in yam, hampering genetic conservation and safe international exchanges of yam germplasm. We report on the implementation of reliable and cost-effective PCR-based detection tools targeting eight different yam-infecting viruses. Viral indexing of the in vitro yam collection maintained by the Biological Resources Center for Tropical Plants (BRC-TP) in Guadeloupe (French West Indies) unveiled a high prevalence of potyviruses, badnaviruses, Dioscorea mosaic associated virus (DMaV) and yam asymptomatic virus 1 (YaV1) and a high level of coinfections. Infected yam accessions were subjected to a combination of thermotherapy and meristem culture. Sanitation levels were monitored using PCR-based and high-throughput sequencing-based diagnosis, confirming the efficacy and reliability of PCR-based detection tools. Sanitation rates were highly variable depending on viruses. Sixteen accessions were successfully sanitized, paving the way to safe yam germplasm exchanges and the implementation of clean seed production programs worldwide.

Yam asymptomatic virus 1, a novel virus infecting yams (Dioscorea spp.) with significant prevalence in a germplasm collection.

A novel virus infecting yams (Dioscorea spp.), tentatively named "yam asymptomatic virus 1" (YaV1), was characterized and sequenced from an asymptomatic D. alata plant from Vanuatu. Sequence comparisons and phylogenetic analysis showed that YaV1 is a novel ampelovirus and has the smallest genome among "subgroup 1" members. RT-PCR-based screening of a yam germplasm collection conserved in Guadeloupe showed that YaV1 is prevalent in D. alata, D. bulbifera, D. cayennensis subsp. rotundata, D. esculenta and D. trifida accessions but causes no apparent symptoms. Additional phylogenetic analysis revealed a low variability of YaV1 in Guadeloupe in a limited part of the genome, and suggested the occurrence of plant-to-plant transmission.

Characterization and genetic diversity of Dioscorea bacilliform viruses present in a Pacific yam germplasm collection

AbstractYam is an important food staple in many Pacific Island countries, but its production is limited by several factors including virus infection. The presence of viruses also hinders the exploitation of the crop by restricting the international dissemination of yam germplasm due to quarantine concerns. In this study, a total of 224 yam accessions present in the Pacific germplasm collection at SPC‐CePaCT, Fiji, were tested for the presence of badnaviruses using a combination of rolling circle amplification (RCA) and sequencing. Of these, 35 tested positive for either Dioscorea bacilliform AL virus (DBALV) or Dioscorea bacilliform AL virus 2 (DBALV2). DBALV was only detected in samples from Vanuatu and Tonga, while DBALV2 was restricted to Papua New Guinean samples. Ten complete genome sequences of DBALV and DBALV2 were obtained and pairwise comparison of the partial reverse transcriptase/ribonuclease H (RT/RNase H)‐coding sequence revealed identities ranging from 89% to 100% and 92% to 100%, respectively. The results suggest that DBALV and DBALV2 are the prevalent badnavirus species infecting yams in the Pacific region.

Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing.

To date, several viruses of different genera have been reported to infect yam (Dioscorea spp.). The full diversity of viruses infecting yam, however, remains to be explored. High-throughput sequencing (HTS) methods are increasingly being used in the discovery of new plant viral genomes. In this study, we employed HTS on yam to determine whether any undiscovered viruses were present that would restrict the international distribution of yam germplasm. We discovered a new virus sequence present in 31 yam samples tested and have tentatively named this virus “yam virus Y” (YVY). Twenty-three of the samples in which YVY was detected showed mosaic and chlorotic leaf symptoms, but Yam mosaic virus was also detected in these samples. Complete genome sequences of two YVY viral isolates were assembled and found to contain five open reading frames (ORFs). ORF1 encodes a large replication-associated protein, ORF2, ORF3 and ORF4 constitute the putative triple gene block proteins, and ORF5 encodes a putative coat protein. Considering the species demarcation criteria of the family Betaflexiviridae, YVY should be considered as a novel virus species in the family Betaflexiviridae. Further work is needed to understand the association of this new virus with any symptoms and yield loss and its implication on virus-free seed yam production.

Development of a cost-effective single nucleotide polymorphism genotyping array for management of greater yam germplasm collections.

Using genome‐wide single nucleotide polymorphism (SNP) discovery in greater yam (Discorea alata L.), 4,593 good quality SNPs were identified in 40 accessions. One hundred ninety six of these SNPs were selected to represent the overall dataset and used to design a competitive allele specific PCR array (KASPar). This array was validated on 141 accessions from the Tropical Plants Biological Resources Centre (CRB‐PT) and CIRAD collections that encompass worldwide D. alata diversity. Overall, 129 SNPs were successfully converted as cost‐effective genotyping tools. The results showed that the ploidy levels of accessions could be accurately estimated using this array. The rate of redundant accessions within the collections was high in agreement with the low genetic diversity of D. alata and its diversification by somatic clone selection. The overall diversity resulting from these 129 polymorphic SNPs was consistent with the findings of previously published studies. This KASPar array will be useful in collection management, ploidy level inference, while complementing accurate agro‐morphological descriptions.

Ethnobotany and Nutritional Value of Two Domestic Yams (Dioscorea spp.) in Abaya Woreda, Southern Ethiopia

Background : From a food security perspective, yam is an important crop in the tropics and subtropics, where it produced both as a subsistence crop and on a commercial scale. This study aimed to assess the ethnobotanical knowledge and nutritional values of two domestic yams in Abaya Woreda, southern Ethiopia. Methods : Data were collected from sixty informants in three kebeles. From each kebele, the most productive top twenty farmers were selected by researchers based on their potential cultivation of yams with the assistance of Development Agency (DA). Ethnobotanical data were collected by semi-structured interviews and edible tubers and bulbils of these crops were collected for nutritional analysis at the Hawassa University Food Laboratory. The data were analyzed with descriptive statistics and Analysis of Variance (ANOVA) using MS-Excel and SPSS. Results : The results showed that farmers of Abaya Woreda have indigenous knowledge about forms of consumption, meal preferences, medicinal use, storage mechanisms and propagation systems of yams. Significant variation was observed in knowledge of edible plant parts and methods of tuber preservation for propagation in the study area. Similarly, the nutritional content of the crops showed variation in some of the measured parameters. For instance, Dioscorea bulbifera had higher carbohydrate content and total energy although it was the lower in moisture content. Conclusions : The present study has attempted to document ethnobotanical knowledge and nutritional values of two domestic Dioscorea species in Abaya Woreda, which should get attention by farmers, researchers, governmental and nongovernmental bodies in order to increase the food potential and indigenous knowledge in the study area. For the results presented here may help to conserve yam germplasm and create awareness about the importance of these crops to alleviate food insecurity. Key words : ethnobotany, nutritional value, yam, Abaya woreda.