Yam Germplasm Research Articles

Search for scutellonema bradys resistance in yams (dioscorea spp.)

A study to examine variability in susceptibility of yams to Scutellonema bradys and to identify possible sources of resistance in Ghanaian yam germplasm (Dioscorea spp.) for use in yam improvement programmes, particularly, in West Africa was undertaken. Pot and field screening methodologies were used. In general, S. bradys and dry rot of tuber symptoms as well as tuber cracking increased during the storage period. The study showed a positive correlation between visual nematode damage and population densities in yam tubers. There was also a linear relationship between dry rot disease and tuber cracking at harvest and during storage. This confirms that S. bradys causes dry rot of tubers resulting in external cracking of yam tubers. Positive linear relationship was also observed between yam tuber weight loss and dry rot disease indicating that dry rot disease may have contributed to the tuber weight loss. Therefore, tuber dry rot symptoms caused by S. bradys of yams could be used to discard susceptible yams at harvest and after a period of storage. However, there was no linear relationship between nematode population densities in yam tubers and roots, therefore, a root protocol cannot be used for assessing resistance in yams as it could lead to misclassification. The yam germplasm screened, reaffirmed resistance to S. bradys in Dioscorea dumetorum var. Nkanfo and D. cayenensis var. Afun.

Yams (Dioscorea spp.) from the South Pacific Islands contain many novel badnaviruses: implications for international movement of yam germplasm

Yam (Dioscorea spp.) samples (n = 690) from seven South Pacific Islands were screened for badnavirus infection by ELISA using two antisera to African badnaviruses. Positive readings were obtained for 26.4-34.6% of samples representing both known (D. bulbifera, D. nummularia and D. pentaphylla) and unreported host species (D. alata, D. esculenta, D. rotundata and D. trifida) in this region. Total DNAs were extracted from 25 ELISA-positive plants and 4 ELISA-negative controls and subjected to PCR amplification with badnavirus-specific primers targeting the reverse transcriptase (RT)-RNaseH genes. All 29 samples yielded the expected size PCR-product for badnaviruses, which were cloned and sequenced. Phylogenetic analyses of the resulting 45 partial (500-527 bp) RT-RNaseH sequences revealed 11 new sequence groups with <79% nucleotide identity to each other or any EMBL sequence. Three sequences (two groups) were highly divergent to the other nine new South Pacific yam badnavirus groups (47.9-57.2% identity) and probably represent either new Caulimoviridae genera or endogenous pararetrovirus sequences. Some sequence groups appeared specific to particular Dioscorea host species. Four 99.9% identical RT-RNaseH sequences possessing nine amino acid deletions from D. esculenta from three islands represent a putative integrated sequence group. The distribution of sequence groups across the islands indicates that badnaviruses have spread extensively between islands and continents through infected germplasm.

Genetic Diversity in Yam Germplasm from Ethiopia and Their Relatedness to the Main Cultivated Dioscorea Species Assessed by AFLP Markers

Yam (Dioscorea spp.) is widely cultivated in southern Ethiopia, where farmers maintain many named landraces. Nevertheless, little is known about their diversity and species identity. In this study, amplified fragment length polymorphism (AFLP) markers were used to investigate the genetic diversity in 48 yam accessions from Ethiopia, and to assess their relatedness to yam species commonly cultivated in West Africa such as D. alata L., D. bulbifera L., D. cayenensis Lam., and D. rotundata Poir. Ten AFLP primer combinations generated 900 fragments, of which 97% were polymorphic. Cluster and principal coordinate analyses revealed that the Ethiopian accessions are distinct from the Dioscorea species widely cultivated in West Africa. A separate analysis of the Ethiopian accessions gave six clusters that represented the various maturity groups and the nonflowering accession in the collection. Analysis of molecular variance (AMOVA) showed that 81% of the variation detected was found within collecting areas, while the variation among collecting areas contributed only 19%. The groups detected by AFLP markers were highly consistent with the local yam classification system and also reflected the main structure of morphological diversity.

Evaluation of Water Yam (Dioscorea alata L.) Germplasm for Reaction to Yam Anthracnose and Virus Diseases and their Effect on Yield

AbstractUse of genetic resistance is the most practical and economic way to manage major diseases of yams. In a search for sources of resistance, 40 water yam (Dioscorea alata L.) accessions from Benin, Ghana, Nigeria and Puerto Rico were screened under natural disease infection conditions in Ibadan, Nigeria. The accessions were evaluated at 1, 3 and 6 months after planting (MAP) for severity of yam anthracnose and viral diseases. The effect of the pathogens on yield was also evaluated at harvest 9 MAP. There were significant differences (P &lt; 0.001) between accessions for severities of anthracnose and viral diseases. Eight (20%) of them had lower anthracnose area under disease progress curves (AUDPC) values than the resistant check while 10 (25%) had AUDPC values below the trial mean. There were significant variations (P &lt; 0.001) in yield components among the accessions. There was significant negative correlation of anthracnose severity with fresh tuber yield (r = −0.51) and with number of tubers per plot (r = −0.40). Similarly, significant negative correlations were observed of virus disease severity with fresh tuber yield (r = −0.78) and number of tubers per plot (r = −0.65). Linear regression models also showed that the fresh yield had significant negative relationships with anthracnose (R2 = 0.26) and viral (R2 = 0.62) diseases. The accessions identified as resistant constitute a valuable resource for breeding of resistant germplasm.

PCR Marker-based Analysis of Wild and Cultivated Yams (Dioscorea spp.) in Nigeria: Genetic Relationships and Implications for ex situ Conservation

Reliable characterization of the variation among wild and cultivated yams in Nigeria is essential for improved management and efficient utilization of yam genetic resources. RAPD and double stringency PCR (DS-PCR) analyses were used to investigate genetic relationships and the extent of redundancy among 30 accessions of two cultivated, and 35 accessions of four wild yam species collected from Nigeria. Twenty-five selected random decamer and two microsatellite primers were used individually and in combination to generate DNA profiles for each accession of the six Dioscorea species. The number of amplified fragments varied from 7 to 18 fragments per primer/primer combination. Different levels of intraspecific genetic diversity were found, with Dioscorea rotundata Poir. being the most variable. Based on identical profiles for the RAPD and DS-PCR primers, 12 duplication groups consisting of a total number of 37 accessions were observed in the present study. An UPGMA analysis grouped the majority of plants according to the species. Cultivated yams belonging to the D. cayenensis–rotundata species complex, which were classified into seven morphotypes/varietal groups, could be clearly separated into two major groups corresponding to D. rotundata Poir. and D. cayenensis Lam. D. cayenensis cultivars exhibited a low level of intraspecific variation and were genetically close to the wild species Dioscorea burkilliana J. Miege. D. rotundata cultivars classified into six varietal groups showed a high degree of DNA polymorphism and were separated into two major groups that appeared most closely related to Dioscorea praehensilis Benth. and Dioscorea liebrechtsiana de Wild. We propose, based on these results, that cultivars classified into D. cayenensis should be considered as a taxon separate from D. rotundata. The implications of intraspecific variability for the ex situ conservation of wild and cultivated yam germplasm in Nigeria are discussed.

English

&nbsp; Yams (Dioscorea&nbsp;spp.) constitute a staple food crop for over 100 million people in the humid and subhumid tropics. They are polyploid and vegetatively propagated. The Guinea yams,&nbsp;Dioscorea rotundata&nbsp;and&nbsp;D. cayenensis,&nbsp;are the most important yams in West and Central Africa where they are indigenous, while&nbsp;D. alata&nbsp;(referred to as water yam) is the most widely distributed species globally. The genetics of yams is least understood among the major staple food crops due to several biological constraints and research neglect. Research to unravel the apparent complexity of the yam genome will have far-reaching implications for genetic improvement of this important tuber crop. Some progress has been made in recent years in germplasm characterization and the development of molecular markers for genome analysis. A genetic linkage map based on amplified fragment length polymorphism (AFLP) markers has been constructed for Guinea and water yams. These linkage maps were used to scan the genome for quantitative trait loci (QTL) associated with genes conferring resistance to&nbsp;Yam Mosaic Virus&nbsp;(YMV) in&nbsp;D. rotundata&nbsp;and anthracnose (Colletotrichum gloeosporioides) inD. alata.&nbsp;In addition, candidate random amplified polymorphic DNA (RAPD) markers associated with major genes controlling resistance to YMV and anthracnose have been identified that could be used for selection and pyramiding of YMV and anthracnose resistance genes in yam improvement. Also, molecular markers such as RAPDs, AFLPs, and microsatellites or simple sequence repeats (SSRs) have been developed for yam genome analysis. An initial c-DNA library has been constructed in order to develop expressed sequence tags (ESTs) for gene discovery and as a source of additional molecular markers. This paper will review the advances made, discuss the implications for yam genetic improvement and germplasm conservation, and outline the direction for future research. &nbsp; Key words:&nbsp;Genetic mapping, genome analysis, molecular breeding, PCR-based markers, QTLs, resistance genes, yam.&nbsp

A comparative assessment of molecular marker assays (AFLP, RAPD and SSR) for white yam (Dioscorea rotundata) germplasm characterization

SummarySeveral DNA‐based marker systems are available for genetic fingerprinting of plants but information on their relative usefulness for yam germplasm characterisation is lacking. The efficiency of RAPD, AFLP and SSR markers for the assessment of genetic relationships, and for cultivar identification and discrimination among 45 West and Central African white yam cultivars belonging to 22 morphotypes/cultivar groups was investigated. Dendrograms were produced based on band pattern scores using the UPGMA method. Results showed that each of the three techniques could unequivocably identify each cultivar, but that techniques differed in the mean number of profiles generated per primer (or primer pair) per cultivar, referred to as genotype index (GI). The order of merit based on this criterion in this study was AFLPs (GI = 2.56), SSRs (GI = 0.39) and RAPDs (GI = 0.35). Yam genotypes classified in the same cultivar group based on morphology were often genetically different, emphasising the need for molecular fingerprinting in yam germplasm characterisation. AFLPs showed the highest efficiency in detecting polymorphism and revealed genetic relationships that most closely reflected morphological classification.

Medium-term and long-term in vitro conservation and safe international exchange of yam (Dioscorea spp.) germplasm

Yam edible tubers feed million of peoples in the intertropical area, where they represent 12% of human feeding. However, as a vegetatively propagated crop, yam is seriously affected by an accumulation of pathogens. Establishing in vitro germplasm collection is a process that cleans the plants from all diseases but viruses. It gives a good control on the preservation of the yam genetic resources and facilitates international exchanges of healthy plant material. Two kinds of in vitro germplasm preservation were considered : slow growth condition culture for mid-term preservation, and cryopreservation using the encapsulation/dehydration technique for long-term preservation. Virus eradication was approached by meristem culture and chemo and thermotherapy. Production of virus-free plants was controlled by ELISA. We succeeded in the introduction and maintenance of 20 yam species, under slow growth conditions. Cryopreservation was applied successfully on two edible yam species, Dioscorea . alata L and D. bulbifera L. Virus-free plants were obtained by meristem culture in D. cayenensis-D. rotundata complex and D. praehensilis . Indexation allowed the detection of different virus (poty-, potex-, badna- and cucumovirus), where the most important potyvirus was YMV. Mid-term conservation of yam germplasm is used routinely, and from these conditions a direct acclimatization is possible. On the cryopreservation aspect, experiments are under way to apply the optimized protocol to genotypes which are more representative of the diversity, to insure a routinely use. More work can be conducted now on virus eradication, based on knowledge accumulated on potyvirus diversity, on several tests available for yam indexing (ELISA, rt/PCR, monoclonal antibodies) and on new sanitation techniques.

Medium-term and long-term in vitro conservation and safe international exchange of yam (Dioscorea spp.) germplasm

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Genetic variation and cultivar identification of Jamaican yam germplasm by random amplified polymorphic DNA analysis

We have used random amplified polymorphic DNA (RAPD) analysis to characterize eleven cultivars of the five economically most important yam species grown in Jamaica (Dioscorea alata, D. cayenensis, D. rotundata, D. trifida and D. esculenta). Amplification of genomic DNA samples with nine different arbitrary 10mer primers revealed a total of 338 different band positions, ranging in size from 0.3 to 2.5 kb. RAPD patterns proved to be highly reproducible and somatically stable. While no variation was observed among plants belonging to the same cultivar, a large number of intervarietal and interspecific polymorphisms enabled us to reliably discriminate between all Jamaican cultivars investigated.