Yam (Dioscorea species)
|Kingdom||Plantae – Plants|
|Subkingdom||Tracheobionta – Vascular plants|
|Division||Magnoliophyta -Flowering plants|
|Species||Around 600 spp.|
For further information on yam breeding/production, visit: - http://www.iita.org/yam
Current Genomics Research Activities:
Identification of duplicates
IITA, in collaboration with 12 national programs (Costa Rica, Cote d’Ivoire, Ghana, New Caledonia, Togo, Fiji, Papua New Guinea, Philippines, Solomon Island, Benin, Vanuatu and Vietnam) and financial support from the GCDT, is engaged in a molecular fingerprinting project aiming at identifying unique/duplicate accessions within and across national and international collections.
Bar coding for species identification
The development of molecular based identification of agriculturally most important Dioscorea species including some wild relatives is underway (Gezahegn Tessema).
The whole genome sequencing of D. rotundata is underway in a collaborative project between JIRCAS and IITA with the objectives of developing new generation markers such as SNPs, for construction of linkage maps, identification of trait-specific QTL (s), and association mapping for marker-assisted selection (MAS) in yam improvement program.
IITA is involved in collaborative project with Australia to develop DArT markers using D. alata accessions.
Evaluation of accession uniformity in yam field genebank (Gezahegn Tessema)
Over the years it was recognized that within the same accession, individuals showed different morphological characters reflecting obvious plant mix up. As the field bank is the source for material introduction to in vitro conservation (including cryopreservation), any mix up at the field bank will reflect in all backup collections. The aim of this study were therefore to assess mismatched individual plants within accessions, to develop distinct morphological characters (descriptors) as a reference for each accession and to identify and maintain uniform individuals within accessions of the field genebank collections.
Three healthy and vigorous tubers were selected for each accession and maximum of ten minisets per accession were used for planting. Morphological characterization was done using 53 yam descriptors. GenStat for Windows software was used to calculate similarity between individuals within the same accession. Descriptive analysis of morphological traits was conducted using SAS software to determine the most descriminant descriptors for identification of individual variation within accession.
Overall 20.60% of the total collection was found misidentified. Registration of two different accessions belonging to different species with the same accession number, occurrence of accession name without passport data reference and loss of accession number either on passport or in field data were some other misidentification problems and causes where germplasm management actions was suggested and implemented. Seven descriptors were found with the most descriminant power among 53 different yam descriptors used in this study. In conclusion, the appropriate management of materials in the field bank was recognized as a fundamental issue for maintenance quality of accessions and reliability of further regeneration techniques (in vitro and cryopreservation).
Understanding flowering phenology and aerial bulbils formation in yam under genebank collection (work in progress, 2010-2012)
Little is known on the flowering pattern and aerial bulbils formation of the accessions of the international collection under IITA. Hence, this study is being conducted with the objective to determine the intensity and seasonal variation in flowering and aerial bulbils formation of yam field genebank accessions and to study the effect of weather on flowering and aerial bulbils formation.
The entire international collections of yam are being evaluated for flowering and aerial bulbils formation. Data being collected based on yam descriptors for flowering and aerial bulbils formation following (IPGRI/IITA, 1997) descriptor list. The weather condition over years at IITA, Ibadan will be obtained from metrology station. Data will be analyzed and interpreted in terms of variation and flowering consistency over years, flowering intensity among species, proportion of male and female, inflorescence type, proportion and characteristics of aerial bulbils in D.alata and correlation with weather condition.
Identification of potential DNA bar-coding regions to distinguish Dioscorea species
Developing molecular tools supported by taxonomic identification is very important for unambiguous species naming or classification. A DNA barcode is an aid to taxonomic identification which uses a standard short genomic region that is universally present in target lineages and has sufficient sequence variation to discriminate among species (Kress and Erickson, 2007). The objective of this study was therefore to identify a candidate DNA barcode region for Dioscorea species that enables to discriminate species unambiguously with high discriminatory power.
Several Dioscorea species was collected from all over the world. Recommended loci suggested for flowering plants (single locus rbcL and matK, 2-locus combination of rbcL + matK, non coding plastid trnH-psbA intergenic spacer region, multicopy nuclear ITS and trnH-psbA paired with coding locus, rbcL) were selected as candidate barcode, amplified by PCR. As a preliminary result only rbcL, matK and trnH-psbA regions were found with better PCR amplification whereas the nuclear region, ITS, was with poor amplification except for few individuals. Hence, only the chloroplast regions were sequenced.
Yam Characterization: Molecular fingerprinting (Ranjana Bhattacharjee)
Similar to cassava fingerprinting, efforts were carried out to fingerprint the yam germplasm collection at IITA and other NARS partners. Towards that effort, a fingerprinting project was started in 2010 through funding from Global Crop Diversity Trust (GCDT) to genotype 1500 accessions from IITA collection and 1500 accessions from NARS germplasm collection from 13 partnering countries representing West Africa, Asia and The Pacific. The objective of the project was to fingerprint 3000 accessions of three priority species of Dioscorea such as D. alata, D. rotundata and D. cayenensis. The germpalsm collection from IITA consisted of 815 accessions of D. alata, 626 accessions of D. rotundata and 59 accessions of D. cayenensis; while only 777 accessions were received from nine NARS countries (Togo, Papua New Guinea, New Caledonia, Ghana, Fiji, Thailand, Philippines, Benin and CATIE) consisting of 461 accessions of D. alata, 252 accessions of D. rotundata and 11 accessions of D. cayenensis. Some of the countries such as Cote d’Ivoire, Solomon Island, Vanuatu and Vietnam did not contribute their germplasm. Further, most of the countries sent lesser number of samples than committed in the original proposal, and there were 11 accessions that belonged to other Dioscorea spp. and 32 accessions for which the species name was not specified. Some of the NARS partners indicated the loss of germplasm as the reason for sending lesser number of samples than committed, and few others indicated that the time available within the project was not enough for them to send the samples. All the 1500 accessions from IITA collection was selected based on available passport data. The passport data of NARS germplasm was not received. The fingerprinting of yam germplasm was carried out following the same strategy as in cassava wherein the accessions were first genotyped using a set of SSR markers following PAGE system and data was recorded in binary format (1 for the presence of an allele per SSR marker and 0 for the absence of the allele for the same marker). The potential duplicates were identified by comparing the genetic distances among the accessions by following the criteria of GD = 0 - 0.15, for at least 3 SSR markers. The potential duplicates were subjected to further genotyping using additional SSR markers following capillary electrophoresis with ABI3130. The data scored based on actual allele sizes in base-pairs were analyzed using modified Roger’s distances to identify absolute duplicates with GD = 0 among accessions.
Following the above strategy, 25 genomic SSRs and 26 EST-SSRs were used to fingerprint yam germplasm collection from IITA and NARS partners. A cost-effective high-throughput DNA extraction protocol was standardized to extract DNA from fresh and dry leaves, tubers and in vitro plantlets from different Dioscorea spp. (Sharma et al., under review). Initially, 25 genomic SSRs were chosen to genotype the accessions following PAGE system, of which 18 showed good amplification and polymorphism across a set of 15 randomly selected accessions from each of D. alata, D. rotundata and D. cayenensis germplasm during optimization of these markers. It is important to note that out of 18 optimized SSR markers, nine were developed from D. alata, four from D. abyssinica and five from D. prahensilis indicating that not all the available genomic SSRs have been developed from a single source or species and the available number of markers from different species is also not enough. No earlier studies reported if these SSR markers are compatible across different Dioscorea spp. In the present study, it was observed during genotyping of entire collection of different Dioscorea spp. that these SSR markers were not compatible across different species and showed poor amplification. Considering the availability of SSR markers mainly from D. alata, a decision was made to continue data scoring and analysis only on D. alata accessions (815 from IITA collection and 461 from NARS collection). The presence (1) – absence (0) data on 1187 D. alata accessions across 18 genomic SSRs was subjected for data analysis and 647 potential duplicates (407 from IITA and 240 from NARS countries) were identified based on GD = 0 – 0.15. The results indicate that 49.9% of D. alata accessions maintained at IITA are potential duplicates. The germplasm collection maintained in different NARS countries represented 52.1% of potential duplicates. The 647 potential duplicates were subjected to further genotyping using additional 26 EST-SSR markers developed recently on a collaborative project between IITA and Virginia State University. This is a randomly selected set of EST-SSRs from a total of 1700 markers, which has not yet been optimized and validated for their allele sizes or used in any other study. Out of 26 EST-SSRs, 23 showed good amplification across randomly selected 15 accessions of D. alata. In the absence of allelic information and amplification of the EST-SSRs at multiple loci (because of polyploidy nature of the accessions, which is yet to be determined) visualized on the ABI runs, it was very difficult to score the alleles. Further, capillary electrophoresis using ABI3130 showed lot of missing values for each EST-SSR marker under study. The data analysis was carried out using only 8 EST-SSR markers. With the whole genome sequencing being completed and more number of species specific molecular markers becoming available, it will be interesting to validate the results of the present study. Even passport and morphological data can be used to validate the duplicates identified in the study.