Novel approaches for the improvement of yam germplasm conservation and breeding

Gezahegn Girma, g.tessema@cgiar.org

IITA, Ibadan, Nigeria

Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Ireland

Efforts are ongoing at IITA, in collaboration with the National University of Ireland Galway, to understand the genetic diversity, evolutionary relationship of yam species, flowering and sex-related genes, polyploidy and its effect on phenotypic performance and somaclonal variation in in vitro regenerated plants. This work is expected to contribute to the development of new tools for assessing yam diversity, and understanding genetic and phenotype linkages for improving yam breeding and germplasm conservation. The status of thrust areas being pursued to address these gaps is summarized here.

Identification of chloroplast or nuclear regions that can help discriminate species

Developing molecular tools supported by taxonomic identification is very important for unambiguous species naming or classification. A DNA barcode aids 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. The single locus rbcL, matK, combination of rbcL+ matK, the noncoding intergenic spacer, trnH-psbA of chloroplast regions, and ITS of nuclear region were evaluated using a criterion for candidate DNA barcode for Dioscorea species identification. All the sequences were assessed for universality (ease of PCR amplification and sequencing), sequence quality, and species discriminatory power.

Genetic polymorphism of cultivated guinea yams and their relationship with wild relatives

Next generation-based genotyping procedures such as genotyping by sequencing (GBS) is now considered as an excellent tool in plant genetics and breeding (Poland and Rife 2012) due to its genome-wide molecular marker discovery, genotyping for multiplexed samples, flexibility, and low cost. A study was conducted to understand the genetic diversity within and between two cultivated guinea yams and five of its wild relatives (D. praehensilis, D. mangenotiana, D. abyssinica, D. togoensis, and D. burkilliana) using GBS, morphology, and ploidy analysis.

In general, the genetic contribution of wild relatives, origin of cultivated species, ongoing domestication practices, potential polyplodization process and utility of GBS in generating genotypic information were demonstrated. Similarly, GBS could further be used for understanding of genetic relationship studies of other species within the genus Dioscorea that holds a large number of species in addition to the guinea yams. Due to the cost effectiveness of GBS, there is major potential for the yam genebank collection in IITA (and other yam germplasm collections) to be genotyped using the GBS procedure. GBS can help to indicate the level of genetic diversity and guide the need for more germplasm collection, duplication, and mismatch identification.

Understanding the molecular genetics of flowering

D. rotundata are mostly dioecious, with separate male and female plants, although a few lines are identified as monoecious. It is also common to find nonflowering, which is perhaps dominant. The dioecy of the crop makes the synchronization of flowering time very difficult. For the efficient improvement of yam crops through conventional breeding, understanding better the genetic mechanisms of flowering in Dioscorea is essential. The tiny and large numbers of Dioscorea chromosomes is also a challenge to make critical observations. Therefore identification of the sex-determining chromosomes is difficult at cytological level. In addition, the genes that control the flowering in yam are not yet known. A study is being conducted to identify gene expression patterns in relation to different flowering habits (male, female, and monoecious) of D. rotundata accessions using the SuperSAGE technique. The study outcome is expected to help understand the flowering biology of the crop in general and once confirmed, identified sex-determining candidate genes can be incorporated in varieties with inconsistent nonflowering to produce regularly flowering cultivars, and hence, improve yam production.

Morphological, ploidy and molecular diversity

The section Enantiophyllum of the genus Dioscorea is generally known to produce only 1-3 underground tubers. Hence, there is a need for exploitation of other options of planting materials such as aerial tubers as an alternative planting material to underground tubers. The study was conducted to investigate the molecular, morphological, and ploidy variation across Dioscorea alata accessions producing aerial tubers in comparison with accessions without aerial tubers. The aerial tuber production of accessions was found correlated with ploidy level, distinct morphological characteristics, and SSR analysis discriminated according to its pattern of aerial tuber production.

Evaluating somaclonal variation under in vitro regeneration

In spite of the several advantages from the tissue culture system in plant ex situ conservation, somaclonal variation is regarded as one of the major problems of many tissue-cultured plants (Bordallo et al. 2004). On the other hand, somaclonal variation is known for its usefulness in crop improvement by creating novel sources of variability that could result in improved yield, resistance to diseases, and quality improvement. Detection and elimination of undesirable variants and spotting variants with useful agronomic traits is therefore essential. The study on meristem derived in vitro clones of D. rotundata accessions with their original genotypes is ongoing to evaluate and verify somaclonal variation using AFLP markers.

References

Bordallo PN, Silva DH, Maria J, Cruz CD, Fontes EP. 2004. Somaclonal variation on in vitro callus culture potato cultivars. Horticultura Brasileira 22:300-304.

Poland JA, Rife TW. 2012. Genotyping-by-Sequencing for Plant Breeding and Genetics. Plant Gen 5:92-102.

Participatory strategies of conserving yam biodiversity in Bénin

A. Dansi (adansi2001@gmail.com), C. Lusty (charlotte.lusty@croptrust.org), R. Asiedu (r.asiedu@cgiar.org), R. Hall, and R. Vodouhè (r.vodouhe@cgiar.org)

Yam (Dioscorea spp.) is an important tuber crop in Bénin. Its production is intensive in Collines (Center), Donga and Borgou (North), but marginal in Atakora (Northwest), Plateau (Southeast), and in Alibori (far north). Four species are cultivated (D. alata, D. cayenensis-rotundata complex, D. dumetorum, and D. bulbifera). Among these, the native African D. cayenensis-rotundata complex remains the most important, preferred, and widely cultivated.

Yam tuber seeds of different accessions ready for transport to IITA genebank for ex situ conservation. Photo from Alexandre Dansi, IRDCAM.
Yam tuber seeds of different accessions ready for transport to IITA genebank for ex situ conservation. Photo from Alexandre Dansi, IRDCAM.

Yam production in Bénin is seriously hampered by numerous constraints including pest and disease pressure, poor soil, and changing climate. Strategic use of existing genetic diversity is thus an appropriate option for addressing these constraints in an affordable and sustainable way. For this diversity to be well studied, conserved, and used, the International Foundation for Science (IFS), Gatsby Charitable Foundation (UK), IITA, Bioversity International, and more recently the Global Crop Diversity Trust (GCDT) sponsored several research projects in Bénin between 1997 and 2009. Within the framework of these projects, different yam germplasm collection surveys have been conducted that led to a unique collection of 1,017 accessions conserved in the field by Crop, Aromatic and Medicinal Plant Biodiversity Research and Development Institute (IRDCAM) in northern Bénin.

The landraces collected were fully documented (origin, agronomic traits, and technological characteristics) and a database was constructed. With the help of farmers, the collected landraces have been fully characterized based on plant morphology and classified into 210 morphotypes. The equivalence of the diverse vernacular names that cause confusion among users has been clearly established. The geographical distribution of the morphotypes, together with genetic diversity analysis, led to the identification of four different zones of diversity. These are Zone 1: Atakora (far Northwest); Zone 2: Bariba cultural area (Northeast); Zone 3: Donga (Northwest); and Zone 4: South-Center.

Yam germplasm collection points. Courtesy of GIS Lab, IITA.
Yam germplasm collection points. Courtesy of GIS Lab, IITA.

Analysis at the community level within each of these four zones revealed the high yam diversity in Bénin in Zone 2 (20–82 varieties per village; 40 on average) and in Zone 3 (13–48 varieties per village; 24 on average). Zone 1 (8–27 varieties per village; 17 on average) and Zone 4 (6–51 varieties per village; 20 on average) had less diversity. Early maturing (double-harvested) varieties dominate Zones 1 and 4, while Zone 3 is dominated by late-maturing (single-harvested) varieties. Both late- and early maturing landraces appeared in almost equal proportions across villages in Zone 2.

Within each of the four diversity zones and at community level, several varieties are disappearing or being abandoned. High rates of genetic erosion (32–48% on average) were recorded almost everywhere. This highlights the necessity and urgency of developing strategies to conserve the existing diversity both in situ and ex situ for use by present and future generations. With the financial support of GCDT, Bénin yam germplasm is already fully regenerated and safely duplicated in IITA’s Genetic Resources Center at Ibadan (Nigeria) where it will be conserved both in vitro and in a field bank.

The causes of the ongoing genetic erosion are diverse (technological, biotic, abiotic, and cultural) and vary in relative importance according to production zones. In the far Northwest (Zone 1), for example, environmental factors, particularly poor adaptation to climate change and susceptibility to poor soils, are the most important. In the Northeast (Zone 2) susceptibility to pests and diseases and cultural beliefs are the principal reasons.

To compensate for the loss in diversity and cope with the environmental (biotic and abiotic) constraints, farmers use different strategies to exploit the existing diversity. In the dry zone of Atakora where climate change is more perceptible, farmers adopt new varieties to adapt production to actual local conditions that are characterized by increasing frequency of drought. They also alter the timing of planting and other agronomic practices. In central Bénin, farmers increasingly neglect D. cayenensis rotundata varieties in favor of those of D. alata since these are better adapted to current agroecological conditions (poor soil, pest and disease pressure, low rainfall, etc.).

To assist farmers with this option for using the genetic diversity, a program for intensive variety exchanges between villages and producers in different diversity zones was launched in 2009 within the framework of the GCDT project. Of 20 to 30 participating villages in each zone, 15 villages have already received new varieties (40 to 50 per village). This year, 15 other villages will also benefit from this program.

Alexandre Dansi (right) and some farmers from Tchakalakou (North Bénin) in a discussion during the participatory yam characterization and classification exercise. Photo from Alexandre Dansi, IRDCAM.
Alexandre Dansi (right) and some farmers from Tchakalakou (North Bénin) in a discussion during the participatory yam characterization and classification exercise. Photo from Alexandre Dansi, IRDCAM.

The exchanges have been conducted, taking into account the preference criteria determined for each zone. This exchange of varieties is a strategic way of conserving diversity on-farm through utilization. It has a multidimensional importance that includes strengthening yam production, food security, poverty alleviation; improvement of household income generation; strengthening diversity, conservation, and use; and improvement of sociocultural conditions of rural women. The results will rapidly become more evident in Zone 1.

In the northern part of this zone negatively affected by climate change, only one to two varieties out of eight to ten are tolerant of drought. The weather is suitable for the production of dry yam chips, which are in high demand and more expensive than fresh yam, but the late-maturing varieties used for this purpose were almost absent. In the south of the zone (Toucountouna and Natitingou region) dominated by lowlands, flooding is a challenge and only a few varieties were reported to be tolerant of high soil moisture.

We believe that by using, through exchanges, a large number of the Bénin yam varieties available, farmers in these regions will have a chance to find at least 50 that will be suitable for their local conditions. A strong network of yam producers in Bénin is actually being organized by IRDCAM to sustain the effort. The farmers highly appreciate the effort.

Cultivated yam are all domesticated from wild relatives co-evolving with the cultivated forms via gene flows. Because these species are sources of useful genes, participatory strategies have also been developed to preserve their diversity in situ while encouraging the domestication process developed by farmers.