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.

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