Hodeba D. Mignouna

Molecular taxonomic, epidemiological and population genetic approaches to understanding yam anthracnose disease

Water yam (Dioscorea alata L.) is the most widely cultivated yam species globally. The major limitation to the profitable and sustainable production of D. alata is its susceptibility to anthracnose disease. The availability of resistant varieties could potentially form the cornerstone of an integrated management strategy for yam anthracnose; however, anthracnose resistance breeding is hampered by the dearth of knowledge on pathogen identity and diversity. Four forms of Colletotrichum are now known to be associated with foliar anthracnose of yam: the slow-growing grey (SGG), the fast-growing salmon (FGS), the fast-growing olive (FGO), and the fast-growing grey (FGG) forms. The close phylogenetic relationship of the first three forms to reference isolates of Colletotrichum gloeosporioides, and the fact that only strains of these forms have been observed to induce typical anthracnose symptoms on D. alata, recently confirmed that C. gloeosporioides is the causal agent of yam anthracnose disease. The FGG form possibly represents a distinct, endophytic, species as indicated by morphological, biological and molecular criteria. Previous research emphasized epidemiology and control but limited progress was made in understanding yam anthracnose disease based on this classical approach. Molecular approaches have started to unravel the systematics and ecology of Colletotrichum strains associated with yam anthracnose, as well the population biology of C. gloeosporioides on yam. Sexual recombination is a likely mechanism contributing to the high genetic diversity of C. gloeosporioides in yam-based cropping systems. Studies have been initiated to understand the mechanisms that generate genetic variation in C. gloeosporioides, and to gain some insight into the biochemistry of the interactions between the pathogen and yam. Our thesis in this article is that integrating traditional and molecular approaches to understanding C. gloeosporioides systematics, epidemiology and population genetics will lead to a much better understanding of yam anthracnose disease, and thus to the development of effective and sustainable control measures. Research successes and challenges are discussed, as well as their implications for future studies on pathogen evolutionary potential, anthracnose resistance breeding, and the deployment of resistance genes. Key words : Anthracnose, Colletotrichum gloeosporioides, Dioscorea spp., molecular markers, molecular systematics, population biology, resistance breeding, yam. African Journal of Biotechnology Vol. 2 (12), pp. 486-496, December 2003

Harnessing modern biotechnology for tropical tuber crop improvement: Yam ( Dioscorea spp.) molecular breeding

Yams (Dioscorea 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, Dioscorea rotundata and D. cayenensis, are the most important yams in West and Central Africa where they are indigenous, while D. alata (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 Yam Mosaic Virus (YMV) in D. rotundata and anthracnose (Colletotrichum gloeosporioides) in D. alata. 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.

Genomics of Yams, a Common Source of Food and Medicine in the Tropics

Yams (Dioscorea spp., Dioscoreaceae), grown either for their starchy tubers or medicinal properties, are important crops in the tropics and subtropics. Yams broaden the food base and provide food security and income to over 300 million people. They are vegetatively propagated and comprise both diploid and polyploid species. Despite their economic and socio-cultural importance, very little is known about the genetics and genomics of yams due to research neglect and several biological constraints. Consequently, conventional breeding efforts have been severely hampered. Research to unravel the apparent complexity of the yam genome will have far-reaching implications for genetic improvement of this important tuber crop. Nevertheless, progress has been made recently towards understanding Dioscorea phylogeny and phylogenetic relationships within the genus. Also, improved molecular technologies have been developed for genome analysis, including germplasm characterization, cytogenetics, genetic mapping and tagging, and functional genomics. Genetic linkage maps have been constructed for D. rotundata and D. alata, and quantitative trait loci associated with resistance to Yam mosaic virus in D. rotundata and anthracnose (Colletotrichum gloeosporioides) in D. alata have been identified. In addition, candidate random amplified polymorphic DNA markers associated with major genes controlling resistance to Yam mosaic virus and anthracnose have been identified. These markers could be converted to sequencecharacterized amplified regions and used formarker-assisted selection for resistance to diseases. An initial cDNA library has been constructed to develop expressed sequence tags for gene discovery and as a source of additional molecular markers. Genetic engineering offers a powerful tool, complementing conventional breeding approaches, for yam improvement. Methods for yam transformation, including in vitro plant regeneration, gene delivery, selection of transformed tissues, and recovery of transgenic plants have been developed but still need improvements. This chapter reviews advances made in yam molecular marker development for genome analysis, phylogeny, molecular cytogenetics, characterization of genetic diversity, genetic mapping and tagging, and progress in functional genomics.

Culturing meristematic tissue and node cuttings from yams (Dioscorea).

This protocol describes how to produce whole yam (Dioscorea) plantlets in vitro through yam meristem culture and from yam node cuttings.

Producing Yam (Dioscorea) Seeds through Controlled Crosses

This protocol describes how to produce yam (Dioscorea) seeds through controlled pollination of flowers on female plants. Pollination by flower thrips takes place naturally in normal yam-growing environments in the presence of flowering male and female genotypes, although it is not efficient. This protocol leads to the production of hybrid seeds of known parentage for genetic studies and use in breeding programs.

Extraction of DNA from Yam (Dioscorea) Leaves

This protocol describes how to extract DNA from the leaves of true yams (Dioscorea) for polymerase chain reaction (PCR) and other analyses.

Yam (Dioscorea) husbandry: cultivating yams in the field or greenhouse.

This protocol describes how to cultivate yams (Dioscorea) in the field or greenhouse. It refers especially to the tropical food species but it will also work for temperate species. The tropical food species of Dioscorea grow in warm, sunny climates with temperatures between 25 degrees C and 30 degrees C. Short days of 10-11 h result in tuber formation, while days longer than 12 h favor vine growth. Yams require deep, loose, textured loamy soil that is rich in organic matter. They are best planted at the beginning of the rainy season. Mulch around the planted sets protects them from excessive heat and desiccation, especially in areas with hot temperatures and dry weather. It also adds organic matter to the soil, prevents soil erosion, preserves water in the soil, and increases microbial activity in the soil. Yams do not tolerate waterlogged conditions. It is important to stake the plants to allow full exposure of their leaves to light for photosynthetic activity and to reduce disease.

Post-flask management of yam (Dioscorea) plantlets.

This protocol describes how to harden or acclimatize tissue culture-derived yam (Dioscorea) plantlets before transplanting them in the soil. Briefly, the plantlets are first put in pots with a vermiculite and peat moss mixture, and the pots are placed in a humidity chamber, where they are sprayed and watered daily. After 2 wk, the plants are transplanted to pots or plastic bags with ordinary or sterile soil and watered daily. After another 2 wk, they are transplanted into the field.