SRA

Yams (genus Dioscorea) are an important source of food and income for millions of smallholder farmers in the tropical and sub-tropical regions of Africa, Asia, the Pacific, and Latin America. Rich in carbohydrates, and containing protein and vitamin C, the year-round availability of yams makes them preferable to seasonal crops. The importance of yams in West Africa is exemplified by their vital role in traditional culture, rituals and religion; yam production is declining, however, due to threats from pests and diseases. Thus, in the context of surging global population growth, improved yam breeding techniques are urgently needed. Water yam, also called greater yam (Dioscorea alata) is the most widely distributed cultivated yam species in the world, and its advantages include high nutritional content, long storability of tubers, and ability to yield in poor quality soil. This project will leverage cutting-edge DNA sequencing and computational analysis to provide a high quality water yam genome assembly and genetic map to the yam community, which will allow breeders to use modern genetic methods to breed the crop more efficiently. The project will also characterize the natural genetic variability present in global collections, yielding insight into how they may be used to improve the crop, and contributing to an understanding of the relationship between water yam DNA sequence and traits important to smallholder farmers. Bringing water yam into the modern genomics era will facilitate the accelerated release of improved varieties to the farmers that need them.The water yam Dioscorea alata is superior to most cultivated yam species due to its potential to yield under low to average soil fertility, ease of propagation, early vigor for weed suppression, and low post-harvest losses. Threats, however, include anthracnose disease, which can cause losses of up to 90% of production, and breeding for desired traits in water yam is arduous due to its autopolyploid and heterozygous nature, long growth cycle, and erratic flowering. This project will accelerate the improvement of water yam by (1) constructing a high quality chromosome-scale genome assembly for D. alata, interpreted through annotation and comparative analysis, (2) producing a framework genetic map for D. alata via analysis of mapcrosses segregating for traits important for farmers, and (3) characterizing the global collection of D. alata cultivars. Advanced technologies such as PacBio de novo sequencing, whole-genome resequencing, genotyping-by-sequencing, flow cytometry for ploidy analysis, and publicly available and custom bioinformatics tools, will be leveraged. The chromosome-scale genome assembly and genetic map will lay the groundwork for more efficient breeding approaches such as genomic selection in water yam. Quantitative trait locus analysis of mapping populations segregating for anthracnose resistance and tuber quality is expected to yield specific sequence variants linked to, and thus mechanistic insight into, those traits. Study of water yam diversity across global collections will elucidate its breeding history, reveal bottlenecks, and suggest strategies for broadening the gene pool. All sequencing resources will be publicly available through the NCBI and the phytozome plant genomics resource.