Chromosome evolution and the genetic basis of agronomically important traits in greater yam

The nutrient-rich tubers of the greater yam, *Dioscorea alata* L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of *D. alata* combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the *Dioscorea* lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

Jessen V. Bredeson, Jessica B. Lyons, Ibukun O. Oniyinde, Nneka R. Okereke, Olufisayo Kolade, Ikenna Nnabue, Christian O. Nwadili, Eva Hřibová, Matthew Parker, Jeremiah Nwogha, Shengqiang Shu, Joseph Carlson, Robert Kariba, Samuel Muthemba, Katarzyna Knop, Geoffrey J. Barton, Anna V. Sherwood, Antonio Lopez-Montes, Robert Asiedu, Ramni Jamnadass, Alice Muchugi, David Goodstein, Chiedozie N. Egesi, Jonathan Featherston, Asrat Asfaw, Gordon G. Simpson, Jaroslav Doležel, Prasad S. Hendre, Allen Van Deynze, Pullikanti Lava Kumar, Jude E. Obidiegwu, Ranjana Bhattacharjee, Daniel S. Rokhsar