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.

African Orphan Crops Consortium Nairobi Kenya

Agricultural Research Council Biotechnology Platform Pretoria South Africa

Chan Zuckerberg BioHub 499 Illinois St San Francisco CA 94158 USA

Cornell University Ithaca NY 14850 USA

Department of Biology University of Copenhagen Copenhagen Denmark

Department of Molecular and Cell Biology University of California Berkeley CA 94720 USA

DOE Joint Genome Institute Berkeley CA USA

Innovative Genomics Institute Berkeley CA USA

Institute of Experimental Botany of the Czech Academy of Sciences Centre of the Region Haná for Biotechnological and Agricultural Research Šlechtitelů 31 CZ 77900 Olomouc Czech Republic

International Institute of Tropical Agriculture PMB 5320 Oyo Road Ibadan Nigeria

International Trade Center Accra Ghana

James Hutton Institute Dundee UK

National Root Crops Research Institute Umudike Nigeria

Okinawa Institute of Science and Technology Onna Okinawa Japan

School of Life Sciences University of Dundee Dundee UK

University of California Davis Davis CA 95616 USA

World Agroforestry Nairobi Kenya

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