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 our new 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.