Identifying Sex Determination Loci in the Highly Heterozygous White Guinea Yam (Dioscorea rotundata Poir.)

White Guinea yam (Dioscorea rotundata Poir.) is a staple crop of great agricultural, cultural and economic significance to Africa, the Americas, the Caribbean, South Pacific and Asia. While demand for yam in sub-Saharan Africa is high, there is a continuing decline in production due to pests, reduced soil fertility and disease. Despite the importance of this crop, there are currently limited genomics resources available for yam that could facilitate breeding initiatives, nor comprehensive phylogenetic or evolutionary studies. The breeding of the white Guinea yam is further impeded by its heterozygosity, long growth cycle, erratic flowering times, and dioecious (both female and male individuals) nature. The latter of which is a rare trait found in only 5 - 6% of angiosperms. To accelerate Guinea yam marker-assisted breeding, as part of an international collaboration, we have sequenced the 594 Mb genome, produced a chromosome anchored assembly and predicted a total of 26,198 genes. Phylogenetic analysis of 2,381 conserved genes has revealed Dioscorea not to form a monophyletic clade with the Poales, Arecales or Zingiberales, indicating an early divergence from the latter taxa in monocotyledons. Additionally, we have observed an expansion of B-lectin genes in Guinea yam genome, potentially involved in tuber defense. The genome and identification of sex loci in Guinea yam will serve as an invaluable resource for genome-assisted breeding in yam and presents a unique opportunity to study the evolution of sex in monocots. Most importantly whole genome re-sequencing of bulked segregants (QTL-seq) in F1 progeny segregating for male and female individuals has led to the identification of a genomic region and candidate genes associated with female heterogametic (male=ZZ, female=ZW) sex determination.