This study provides a complete, haplotype-resolved genome assembly of a male greater yam (Dioscorea alata) cultivar, shedding new light on the sexual genetics of this crop :
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Sex chromosome architecture : Identification of the sex-determining region (SDR) on chromosome 6 and discovery of a major 7.6-Mb Y-specific chromosomal inversion.
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Evolution : Characterization of young sex chromosomes (~4.32 million years old), formed after divergence from the species Dioscorea rotundata.
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Breeding tools : Validation of new molecular markers enabling early sex identification at the seedling stage.
Why this discovery is essential : A detailed understanding of the SDR alongside early-stage molecular markers addresses a major bottleneck in D. alata, where asynchronous and unpredictable flowering traditionally hampers genetic improvement. By predicting sex early in nursery development, breeders can optimize field sex ratios, efficiently plan controlled crosses, and save valuable time in developing more productive and resilient cultivars.
Dossa, K., Su, X., Zoclanclounon, Y. A. B., Chen, Y., Nawaz, M. A., Ni, P., Qiu, T., Chen, G., & Malédon, E. (2026). Haplotype-resolved genome assembly of a male Dioscorea alata cultivar reveals the structure and evolution of young sex chromosomes. The Plant Journal. https://doi.org/10.1111/tpj.71091
The figure characterizes the structure of the sex-determining region (SDR) in Dioscorea alata by integrating (a) a Hi-C interaction map visualizing contact patterns between the Y (Chr6A) and X (Chr6B) sex chromosomes, (b) genomic synteny revealing four major inversions (INV1 to INV4) on the Y chromosome, (c) the genetic variant landscape illustrating fixation index and male SNP density across all 20 chromosomes, (d) a GWAS Manhattan plot for SNPs and (e) a GWAS Manhattan plot for InDels identifying sex-associated signals, complemented by regional zoom-ins showing the distribution of significant SNPs (f) and InDels (g) on Chr6A, (h) differential sequencing coverage between males and females, (i) the mapping of male-specific 27-bp k-mers, and (j) a global map of the X and Y chromosomes detailing gene density, centromeres, telomeres, pseudoautosomal regions (PARs), and the SDR zone.