Chinese yam (Dioscorea polystachya) is extensively cultivated for nutritional and medicinal applications. However, the lack of a high-quality reference genome has hindered molecular genetic analysis and breeding advancements. Here, we present a haplotype-resolved chromosome-level assembly for this autotetraploid species, featuring a 1.56-Gb genome anchored to 80 chromosomes across four haplotypes and comprising 95 668 protein-coding genes. Following divergence from Dioscorea alata about 4.64 million years ago (Mya), D. polystachya underwent a specific whole-genome duplication ~1.42 Mya, resulting in an autotetraploid species without subgenomic dominance. Notably, the biosynthetic pathway genes of dioscin, an important steroidal saponin primarily accumulating in tubers, were generally over-retained in D. polystachya compared to the diploid species D. alata. Of these genes, 7-dehydrocholesterol reductase (Dp7-DR) promoted the accumulation of dioscin, exhibiting tuber-specific expression and strong inducibility by abscisic acid, based on transcriptome and gene function analyses. We determined that the transcription factor DpbZIP12 activates Dp7-DR transcription, as supported by yeast one-hybrid, dual-luciferase reporter, and electrophoretic mobility shift assays. Notably, overexpressing Dp7-DR or DpbZIP12 resulted in lower cholesterol levels and elevated dioscin levels, while silencing either gene produced opposite metabolic profiles. These findings delineate promising targets for manipulating dioscin content and expand genetic resources for enhancing yam nutritional quality.

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