Genomic analyses provide insights into the genetic basis of quality traits in Amomum tsaoko

•A chromosome-level genome of Amomum tsaoko (1.967 Gb, 93.9% completeness) provides an improved genomic resource.•Expanded terpene synthase families likely enhance medicinal terpenoid accumulation.•Population genomics reveals low genetic differentiation linked to historical domestication.•GWAS identifies zinc finger and AP2/EREBP genes significantly associated with fruit length.•Integrated multi-omics analyses highlight plant hormone regulators influencing fruit morphology.