Integrated Analysis of Metabolomics, Flavoromics, and Transcriptomics for Evaluating New Varieties of Amomum villosum Lour.

<i>Amomum villosum</i> Lour. (<i>A. villosum</i>) is the original plant of the medicinal and culinary spice Amomi Fructus (Sharen) and is an important economic crop in the Lingnan region of China. During the cultivation and production of <i>A. villosum</i>, prolonged reliance on single asexual reproduction has exacerbated the degradation of its varieties, leading to inconsistent yields and quality. Building upon earlier cultivar selection efforts, this study provides a comprehensive evaluation of two newly bred <i>A. villosum</i> varieties (A11 and A12) from perspectives including plant traits, product characteristics, active ingredients, and multi-omics analysis. It was found that A12 plants display enhanced robustness, more aromatic fruits, higher yields, and elevated levels of bornyl acetate, A11 shows the advantage of a high camphor content, and the different metabolites and differentially expressed genes of the two varieties were significantly enriched in multiple metabolic pathways. Additionally, A12 contained more terpenoids and substances with aromatic odors such as sweet, fruity, floral, and green. Furthermore, a key gene (Wv_032842) regulating the acetylation of bornyl was discovered, and its significantly higher expression, in A12. In conclusion, this study has a guiding significance for the evaluation of germplasm resources and the breeding of excellent varieties of <i>A. villosum</i>.