Transcriptome-Based Discovery of Tuber Formation Genes in Asparagus cochinchinensis and A. taliensis Provides Targets for Breeding Improvement

The genus Asparagus L. is a traditional Chinese herb valued for its medicinal and culinary properties, with root tubers being the primary organ of interest. To elucidate the genetic mechanisms underlying tuber formation, we conducted a comparative transcriptome analysis of two species, Asparagus cochinchinensis (Lour.) Merr. and Asparagus taliensis F. T. Wang & Tang ex S. C. Chen, which exhibit distinct differences in root tuber number. High-throughput sequencing generated 6.68 Gb and 7.60 Gb of clean data for the respective species, leading to the annotation of 115,080 non-redundant unigenes. Comparative analysis identified 26,013 differentially expressed genes (DEGs), including 1096 associated with carbohydrate metabolism. Weighted gene co-expression network analysis (WGCNA) revealed that the MEred and Megreenyellow modules which included genes involved in material and energy metabolism were significantly correlated with tuber development. From these modules, we identified two candidate genes involved in carbon and sugar metabolism, designated Ac_uniYEAD and Ac_uniRPE. Quantitative real-time PCR validation confirmed that their expression levels were positively correlated with root tuber number, consistent with the transcriptomic data. These results highlight Ac_uniYEAD and Ac_uniRPE as promising targets for genetic improvement of tuber yield in Asparagus breeding programs.