Genetic diversity and association analysis between agronomic traits and EST-SSR markers in Chinese chive (Allium tuberosum)

Chinese chive ( Allium tuberosum ) is an economically important vegetable and medicinal crop, yet research on its genetic diversity and population structure remains limited. In this study, we identified 68,248 SSR loci from chive transcriptome data and developed a set of corresponding SSR markers. After validation and screening, 59 polymorphic SSR markers were used to genotype 82 chive germplasm accessions. Clustering analysis and population structure d analysis assigned these accessions into three distinct groups. We conducted principal component analysis, correlation analysis, and marker-trait association analysis with FDR correction for 18 agronomic traits using GLM (Q) and MLM (Q+K) models. At the P ≤ 0.05 significance level, 2 and 30 significant trait-associated markers were identified by GLM and MLM, respectively. The marker sxauAt427 was significantly associated with anthocyanin content in both models, and its linked gene Unigene-84067 participates in the flavonoid biosynthesis pathway, which supplies critical precursors for anthocyanin production. Expression analysis further showed that key flavonoid biosynthesis genes were significantly upregulated in purple-rooted chives compared with white-rooted chives, providing a molecular basis for the root color difference. These results offer valuable genetic resources and theoretical support for gene mining, functional dissection of agronomic traits, and molecular breeding in Chinese chive.