From multi-clove to single-clove: integrative analysis uncovers the genetic architecture of bulb type transition in garlic by GWAS combined with transcriptomics

Abstract Single-clove garlic represents a valuable market variant characterized by uniform morphology and enhanced bioactive compounds, yet its genetic architecture and developmental mechanisms remain poorly understood. In this study, 363 garlic accessions from 40 countries were evaluated for multi-clove to single-clove transition, identifying six elite lines with up to 100% single-clove formation. Phenotypic analysis confirmed that low clove number under conventional conditions predicts high single-clove potential, a process associated with genetic mechanisms distinct from bulb enlargement. GWAS identified 218 SNPs linked to clove number variation, of which 44% clustered on chromosome 1. Selective sweep analysis revealed 23 925 genomic regions under selection, with 192 genes overlapping GWAS candidates and functionally enriched in hormone response, ribonucleotide biosynthesis, and energy metabolism. GWAS for single-clove rate identified 171 significant SNPs and 302 candidate genes, with sphingolipid metabolism as the most significantly enriched KEGG pathway. Transcriptomic analysis across six developmental stages revealed six distinct gene clusters (C1-C6), showing that single-clove garlic upregulates MAPK signaling genes (C2) while downregulating cell wall biosynthesis genes (C3). WGCNA identified two antagonistic modules: a turquoise module (r = 0.83 with single-clove rate) and a brown module (r = 0.74 with clove number). Integrated GWAS, selective sweep, transcriptomic, and WGCNA analyses suggest, for the first time, a functionally coordinated ‘Accelerator-Brake’ two-module candidate network associated with bulb-type fate in garlic. Sufficient acceleration coupled with precise braking may potentially redirect developmental resources from multi-clove differentiation to single-bulb expansion. Our study provides insights into the candidate regulatory hierarchy underlying storage organ development and offers precise targets (Asa7G03712.1, Asa1G03229.1) for engineering bulb architecture.