Elucidating the genetic basis of bulb-related traits in garlic (Allium sativum) through genome-wide association study

The genetic architecture of garlic bulb related traits were still not well elucidated due to its big and complex genome. In this study, genotyping-by-sequencing (GBS) in 163 garlic accessions mainly from China were conducted. All the 163 garlic accessions were divided into three subpopulations, and largely consistent with geographic origins. Genome-wide association study (GWAS) was conducted for 5 garlic bulb related traits across four environments. Totally, 26 significantly loci were identified in two or more environments and located within or near 431 genes, and explain 14.0-31.7 % of the phenotypic variances. Among these, qBW5.1 was nearly with the qBH5.1. Four loci were reported previously, whereas the remaining 22 are likely to be new. Gene ontology enrichment analysis showed that the candidate genes were significantly enriched in metabolic process, biosynthetic process and catalytic activity. Nine candidate genes encode the zinc finger domain-containing protein, serine/threonine-protein kinase, peroxygenase, auxin-induced protein, ethylene-responsive transcription and E3-Ubiquitin protein ligases were identified and validated. Additionally, a meaningful achievement is one kompetitive allele-specific PCR marker, Kasp_chr7_BW for bulb weight were successfully developed and validated in a diverse panel. These results uncover the genetic mechanism of garlic bulb related traits and provide accessions and KASP markers for further garlic molecular breeding.