Genome-wide association analysis identifies candidates of three bulb traits in garlic

Garlic bulbs generally possess several swelling cloves, and the swelling degree of the bulbs determines its yield and appearance quality. However, the genetic basis underlying bulb traits remains poorly known. To address this issue, we performed a genome-wide association analysis for three bulb traits: bulb weight, diameter, and height. It resulted in the identification of 51 significant associated signals from 38 genomic regions. Twelve genes from the associated regions, whose transcript abundances in the developmental bulb showed significant correlations with the investigated traits in 81 garlic accessions, were considered the candidates of the corresponding locus. We focused on five of these candidates and their variations and revealed that the promoter variations of fructose-bisphosphate aldolase-encoding Asa8G05696.1 and beta-fructofuranosidase-encoding Asa6G01167.1 are responsible for the functional diversity of these two genes in garlic population. Interestingly, our results revealed that all candidates we focused on experienced a degree of selection during garlic evolutionary history, and different genotypes of them were retained in two China-cultivated garlic groups. Taken together, these results suggest a potential involvement of those candidates in the parallel evolution of garlic bulb organs in two China-cultivated garlic groups. This study provides important insights into the genetic basis of garlic bulb traits and their evolution.