A Genome-wide association study identifies candidate genes for cold tolerance in garlic overwintering period

Cold stress severely limits growth and yield of garlic (Allium sativum L.). However, the genetic basis of cold tolerance in garlic remains poorly understood. Here, we evaluated freezing-injury indices (DI) of 71 garlic accessions representing diverse ecotypes in two open-field sites across two years. Fifteen accessions were classified as highly cold-tolerant and 23 as highly cold-sensitive. A genome-wide association study (GWAS) using BLUP values and resequencing data identified five loci significantly associated with cold tolerance (chr2-1048886093, chr3-1062979463, chr2-386689956, chr3-1063009679 and chr6-389186607). Candidate-gene analysis prioritized five genes within these intervals: Asa2G03892 (sulfiredoxin, SRX), Asa3G03882 (nucleobase-ascorbic acid transporter, NAT6), Asa2G01375 (poly (ADP-ribose) polymerase 1, PARP1), Asa3G03883 (fatty acid export 1, FAX1) and Asa6G01495 (SWEET14-like sugar transporter). Asa3G03882 and Asa2G01375 Functional annotation, haplotype analysis, and qRT-PCR revealed nonsynonymous SNPs and cold-induced expression changes in several genes, suggesting roles in ROS detoxification, membrane lipid metabolism, and sugar transport. Sequence polymorphisms in Asa3G03883 and Asa2G03892 were located in intronic regions; notably, expression of Asa3G03883 was lower in cold-tolerant than in cold-sensitive accessions. These candidate genes provide a foundation for dissecting cold-tolerance mechanisms in garlic and represent potential targets for marker-assisted or molecular breeding to develop cold-resilient cultivars.