Genome-wide association study of salt tolerance at the germination stage in hemp

Seed germination is the first stage of the plant life cycle, and salinity is a major environmental stress for the inhibition of seed germination in plants. Hemp (Cannabis sativa. L) has high economic value and is widely used in textiles, building materials, food, health care, and so on. Unfortunately, research on the salt tolerance of hemp is very limited. In this study, 202 hemp accessions from 11 countries were used to conduct a genome-wide association study (GWAS) on salt tolerance at the germination stage. Based on 762,634 high-quality SNPs, 70 SNP loci were identified to be associated with salt tolerance-related traits (RGR-T1, RGR-T2, RSRL-T1, RSRL-T2, RSW-T1 and RSW-T2). Among the 70 SNPs, nine were further analyzed as candidate SNPs, and 55 genes were annotated within 100 kb upstream and downstream of the nine SNPs. Combined with RNA-seq data and qRT-PCR results, XM_030641043.1, XM_030641906.1, XM_030648362.1, XM_030648308.1 and XM_030646898.1 may play a key role in regulating salt tolerance of hemp during germination. To our knowledge, this is the first study of hemp GWAS, and the information obtained in this study will be useful for gene cloning and marker-assisted selection (MAS) of salt tolerance in hemp.