Abstract

A total of 120 quinoa (Chenopodium quinoa Willd.) accessions were classified into two distinct genetic groups, Andean highland type and Chilean lowland type, based on a genetic differentiation index (FST) of 0.14. Within this framework, accession M065 was identified as drought-tolerant, whereas M084 exhibited drought sensitivity. 735 SNP loci were obtained by using the MultipleSeq multiplex PCR amplicon capture sequencing technology. GWAS-based SNP-trait association indicated that 5 SNP loci were significantly associated with plant height (PH, R-2: 10.03%), branch number (BN, R-2: 13.13%), yield per plant (YPP, R2: 10.77%) and panicle width (PW, R-2: 10.38%), respectively. Under drought stress, M065 exhibited significantly smaller reductions-by 5.93%, 6.99%, 6.02%, 9.45%, 6.87%, 10.24%, 8.59%, 2.58%, and 3.80%, respectively-than M084 in plant height, leaf area, biomass, relative leaf water content, chlorophyll content, net photosynthetic rate, transpiration rate, intercellular CO2 concentration, and stomatal conductance. Root system scanning indicated that under drought stress, M065 root cells maintained near-normal volume with only mild shrinkage, whereas M084 root cells exhibited pronounced shriveling. The physiological analysis showed that both accessions exhibited elevated MDA and H2O2 levels under drought stress, with M084 showing greater increases than M065. SOD activity increased in both accessions under D1 (SMC: 45%-55%) and D2 (SMC: 25%-35% stresses, but the rise was slightly higher in M065. POD activity increased significantly in M065, while M084 showed no significant change under D2. CAT activity increased in both accessions under D1, but only M065 showed a significant increase under D2.