• Natural variation analysis provides important insights into the genetic basis of explant browning in jujube. • Multi-omics integration highlights ZjSBT3.6 and ZjNOLC1 as potential candidate genes functioning beyond canonical oxidases. • Our findings propose that browning may represent a maladaptive consequence linked to structural defense and programmed cell death. Explant browning represents a persistent bottleneck in plant tissue culture, severely hampering regeneration and genetic transformation efficiencies . Despite its widespread prevalence, the genetic architecture and regulatory mechanisms underlying this recalcitrant trait remain largely unexplored. Here , we evaluated in vitro leaf browning across 139 jujube ( Ziziphus jujuba Mill.) accessions. By integrating genome-wide association studies (GWAS) with comparative transcriptomics between resistant (‘ZS4’ and ‘Pozao’) and susceptible (‘Lincui1’ and ‘Linzedazao’) genotypes, we comprehensively dissected the molecular basis of this phenomenon. This multi-omics approach pinpointed 10 high-confidence candidate loci ( including Zj4CL2, ZjPOD15, ZjBBE-like13, ZjCOMT, ZjPOD55, ZjPRX1, ZjSBT3.6, ZjCOR2, ZjABCA2 , and ZjNOLC1 ) strongly associated with the necrotic phenotype. Functional analysis revealed that the core differentially expressed genes (DEGs) predominantly mapped to secondary metabolite biosynthesis, particularly the phenylpropanoid and glutathione pathways. Overall, our findings suggest that jujube explant browning is associated with specific metabolic shifts, providing potential genetic targets for further investigation into improving tissue culture efficiency.
Gao et al. (2026) studied this question.