Lycium ruthenicum Murr. (Black goji), a medicinal and economically valuable crop rich in bioactive compounds, remains genomically understudied despite its expanding cultivation. To overcome limitations of traditional markers in genetic diversity analysis and molecular breeding, we employed specific-locus amplified fragment sequencing (SLAF-seq) to develop genome-wide SNP markers and elucidate the genetic structure of 213 L. ruthenicum accessions from natural and cultivated populations in Alxa, China. We identified 827,630 SLAF tags and 33,121 high-quality SNPs uniformly distributed across 12 chromosomes, establishing the first high-density SNP database for this species. Population genetic analyses revealed three distinct genetic clusters with <60% geographic origin consistency, indicating weakened isolation due to anthropogenic germplasm exchange. The Qinghai Nuomuhong population exhibited the highest genetic diversity (Nei’s index = 0.253; Shannon’s index = 0.352), while low overall polymorphism (average PIC = 0.183) likely reflects SNP biallelic limitations and domestication bottlenecks. Notably, SNP-based clustering showed <40% concordance with phenotypic trait clustering (31 traits), underscoring environmental plasticity as a key driver of morphological variation. This study provides the first genome-wide SNP resource for L. ruthenicum, enabling marker-assisted breeding and highlighting the need for standardized germplasm management to mitigate genetic erosion.

Aphid infestation constrains goji berry production, yet its defense architecture remains poorly resolved. We integrated comparative transcriptomics, phytohormone profiling, small RNA sequencing, and genome-wide nucleotide-binding leucine-rich repeat (NLR) analysis to dissect aphid defense in Lycium barbarum (cv. Ningqi-10)and susceptible L. chinense. Aphid bioassays confirmed that L. barbarum imposes a significant fitness cost on aphids, reducing survival, longevity, and fecundity. Transcriptomic comparison revealed fewer but more defense-enriched differentially expressed genes in the resistant accession. Weighted gene co-expression network analysis (WGCNA) identified a stress-associated turquoise module (288 genes, r = 0.981) receptor-like kinases and mitogen-activated protein kinase (MAPK) components, bridging extracellular signals sensing and hormone signaling. Phytohormone profiling showed that salicylic acid (SA) accumulated to 72 h, whereas jasmonic acid (JA) peaked transiently at 24 h, producing an increased SA/JA ratio suggesting a shift to SA-dominated signaling. MiR398a-3p and miR319-3p dynamics coincided with this SA/JA shift, suggesting a possible link to hormone-coordinated regulation and candidate targets for validation. NLR analysis identified 151 candidate genes, including 18 L. barbarum-biased NLRs up-regulation under SA-dominated signaling, implying a link to SA signaling. Collectively, these findings support a multi-layered framework integrating SA signaling, transcriptional reprogramming, and coupled miRNA and NLR responses in aphid defense.