The recognition of pollen and pistil in the self-incompatibility process is generally determined by the interaction between the pollen S gene and pistil S gene located at the S locus. However, the regulatory mechanism of self-incompatibility in goji remains unknown. In this study, we used the self-compatible strain ‘13–19’ and self-incompatible strain ‘xin9’ from Ningxia as parents to create an F1 hybrid population. Reciprocal cross-pollination was performed within the same plant to evaluate the self-compatibility of the parents and F1 progeny. The parents and progeny were subjected to whole-genome resequencing, and mixed pools of DNA were constructed using 30 self-compatible and 30 self-incompatible individuals. Association analysis using the SNP-index method and Euclidean distance was employed to identify the key candidate region of the S locus. The candidate region was further annotated using the Swiss-Prot database to identify genes within the region. Additionally, transcriptome sequencing data from different organs/tissues, as well as from pistils of self-compatible and self-incompatible strains at control (0 h), short (0.5 h), medium (8 h), and long (48 h) time points after self-pollination and cross-pollination, were analyzed to assess differential gene expression and screen for self-compatibility-related loci. Specific primers were designed for PCR amplification to determine the S-RNase genotypes of the extreme parents. The results revealed that the S locus in goji is located within a 32.2 Mb region on chromosome 2 that contains a total of 108 annotated genes. Differential expression analysis showed that ten genes, including Lba02g01064, were specifically expressed in stamens, with four of them annotated as F-box genes, potentially serving as determinants of self-compatibility in stamens. Lba02g01102 was exclusively expressed in pistils and annotated as an S-RNase gene, likely involved in self-compatibility. The expression of Lba02g01102 in pistils decreased after self-pollination and cross-pollination. Six candidate genes exhibited significant changes after self-pollination and cross-pollination. Both parents and progeny carried two S-RNase alleles, and the S-RNase genotypes showed a significant correlation with self-compatibility, with the self-compatible progeny containing the S8-RNase allele. The identification of the S locus in goji provides molecular markers for future marker-assisted breeding and offers genetic resources for studying the mechanism of self-incompatibility in goji, thus contributing to the improvement of goji varieties.

Background: Lycium barbarum L. is gaining significant interest as a medicinal and culinary raw material. The quality and aroma are significantly influenced by metabolite accumulation, which differs based on origins and drying methods. Methods: This study utilizes gas chromatography–mass spectrometry (GC-MS) to analyze the metabolic profiles of the ‘Ningqi’ No. 1 variety from three distinct origins employing two drying techniques (natural sun drying, NSD; hot-air drying, HAD). The samples include Zhongping, Ningxia, with HAD (1-1); Zhongning, Ningxia, with NSD (1-2); Wuwei, Gansu, with NSD (1-3); Nuomuhong, Qinghai, with NSD (1-4); and Nuomuhong, Qinghai, with HAD (1-5). Results: The study found that aldehydes, esters, ketones and alcohol are key secondary metabolites generated during NSD and HAD treatments of goji berry from various regions. Flavor analysis revealed the compound Ethanol, 2-phenoxy- (balsamic) was up accumulated in goji berry from Qinghai drying with NSD compared with HAD; goji berry drying with HAD collected from Ningxia compared with Qinghai; goji berry drying with NSD collected from Gansu compared with Ningxia; and goji berry drying with NSD collected from Qinghai compared with Ningxia. The compound 2-Thiophenemethanol (burnt) was up accumulated in goji berry drying with HAD collected from Ningxia compared with Qinghai. Further flavor analysis revealed that the compound Undecanal (floral) was up accumulated in goji berry drying with NSD collected from Qinghai compared with Ningxia and Gansu. 1H-Pyrrole-2-carboxaldehyde (burnt), 1-ethyl- (burnt) was up accumulated in goji berry drying with NSD collected from Qinghai compared with Gansu. KEGG enrichment analysis suggests that ‘Arginine and proline metabolism’ could be the primary metabolic pathway in the goji berry drying process. Conclusions: This study examined how origins and drying methods affected the metabolites and metabolic pathways of goji berries to elucidate the mechanisms impacting their quality and flavor. The findings provide important insights into the use of goji berries in functional foods and pharmaceuticals.

Powdery mildew severely constrains the production of Lycium barbarum L., yet the molecular mechanisms underlying its response to infection remain poorly understood. Here, ‘Ningqi-1’ plants were inoculated with the powdery mildew pathogen and sampled at 0, 12, 24, and 48 hpi for integrated transcriptomic, proteomic, and metabolomic analyses. Quantitative PCR and CRISPR/Cas9-mediated gene editing were further used to evaluate the candidate susceptibility gene LbMLO6. Infection induced extensive molecular reprogramming, yielding 1299 differentially expressed genes with sustained changes, 75 DAPs shared across all three time points, and 127 shared differentially accumulated metabolites. These molecules were mainly enriched in plant–pathogen interaction, plant hormone signal transduction, MAPK signaling, phenylpropanoid biosynthesis, and α-linolenic acid metabolism pathways, suggesting coordinated roles for Ca²⁺ signaling, reactive oxygen species, defense-related proteins, and secondary metabolism in the host response. Integrated multi-omics analysis identified LbMLO6 as a candidate gene associated with powdery mildew susceptibility, its expression was markedly induced from 24 hpi onward. CRISPR/Cas9-edited LbMLO6 lines showed reduced fungal development compared with the control, particularly during the early stages of infection. These findings provide preliminary evidence that LbMLO6 may be associated with powdery mildew susceptibility in L. barbarum.