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.

Quantifying the genetic diversity present in plant populations is crucial for the success of selection of elite plants and breeding programs. The population structure and partition of genetic variance within and between plant populations allows inferences about the distribution and extent of variation available in plant breeding populations. The Chinese pine (Pinus tabuliformis Carriere) is a native species that is ecologically and economically important to Northern China. Studying the genetic variation and partition of P. tabuliformis will be invaluable for its efficient utilization. In this study, we selected 21 pairs of SSR primers to estimate the genetic diversity of 35 clones from four populations and 216 progenies from 22 full-sib families of P. tabuliformis. Our results showed that P. tabuliformis was a typical outcrossing plant (F_IS = −0.053/−0.165) containing moderately high genetic diversity (He = 0.542/0.605) both for the clone populations and the progenies produced by the clone crosses via controlled pollination. The genetic differentiation between the clones (F_ST = 0.076) was lower than that between the full-sib progenies (F_ST = 0.155). Such diverse F_ST may be promoted by different gene flows (Nm = 3.881/1.546) due to distinct pollination patterns. The clustering methods showed a lack of significant division of the clone populations, with a similar genetic admixture found for each of the clones. However, two groups were found between the full-sib families with genetic admixture between them. The analysis of molecular variance (AMOVA) showed that the most plentiful genetic variability exists between the cloned individuals (98%) as well as within the full-sib progenies (89%). Such distribution of genetic variation suggests rich internal variance and thus it is feasible to select the elite plants within each population or family. These results provide genetic materials and theoretical guidance for the selection and breeding of the Chinese pine.

Microtubules, polymerized from α-tubulin (TUA) and β-tubulin (TUB) monomers, play a pivotal role in shaping plant morphogenesis according to developmental and environmental cues. Salix psammophila C. Wang & C. Y. Yang is an important shrub plant in sand-fixing afforestation in arid regions, with three significantly distinct plant types shaped under various environments, namely, upright, intermediate, and scattered types. However, how tubulin genes respond to the developmental and environmental signs in S. psammophila has been far less studied. Here, based on RNA-seq, Sanger sequencing, and real-time PCR (RT-PCR) data, we analyzed the phylogeny of tubulins and their expression profiles in S. psammophila among the three plant types. Furthermore, we analyzed the genetic structure and expression pattern of SpsTUB10 in S. psammophila under various abiotic stress treatments. In total, we identified 26 SpsTubulin genes in S. psammophila. The homologous alignment and phylogenetic analysis revealed that these SpsTubulin genes can be classified into two groups, corresponding to the TUA and TUB genes. The expression profiles of these SpsTubulin genes in various organs showed that most SpsTubulin genes were mainly expressed in the root. SpsTUB10 is a member of the TUB IIa group, consisting of two intros and three exons. The SpsTUB10 protein contains a typical GTPase domain and a C-terminal domain, with α-helix and random coil dominant in the secondary and tertiary structures. The RT-PCR results of SpsTUB10 showed an extremely significant difference in expression levels among the root and stem-developing organs between the upright and scattered types, and the transcript level of SpsTUB10 had a significantly negative correlation with the crown-height ratio. Under different treatments, we found that cold, osmotic stress, and short daylight could significantly increase SpsTUB10 expression levels compared to those in the controls, thereby supporting the positive role of SpsTUB10 in stress-induced responses. These results will provide evidence for the SpsTubulin genes’ response to the developmental and environmental cues in S. psammophila.