Chinese pine (Pinus tabuliformis) is a conifer species endemic to the temperate, warm temperate, and semi-arid regions of China. It has important ecological and economic values, but lacks suitable molecular markers for genetic studies. In this study, we collected open-pollinated progeny seeds from four provenances: Ningcheng (Nc), Qinyuan (Qy), Weichang (Wc), and Pingquan (Pq). We sequenced the transcriptomes of open-pollinated progeny seedlings from four provenances and annotated 18,244 unigenes. We analyzed the expression of genes involved in the auxin indole-3-acetic acid (IAA), cytokinin (CTK), and gibberellin (GA) signaling pathways among the provenances. Additionally, we detected 2811 expressed sequence tag simple sequence repeat (EST-SSR) loci in 2360 unigenes, with a frequency of 14.83% and an average of one locus per 14,556 base pairs (bp). We developed 10 polymorphic primers from 67 pairs and tested them on 56 samples from the four provenances. These primers exhibited moderate to high polymorphism and distinguished all samples clearly. Our study reveals variation in growth and development among open-pollinated progeny seedlings from different provenances of Chinese pine and provides novel markers for its genetic diversity study and marker-assisted breeding.

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.