Loblolly pine (Pinus taeda L.) is an important tree for afforestation with substantial economic and ecological value. Many metabolites with pharmacological activities are present in the tissues of P. taeda. However, the biosynthesis regulatory mechanisms of these metabolites are poorly understood. In the present study, transcriptome and metabolome analyses were performed on five tissues of P. taeda. A total of 40.4 million clean reads were obtained and assembled into 108,663 unigenes. These were compared with five databases, revealing 39,576 annotated unigenes. A total of 13,491 differentially expressed genes (DEGs) were observed in 10 comparison groups. Of these, 487 unigenes exhibited significantly different expressions in specific tissues of P. taeda. The DEGs were explored using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis. We identified 343 and 173 candidate unigenes related to the biosynthesis of terpenoids and flavonoids, respectively. These included 62 R2R3-MYB, 30 MYB, 15 WRKY, seven bHLH, seven ERF, six ZIP, five AP2, and one WD40 genes that acted as regulators in flavonoid and/or terpenoid biosynthesis. Additionally, metabolomics analysis detected 528 metabolites, among which 168 were flavonoids. A total of 493 differentially accumulated metabolites (DAMs) were obtained in 10 comparison groups. The 3,7-Di-O-methyl quercetin was differentially accumulated in all the comparison groups. The combined transcriptome and metabolome analyses revealed 219 DEGs that were significantly correlated with 45 DAMs. Our study provides valuable genomic and metabolome information for understanding P. taeda at the molecular level, providing a foundation for the further development of P. taeda-related pharmaceutical industry.

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is a fast-growing conifer with great forestation value and prefers outcrossing with high inbreeding depression effect. Previously, we captured a special Chinese fir parent clone named as ‘cx569’ that lacks early inbreeding depression. In view of the fact that very little has been published about the rare self-fertilizing event in Chinese fir from a genetic view, herein, we conduct an SSR-based study on the variation of open- and self-pollinated offspring of this parent to gain a view of the rare self-fertilizing event. The results indicated that genetic diversity of self-pollinated offspring was significantly reduced by half (Ho: 0.302, vs. 0.595, p = 0.001; He: 0.274 vs. 0.512, p = 0.002) when compared to an open-pollinated set. Self-pollinated offspring also had significantly positive FIS values (FIS = 0.057, p = 0.034) with a much higher proportion of common allele (20.59% vs. 0), reflecting their heterozygote deficiency. Clustering analysis further indicated a separation of the self- and opened- pollinated groups, implying a natural preference of outcrossing for cx569. However, the cx569 still had 6% acceptance for selfing. When accepted 100% for its own pollen, the cx569 led to a genetically unique selfing group. Additionally, this selfing group seemed to be consistently homozygous at seven particular loci. These findings gave us more genetic clues to gain insight into the rare self-fertilizing event in conifer (Chinese fir).

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Accurate estimation of genetic relationships among breeding materials and their genetic diversity contributes to the optimal design of breeding programs. For Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.), an important indigenous tree species in China, breeders have attempted to employ different molecular markers to address the genetic architecture of their target population, but the power of an advanced parent tree population with a complex pedigree relationship is still rather limited. In this study, a partly known pedigree map combined with marker-derived (SSRs and SNPs) information was implemented for the first time in the assessment of the genetic relatedness of a complex advanced parent tree population (n = 50) in Chinese fir. The bivariate analysis showed that relatedness coefficients between individuals based on SSRs were significantly correlated with SNPs (r = 0.690, p < 0.01). Moreover, the heatmap generated by the SSR-based coefficient matrix was largely consistent with that derived from the SNP-based matrix. Additionally, STRUCTURE and ADMIXTURE analyses based on the two markers showed an analogical genetic clustering result. When compared to the recorded pedigree information, the genetic relationships estimated by the two molecular markers were broadly parallel with pedigree relatedness. These results indicated that SSRs and SNPs can be used as effective tools to clarify genetic relationships when complete pedigree records are not available in Chinese fir. Based on the two markers, the present study revealed a relatively wide genetic variation (SSRs: PIC = 0.573; SNPs: PIC = 0.231) in the selected parent trees. This investigation provides important input into the progress of Chinese fir advanced-generation breeding.