The mechanisms underlying plant response to drought involve the expression of numerous functional and regulatory genes. Transcriptome sequencing based on the second- and/or third-generation high-throughput sequencing platforms has proven to be powerful for investigating transcriptional landscape under drought stress. However, the full-length transcriptomes related to drought responses in the important conifer genus Pinus L. remained to be delineated using the third-generation sequencing technology. With objectives to identify the candidate genes responsible for drought and/or rehydration and clarify the expression profile of key genes involved in drought regulation, we combined the third- and second-generation sequencing techniques to make transcriptome analysis on seedling roots under drought stress and rewatering in the drought-tolerant conifer Pinus massoniana Lamb.. A sum of 294,114 unique full-length transcripts were produced with a mean length of 3,217 bp and N50 estimate of 5,075 bp, including 279,560 and 124,438 unique full-length transcripts being functionally annotated and gene ontology enriched, respectively. Totally 4,076, 6,295 and 18,093 differentially expressed genes (DEGs) were identified in three pair-wise comparisons of drought-treatment versus control transcriptomes, including 2,703, 3,576 and 8,273 upregulated and 1,373, 2,719 and 9,820 downregulated DEGs, respectively. Moreover, 157, 196 and 691 DEGs were identified as transcription factors in the three transcriptome comparisons and grouped into 26, 34 and 44 transcription factor families, respectively. Gene ontology enrichment analysis revealed that a remarkable number of DEGs were enriched in soluble sugar-related and cell wall-related processes. A subset of 75, 68 and 97 DEGs were annotated to be associated with starch, sucrose and raffinose metabolism, respectively, while 32 and 70 DEGs were associated with suberin and lignin biosynthesis, respectively. Weighted gene co-expression network analysis revealed modules and hub genes closely related with drought and rehydration. This study provides novel insights into root transcriptomic changes in response to drought dynamics in Masson pine and serves as a fundamental work for further molecular investigation on drought tolerance in conifers.

Clonal testing is crucial for estimating genetic parameters and selecting elite clones. However, few studies have tested clones over two or more rotations. In this study, a clonal trial of the sibs from a Eucalyptus urophylla × Eucalyptus tereticornis cross was used for genetic parameter analyses and multitrait selection based on traits such as across-rotation growth, wood properties, coppicing ability, and coppice chlorophyll fluorescence. Clonal repeatability (H²) estimates for growth traits in the first rotation ranged from 0.73 (diameter at breast height at age 15) to 0.84 (single-tree volume at age 2.5) and were generally higher than those for growth traits in the second rotation (0.11–0.62). H² estimates for coppicing and chlorophyll fluorescence traits ranged from 0.35 to 0.57 and 0.03 to 0.53, respectively, indicating low to medium genetic control of these traits. Phenotypic correlations (rp) and additive genetic correlations (rg) were generally high among growth traits within a single rotation and among coppicing traits but varied considerably across other trait pairs. In particular, second-rotation volume at 2.5 years showed a very weak rp but a moderately positive rg with early-stage volumes from the first rotation. Multitrait selection index (SI) and multitrait genotype–idiotype distance index (MGIDI) methods were applied at a selection intensity of 15% under four scenarios, each combining two to five traits. Relative genetic gain (RG) and selection efficiency (E) estimates were positive for all traits included in multitrait selection, indicating the usefulness of all selection scenarios. Compared to SI, the MGIDI method produced slightly lower RG and E values for volumes at ages 8 and 15 years, but higher RG and E values for wood basic density and cellulose content at age 8 in the first rotation. This study has important implications for eucalypt clonal breeding and management.

Archidendron clypearia (Jack) I. C. Nielsen is an important tree species for traditional medicine purposes such as anti-inflammatory, detoxification, uric acid control and neuro-protection. Here, a set of 15 microsatellite markers were used to fingerprint 248 elite genotypes from six origins of A. clypearia and investigate the genetic structure of these genotypes. A total of 170 alleles were amplified. The elite genotypes showed moderate genetic variability, with mean observed heterozygosity (H_o) and expected heterozygosity (H_e) being 0.651 and 0.699, respectively. Each of the elite genotypes could be fingerprinted uniquely. The cumulative probability of identity (PI) and the cumulative probability of paternity exclusion (PE) were 2.25 × 10⁻¹² and 0.999992, respectively, demonstrating the extremely high power of the markers for genotype identification. In STRUCTURE and clustering analyses, the same origin of elite genotypes tended to be grouped in a sub-population and clustered closely, but some genotypes from different geographic origins were mixed, suggesting a low level of genetic differentiation between the origins. These results can contribute to the protection and management of the elite genotype resources of A. clypearia and the comprehensive understanding of its genetic structure.