Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low F_ST (0.0285–0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies.

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is one of the major commercial conifer species in China. The present study concentrated on the assessment of growth, wood property traits, and strobili number in a 12-year grafted clone test of 62 Chinese fir breeding parents, aiming to describe the variation and correlations between these traits and to identify parent clones with the highest potential for future breeding. The results indicate that all of the growth (height, diameter at breast height, stem volume, crown-width) and wood property (wood basic density and hygroscopicity) traits varied significantly (p < 0.01) among clones, with coefficients of variation ranging from 7.6% to 30.6%. Furthermore, these traits consistently had a moderate to high (0.39–0.87) repeatability estimate (broad-sense heritability). Remarkable clonal differences were also observed for the production of male and female strobili. Phenotypic correlations among growth traits were strong (p < 0.01) and positive. Significantly negative correlations (p < 0.01 or 0.05) were found between wood basic density and growth (except for height) and hygroscopicity. The production of male and female strobili appeared to be significantly (p < 0.01) positively correlated with each other. A notable number of faster-growing parent clones were identified (n = 30); 11 of these had higher density wood with an average realized gain of 10.5% in diameter, and a 5.4% gain in wood basic density. When selection was made for growth and strobili, 10 faster-growing parent clones with medium to high production of female strobili were identified.

Cunninghamia lanceolate (Lamb.) Hook. (Chinese fir) is one of the most important wood-producing species, supplying ~20% of commercial timber by plantations in China. However, the genetic potential of the bred variety is limited by soil degrading in the long term and requiring continuous replanting, and especially the shortage and supply of active and efficient phosphorus. Recently, great attention has been paid to the genotypic variation in phosphorus conversion and utilization efficiency by tree breeders. In this study, the morphological characteristics were used to evaluate the Chinese fir clonal Pi-efficiency stress. A Pi-tolerant clone and a Pi-sensitive clone were selected for RNA sequencing, respectively. In addition, gene function annotation and weighted correlation network analysis (WGCNA) were performed. A total of 60 hub genes were selected, combining phosphate accumulation under Pi-deficiency stress. We also used RNA-seq data to analyze the differences in the response of Pi-sensitive clones and Pi-tolerant clones to Pi-deficiency stress, and real-time quantitative polymerase chain reaction (RT-PCR) analyses were used to test the validity of transcriptome data. The present study provided new insights into the molecular mechanisms of Pi-efficient utilization in Chinese fir clones.