Advancement of the oil tea industry requires the development of high-yielding and superior-quality varieties of Camellia oleifera, a major oilseed crop. However, traditional breeding methods, hampered by lengthy cycles and low selection accuracy, significantly constrain the breeding process. Identifying single nucleotide polymorphisms (SNPs) associated with target traits, and applying molecular marker-assisted selection (MAS) for these traits, can thereby shorten the breeding cycles and amplify the breeding efficiency. In this study, we utilized the hexaploid C. oleifera as the reference genome to identify high-quality SNPs and constructed a high-density genetic linkage map of C. oleifera that spanned 1566.733 cM, included 3097 SNPs, and was anchored to 15 linkage groups. Using interval mapping, we localized quantitative trait loci (QTLs) for 11 juvenile traits in C. oleifera, identifying 15 QTLs for growth traits and 24 QTLs for leaf traits, including 4 stable QTLs. The logarithm of odds (LOD) scores for individual QTLs ranged from 3.48 to 14.62, explaining 9.86–48.61% of the phenotypic variance. We further identified 2 SNPs associated with growth traits (marker11-951 and marker12-68) and 10 SNPs associated with leaf traits (marker11-276, marker11-410, marker11-560, marker13-16, marker13-39, marker13-110, marker13-731, marker14-701, marker14-910, and marker14-1331). These results provide valuable insights into the genetic mapping of key traits in C. oleifera and will contribute to the development of new varieties with high yield and superior quality in the future.

Tea oil is an important high-quality edible oil derived from woody plants. Camellia oleifera is the largest and most widely planted oil-producing plant in the Camellia genus in China, and its seeds are the most important source for obtaining tea oil. In current research, improving the yield and quality of tea oil is the main goal of oil tea genetic breeding. The aim of this study was to investigate the degree of genetic variation in an early crossing population of C. oleifera and identify single nucleotide polymorphisms (SNPs) and genes significantly associated with fruit traits, which can provide a basis for marker-assisted selection and gene editing for achieving trait improvement in the future. In this study, we selected a crossing population of approximately 40-year-old C. oleifera with a total of 330 samples. Then, ddRAD sequencing was used for SNP calling and population genetic analysis, and association analysis was performed on fruit traits measured repeatedly for two consecutive years. The research results indicate that over 8 million high-quality SNPs have been identified, but the vast majority of SNPs occur in intergenic regions. The nucleotide polymorphism of this population is at a low level, and Tajima’s D values are mostly greater than 0, indicating that the change in this population was not suitable for the model of central evolution. The population structure analysis shows that the population has seven theoretical sources of genetic material and can be divided into seven groups, and the clustering analysis results support the population structure analysis results. Association analysis identified significant SNPs associated with genes related to the seed number of a single fruit and seed kernel oil content. Our findings provide a basis for molecular breeding and future genetic improvement of cultivated oil tea.

Plantations of the valuable Chinese timber species, Chamaecyparis hodginsii, established by planting, primarily rely on seed orchards for propagation. Therefore, effective management of the genetic composition of these orchards is essential to ensure a sustainable supply of high-quality seeds. However, the mating system and pollen dispersal mechanisms in its high-generation seed orchards remain unclear, limiting precise genetic management. To address this, we analyzed 30 parental clones and 75 of their open-pollinated progeny from a second-generation seed orchard using 15 polymorphic EST-SSR markers. Compared to reported natural populations of C. hodginsii, both parental and progeny populations maintained high genetic diversity (mean uHe = 0.438 and 0.449, respectively), with a significant excess of heterozygotes (mean Fis = −0.084 and −0.066, respectively). Population genetic structure analysis indicated weak genetic differentiation among the parental genetic groups (mean Fst = 0.012), which was further reduced in the progeny population (mean Fst = 0.003) due to open pollination, reflecting a trend toward genetic homogenization. The mating system was characterized exclusively by outcrossing (tm = 1.000). However, paternity analysis revealed highly skewed paternal contributions, a low effective number of pollen donors (Nep = 8.13), and contributions of S5, S11, and S17 as dominant pollen parents, with 17.33% external pollen flow. These findings elucidate the mechanisms underlying sustained genetic diversity despite unequal paternal contributions and provide a theoretical basis for optimizing parental configuration and pollen management.