SNP screening and genetic richness analysis
Tea, as a self-incompatible plant (Liang et al. 2015), exhibits high variation, which facilitates the generation of new varieties. However, this trait also makes it challenging to maintain the quality of improved varieties. In recent years, advances in biological sequence technology have deepened our understanding of tea plant genomics and genetics. Several reports have been published on the tea genome of various varieties and strains (Xia et al. 2020; Zhang et al. 2020; Zhang et al. 2021; Zhang et al. 2020; Wang et al. 2021). SNP technology is an efficient tool for genetic analysis of complex traits and identification of genes that cause population differences. SNPs are widely distributed in biological genomes and exhibit high genetic stability (Mammadov et al. 2012; Guajardo 2020).
During testing, 28 primer pairs failed, and only one SNP was identified in some of the primers. These single-state markers may be due to the absence of single nucleotide polymorphism in the identification materials or EST sequence errors. The other party did not identify any SNP marker pairs, possibly because of the sequence's complexity, polymorphism of the flanking sequence, or lack of specificity of the primers for the identification materials. In the preliminary data analysis, we identified 58 sites with MAF ≥ 0.05 for subsequent analysis to ensure the reliability of the results. We analyzed the genetic diversity and relationship of 76 tea plant materials from Gushan Mountain and its surrounding areas using the selected SNP loci.
Ho represents the probability that the alleles of two random samples are different, while the value of He indicates the level of population polymorphism. The results of I, Ho, He, and F of 58 pairs of SNP loci in the study (Table 3) show that Ho ranges from 0.081 to 0.871, with an average of 0.384. He ranges from 0.114 to 0.4901, with an average of 0.329. The lower the expected heterozygosity (Ho), the higher the genetic consistency of the population, which suggests that the Gushan semi-rock tea plant population has high genetic diversity.
Genetic relationship analysis of Gushan semi-rock tea
The Gushan Mountain and Kuling regions belong to the same mountain range, and the distance between sample collection points of Gushan semi-rock tea is small. The tea plant materials of Gushan Mountain and Kuling are derived from semi-wild and wild tea plants, while the materials collected from SF, NF, FZ, and EF also include some mainstream cultivated varieties. Tea production is a commercial activity that involves targeted screening of tea resources to increase benefits. Artificially selected varieties can have a large spatial distance between the parents, as has been reported in both Guiyuan (Wang et al. 2015) and loquat (Nagano et al. 2022) germplasm. This human intervention accelerates the evolutionary direction of species and increases genetic differences between resources, unlike cross-breeding under natural conditions (Chen et al. 2007; Kottawa et al. 2019). wild plants usually had higher genetic diversity than artificially selected plants (Chen RK et al. 2016; Niu et al. 2019), but cultivated materials exhibit greater heterozygosity than wild materials (Yang et al. 2016).
The genetic relationship between Gushan semi-rock tea and tea plants from SF, NF, and EF regions showed significant differences in genetic diversity between Gushan semi-rock tea plant resources and those from SF, NF, and EF regions. Based on a review of the history of the Gushan region, it is speculated that the low gene exchange among tea plants in and around the region may be due to the fact that Gushan semi-rock tea has been used as tribute tea in history (Chen and Yang 2011). To ensure its excellent germplasm, closed management is usually carried out, which limits gene exchange between tea plants. The geographical difference between the Gushan region and FZ is relatively small, which is conducive to the exchange of genetic material between tea plants in them. Although there are significant geographical differences among SF, NF, and EF tea plants, they share a close connection. This relationship is also confirmed by previous studies (Chen et al. 2012; Lin et al. 2017). SF, NF, and EF are the main producing areas of tea in Fujian. Since the 1990s, the tea industry has been moving towards intensification, resulting in monoculture of tea plant varieties and a decline in local tea plant group species and bitter tea resources. Currently, the parental materials used for innovative varieties in Fujian are mainly Fuding Da Bai tea, Tieguanyin, Huang Dan, and few other varieties (Liu et al. 2009). This has resulted in decreasing genetic diversity, loss of certain excellent tea plant resources, and a narrowing of the genetic base of varieties.
Furthermore, The results of Nei’s genetic distance indicated a small difference between the GS and GL populations,This coincides with the geographical differences between the two, while there was a significant difference between GS and NF, SF, and EF regions. According to the results of Fst, the Fst value between GS and GL is only 0.043, which is much lower than those in regions such as NF, SF, and EF. The genetic variation between regions accounted for only 18% of the total variation, while genetic variation within regions accounted for 82%, indicating that the main genetic variation comes from intraregional differentiation. The population has varying degrees of genetic differentiation, similar to previous reports (Yao et al. 2012; Zhao et al. 2022). These results have lower gene exchange between the Gushan semi-rock tea and the resources of SF, NF, and EF, making the tea resources of the Gushan Mountain region significantly different from those of SF, NF, and EF regions.
Genetic structure analysis of Gushan semi-rock tea
To further validate their phylogenetic relationships, we analyzed the population structure of 76 tea plant materials. The results of groups I and II were highly similar to those of NJ clustering, indicating that the clustering results were highly reliable. Moreover, the FZ resources are always closely related to the two populations mentioned above. This result is similar to the structure of the tomato population in the fresh market described by Sim et al. (2011). Of course, introduced varieties are mainly determined by human activities rather than natural factors (Guo et al. 2021). These cultivated varieties may then hybridize with wild tea plants due to geographical distance, weather influences (Hegland et al. 2009; Malyshev et al. 2022), and wildlife (Huo et al. 2019; Godley et al. 1967; Gervasi et al. 2017). The population structure information also showed that Gushan semi-rock tea had little communication with the genetic material of other populations. This confirms the previous conclusion from PCoA analysis that Gushan semi-rock tea resources are distinct from tea tree resources in the NF, SF, and EF regions. The results of hierarchical clustering can verify this and complement each other. Overall, the genetic information of Gushan semi-rock tea is unique.