Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

Abstract

Background Tea plants originated in southwestern China. Guizhou Plateau is an original center of tea plants, and is rich in germplasm resources. However, the genetic diversity, population structure and distribution characteristics of cultivated-type tea plants in the region are unknown. In this study, we explored the genetic diversity and geographical distribution of cultivated-type tea accessions in Guizhou Plateau. Results We used 112,072 high-quality genotyping-by-sequencing to analyze the genetic diversity, principal components, phylogeny, population structure, and linkage disequilibrium, and develop a core collection of 253 cultivated-type tea plant accessions from Guizhou Plateau. The results showed Genetic diversity of the cultivated-type tea accessions of the Pearl River Basin was significantly higher than that of the cultivated-type tea accessions of the Yangtze River Basin. Three inferred pure groups (CG-1, CG-2 and CG-3) and one inferred admixture group (CG-4), were identified by a population structure analysis, and verified by principal component and phylogenetic analyses. The highest genetic distance and differentiation coefficients were determined for CG-2 vs CG-3. The lower genetic distance and differentiation coefficients were determined for CG-4 vs CG-2 and CG-4 vs CG-3, respectively. We developed a core set and a primary set. The primary and core sets contained 77.0 and 33.6% of all individuals in the initial set, respectively. The primary set may serve as the primary population in genome-wide association studies, while the core collection may serve as the core population in multiple treatment setting studies. Conclusions The present study demonstrated the genetic diversity and geographical distribution characteristics of cultivated-type tea plants in Guizhou Plateau. Significant differences in genetic diversity and evolutionary direction were detected between the ancient landraces of the Pearl River Basin and the those of the Yangtze River Basin. Major rivers and ancient hubs were largely responsible for the genetic exchange between the Pearl River Basin and the Yangtze River Basin ancient landraces as well as the formation of the ancient hubs evolutionary group. Genetic diversity, population structure and core collection elucidated by this study will facilitate further genetic studies, germplasm protection, and breeding of tea plants.

Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

“…In this study, a positive value of Tajima’s D was detected in the wild tea plant population, suggesting that the wild tea plant population underwent population bottlenecks and/or balancing selection (Table 2 ). Fst (differentiation coefficient) is used as a measure of population structure; Fst values of 0–0.05 and 0.05–0.15 indicate little and moderate divergence, respectively [ 25 , 26 ]. In this study, the Fst value of C. gymnogyna and C. tachangensis was 0.075, suggesting that the moderate divergence occurred in the wild tea plant population between C. gymnogyna and C. tachangensis (Table 3 ).…”

“…Previous studies showed that Fst in the range of 0.00 to 0.05 indicate little divergence, Fst in the range of 0.05 to 0.15 indicate moderate divergence and 0.15 to 0.25 indicate large divergence [ 26 , 27 ]. The pairwise Fst was analyzed among three inferred groups (Fig.…”

“…Fst has been widely used as a measure of population structure. The Fst values for wild tea plant populations of C. tachangensis and C. gymnogyn , H1 and H3, H2 and H3, areas II and III, and areas II and IV were 0.05–0.15, indicating that moderate divergence occurred in wild tea plant populations between C. tachangensis and C. gymnogyn , between H1 and H3, between H2 and H3, between areas II and III, and between areas II and IV [ 25 , 26 ].…”

“…In particular, altitude and geological environment played important roles in the distribution, population structure, and evolutionary direction of germplasm resources of wild plants [ 41 , 42 ]. Zhao et al [ 26 ] divided cultivated tea plants in the Guizhou Plateau into four groups with reference to the river basin distribution. Our results showed that 159 wild tea plants from the Guizhou Plateau were divided into three groups—two pure groups (GP01 and GP02) and one mixed group (GP03)—and this grouping was consistent with that of the PCA and phylogenetic analysis.…”

Genome‐wide diversity evaluation and core germplasm extraction in ex situ conservation: A case of golden Camellia tunghinensis

“…First, the genetic distance matrix of 229 individuals in the wild and ex situ populations was calculated using Plink. The sampling intensity of previous core germplasms of woody plants usually ranges between 30% and 45%(Duan et al, 2017;Lv et al, 2020;Wang et al, 2016;Zhao et al, 2022). In the Camellia genus,Zhao et al (2022) determined a sampling intensity of 33.6%…”