Additional file 3 of Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

Additional file 3: Table S1. Sampling localities of 159 wild tea accessions

Additional file 4 of Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

Additional file 4: Table S1. Genotyping of 98,241 SNPs based on GBS in 159 wild tea accessions

Additional file 2 of Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

Additional file 2: Figure S1. Geographic distribution of 159 materials collected at different altitudes and rock types. Note: (A) Geographical position. (B) Distribution map of altitude, rock type and sample point in Guizhou Plateau. Figure S2. Graph for CV error in the range of K=1-9 of 159 wild tea accessions. Figure S3. ML tree of four geologically suitable areas. Note: I Dolomite sub-suitable area, II Dolomitic limestone suitable area, III Clastic rock most suitable area, IV Purple clastic rock suitable area

Additional file 1 of Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

Additional file 1: Table S1. Information of 159 wild tea accessions used in this study. Table S2. The quality control data of 159 wild tea accessions. Table S3. Statistics of Heterozygosity Rate of 98,241 SNPs in 159 wild tea accessions. Table S4. SNP density. Table S5. Statistics of the number and ratio of the accessions of species, rock classes and geologically suitable area in three inferred populations. Table S6. Statistics of the number and ratio of the accessions of altitude gradient in three inferred populations. Table S7. The soil nutrient content and altitude factor of 159 wild tea accessions

Additional file 1 of Genome-wide association study, population structure, and genetic diversity of the tea plant in Guizhou Plateau

Additional file 1: table S1. Information of 415 tea accessions used in this study. Table S2. Statistics of the number and ratio of the accessions of cultivation status, species classification and indigenous communities in six inferred populations. Table S3. Statistics of the number and ratio of the accessions of near ancient hubs and near rivers in six inferred populations

Additional file 1 of Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing

Additional file 1: Figure S1. Dynamics of population structure under different K (K = 2-9) values of 338 tea accessions. Figure S2. The Q-Q plots and Manhattan plots of other models of 4 traits except the optimal model. (A1) MLZ-2019-cMLM-Q+K; (A2) MLZ-2019-GLM-P; (A3) MLZ-2019-GLM-Q; (A4) MLZ-2019-MLM-P+K; (A5) MLZ-2019-MLM-Q+K; (B1) MLZ-2020-cMLM-Q+K; (B2) MLZ- 2020-GLM-P; (B3) MLZ-2020-GLM-Q; (B4) MLZ-2020-MLM-P+K; (B5) MLZ-2020-MLM-Q+K; (C1) MLZ-2021-cMLM-Q+K; (C2) MLZ-2021-GLM-P; (C3) MLZ-2021-GLM-Q; (C4) MLZ-2021-MLM-P+K; (C5) MLZ-2021-MLM-Q+K; (D1) MLC-cMLM-P+K; (D2) MLC-cMLM-Q+K; (D3) MLC-GLM-P; (D4) MLC-MLM-P+K; (D5) MLC-MLM-Q+K; (E1) MLS-cMLM-Q+K; (E2) MLS-GLM-P; (E3) MLS-GLM-Q; (E4) MLS-MLM-P+K; (E5) MLS-MLM-Q+K; (F1) MLT-cMLM-P+K; (F2) MLT-cMLM-Q+K; (F3) MLT-GLM-Q; (F4) MLT-MLM-P+K; (F5) MLT-MLM-Q+K. Figure S3. The labeled complete gels of PCR products of six tea accessions using the dCAPS primer. Table S1. The quality control (QC) data of each sample. Table S2. Genotyping of 100,829 SNPs based on GBS in 168 tea accessions. Table S3. Genotyping of 100,829 SNPs based on GBS in 170 tea accessions. Table S4. Distribution information of 100,829 SNPs on 15 chromosomes of tea plant.Table S5. Information of 338 tea accessions used in the present study. Table S6. Statistics of the number and ratio of the accessions of species, and both cultivation status in five inferred populations.Table S7. Analysis of TEA005350.1 gene expression of 15 tea plant accessions. Table S8. Analysis of TEA027527.1 gene expression of 20 tea plant accessions. Table S9. Four leaf phenotypic traits (mature leaf size, mature leaf color, mature leaf shape and mature leaf texture) data and their assignment of 338 tea accessions in 2019, 2020 and 2021, respectively

Additional file 3: of Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing

Figure S1. Graphical method allowing the detection of the number of groups using ∆K inferred population structure of the 263 Pure Cultivation Type. Figure S2. Inferred population structure of the 263Pure Cultivation Type using STRUCTURE software. Bar plot of individual ancestry proportions for the genetic clusters inferred using STRUCTURE (K = 2) and the reduced dataset. Individual ancestry proportions (q values) are sorted within each cluster. Admixture model, independent frequencies, 30,000 burn-in iterations, 100,000 Markov Chain Monte Carlo iterations were used for this analysis. Ancient landraces (GP03–1) and modern landraces (GP03–2) are shown in yellow and green, respectively. Figure S3.. Four inferred populations of the 415tea accessions using STRUCTURE (K = 3). GP01 are shown in red, GP02 are shown in red and blue, GP03–1 are shown in blue, and GP03–2 are shown in green. (PDF 207 kb

Additional file 1: of Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing

Table S1. The quality control (QC) data of each sample. Table S2. Statistics of individual heterozygosity of 287,408 SNPs based on GBS. Table S3.. Statistics of individual heterozygosity of 79,016 SNPs based on GBS. Table S4. SNP density of scaffolds based on GBS. Table S5. The p-value of genetic diversity parameters in Table 2 based on independent-samples T-test. Table S6. Genetic diversity parameters of three species of tea plants in Guizhou Plateau. Table S7. Fst and pairwise genetic distance among three Species of tea plant in Guizhou Plateau (XLSX 117 kb

Additional file 5: of Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing

Geographic distribution of tea accessions analyzed in the current study according to the collection. (A) The geographical position of Guizhou province in China. (B) Agriculture climate regionalization map for tea plant growth in Guizhou Plateau [35]. Ia: Area with a very suitable climate for tea plant growth in North of Guizhou; Ib: Area with a very suitable climate for tea plants growth in East of Guizhou; Ic: Area with a very suitable climate for tea plants growth in South of Guizhou; II: Area with a suitable climate for tea plant growth in Center of Guizhou; III: Area with a minor suitable climate for tea plant growth in West of Guizhou; IV: Area with an unsuitable climate for tea plants growth in West of Guizhou. (PDF 157 kb

Additional file 4: of Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing

Average LD decay (r2) estimated against the genetic distance for pairs of linked SNP across all scaffolds longer than 500 kb in the 415 accessions (ALL) and four inferred groups (GP01, GP02, GP03–1and GP03–2). (PDF 220 kb