Additional file 2 of Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits

Additional file 2: Table S1. Summary of all accessions sequenced in this study. Table S2. Distribution of SNPs within various genomic regions in Tartary buckwheat. Table S3. Distribution of indels within various genomic regions. Table S4. The validation of random selected SNPs by PCR methods. Table S5. Levels of genetic differentiation in different chromosomes. Table S6. 13 agronomic and quality traits used in GWAS. Table S7. Putative regions and genes experiencing domestication sweep between HW and SL. Table S8. Putative regions and genes experiencing domestication sweep between HW and NL. Table S9. Putative regions and genes experiencing domestication sweep between HW and SL calculated by DCMS. Table S10. Putative regions and genes experiencing domestication sweep between HW and NL calculated by DCMS. Table S11. Putative regions and genes experiencing differentiation sweep between SL and NL. Table S12. Putative regions and genes experiencing domestication sweep between HW and SL. Table S13. Putative regions and genes experiencing domestication sweep between HW and NL. Table S14. Regions identified by Fst approaches overlapped with the SL or NL unique selective sweep regions. Table S15. Overlaps between domesticated regions and GWAS signals for all traits. Table S16. Overlaps between domesticated regions and GWAS signals for all traits calculated by DCMS. Table S17. Overlaps between differentiated regions and GWAS signals for all traits. Table S18. SNP analysis associated with Ft1:4617722 for kaempferol-3-O-rutinoside content (-logP > 5). Table S19. Identification of candidate genes associated with Ft1:4617722 on Chr.1 for kaempferol-3-O-rutinoside content. Table S20. Information of the candidate genes from GWAS analysis. Table S21. Total SNPs for GWAS on 1000-gain-weight (-logP > 5). Table S22. Identification of candidate genes associated with Ft4:46350596 on Chr.4 for 1000-gain-weight. Table S23. The information of FtPinG0404616900 potential target genes from GWAS on 1000-gain-weight. Table S24. Primers used in this study.

附加文件2：
表S1：本研究中所有测序种质材料的汇总信息。
表S2：鞑靼荞麦（Tartary buckwheat）不同基因组区域内的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）分布情况。
表S3：不同基因组区域内的插入缺失变异（Insertions and Deletions, indels）分布情况。
表S4：采用聚合酶链式反应（Polymerase Chain Reaction, PCR）方法对随机选取的单核苷酸多态性位点进行验证的结果。
表S5：不同染色体的遗传分化程度。
表S6：全基因组关联分析（Genome-Wide Association Study, GWAS）中使用的13个农艺性状与品质性状。
表S7：HW与SL之间存在驯化选择性清除的推定区域及相关基因。
表S8：HW与NL之间存在驯化选择性清除的推定区域及相关基因。
表S9：采用DCMS方法计算得到的HW与SL之间存在驯化选择性清除的推定区域及相关基因。
表S10：采用DCMS方法计算得到的HW与NL之间存在驯化选择性清除的推定区域及相关基因。
表S11：SL与NL之间存在分化选择性清除的推定区域及相关基因。
表S12：HW与SL之间存在驯化选择性清除的推定区域及相关基因。
表S13：HW与NL之间存在驯化选择性清除的推定区域及相关基因。
表S14：通过固定指数（Fixation Index, Fst）方法鉴定出的与SL或NL特异性选择性清除区域重叠的区域。
表S15：所有性状的驯化选择性清除区域与全基因组关联分析（GWAS）信号的重叠情况。
表S16：采用DCMS方法计算得到的所有性状的驯化选择性清除区域与全基因组关联分析（GWAS）信号的重叠情况。
表S17：所有性状的分化区域与全基因组关联分析（GWAS）信号的重叠情况。
表S18：与山奈酚-3-O-芸香糖苷（kaempferol-3-O-rutinoside）含量相关的Ft1:4617722位点的单核苷酸多态性分析（-logP > 5）。
表S19：位于1号染色体上与山奈酚-3-O-芸香糖苷含量相关的Ft1:4617722位点候选基因的鉴定结果。
表S20：全基因组关联分析（GWAS）得到的候选基因信息。
表S21：针对1000-gain-weight开展全基因组关联分析（GWAS）的总单核苷酸多态性位点（-logP > 5）。
表S22：位于4号染色体上与1000-gain-weight相关的Ft4:46350596位点候选基因的鉴定结果。
表S23：针对1000-gain-weight开展全基因组关联分析（GWAS）得到的FtPinG0404616900潜在靶基因的信息。
表S24：本研究中使用的引物信息。