Additional file 1 of Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat

Additional file 1: Table S1. Summary of the 567 Tartary buckwheat accessions and 7 outgroup accessions used in this study with the mapping rate, depth and coverage. Table S2. Distribution of SNPs into various genomic regions in Tartary buckwheat. Table S3. Statistical differences between pairwise FST values between the different populations. Table S4. Genomic fragments with evidence for introgression based on Fd and FdM.Table S5. Interpopulation introgression based on D- statistics. Table S6. Putative selective sweeps between HW and SL based on XP-CLR analysis. Table S7. Putative selective sweeps between HW and NL based on XP-CLR analysis.Table S8. Genes in selective sweeps in both between HW and SL and between HW and NL based on XP-CLR analysis. Table S9. Putative selective sweeps between HW and SL based on DCMS analysis. Table S10. Putative selective sweeps between HW and NL based on DCMS analysis. Table S11. Genes in selective sweeps in both between HW and SL and between HW and NL based on DCMS analysis. Table S12. Candidate genes associated with disease index identified by GWAS with MAF >= 0.01. Table S13. Putative selective sweeps between SL and NL based on XP-CLR. Table S14. Putative selective sweeps between SL and NL based on DCMS. Table S15. Salt tolerance of Tartary buckwheat accessions. Table S16. Candidate genes associated with salt tolerance identified by GWAS. Table S17. Sequencing reads used for assembly of EDT. Table S18. Assembly statistics of the EDT genome. Table S19. BUSCO analysis of the EDT genome. Table S20. Genetic differences between EDT and DDT. Table S21. The expression of genes with insertions and deletions within the QTL inverval. Table S22. Summary of FtXIP insertion promoter cis-acting elements prediction in 1,400 bp region. Table S23. Primers used in this study.

附加文件1：表S1。本研究使用的567份苦荞（Tartary buckwheat）种质资源与7份外类群种质资源的概况，包含比对率、测序深度及覆盖度信息。
表S2。单核苷酸多态性（Single Nucleotide Polymorphism, SNP）在苦荞不同基因组区域的分布情况。
表S3。不同种群间成对FST值的统计学差异。
表S4。基于Fd和FdM检测到存在基因渐渗证据的基因组片段。
表S5。基于D-统计量（D-statistics）的种群间基因渐渗分析结果。
表S6。基于XP-CLR分析得到的HW与SL种群间的潜在选择性清除区域。
表S7。基于XP-CLR分析得到的HW与NL种群间的潜在选择性清除区域。
表S8。基于XP-CLR分析，在HW与SL、HW与NL两组种群对比中均检测到的选择性清除区域内的基因。
表S9。基于DCMS分析得到的HW与SL种群间的潜在选择性清除区域。
表S10。基于DCMS分析得到的HW与NL种群间的潜在选择性清除区域。
表S11。基于DCMS分析，在HW与SL、HW与NL两组种群对比中均检测到的选择性清除区域内的基因。
表S12。通过最小等位基因频率（Minor Allele Frequency, MAF）≥0.01的全基因组关联分析（Genome-Wide Association Study, GWAS）鉴定得到的与病害指数相关的候选基因。
表S13。基于XP-CLR分析得到的SL与NL种群间的潜在选择性清除区域。
表S14。基于DCMS分析得到的SL与NL种群间的潜在选择性清除区域。
表S15。苦荞种质资源的耐盐性鉴定结果。
表S16。通过全基因组关联分析（GWAS）鉴定得到的与耐盐性相关的候选基因。
表S17。用于EDT基因组组装的测序读段信息。
表S18。EDT基因组的组装统计结果。
表S19。EDT基因组的BUSCO（Benchmarking Universal Single-Copy Orthologs）评估结果。
表S20。EDT与DDT之间的遗传差异信息。
表S21。数量性状基因座（Quantitative Trait Locus, QTL）区间内存在插入缺失变异的基因的表达情况。
表S22。1400 bp区域内FtXIP插入位点启动子的顺式作用元件预测结果汇总。
表S23。本研究中使用的引物序列信息。