Additional file 2 of Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment

Additional file 2: Table S1. List of samples included in the study, including their origin and group. Table S2. Summary of sequenced genes and primer sequences used in this study. Table S3. Summary of nucleotide polymorphisms and neutrality tests. Table S4. The genetic diversity of rice landraces based on 48 SSRs. Table S5. The genetic diversity of rice landraces in each population. Table S6. Putative selective-sweep regions in subgroup jap-N. Table S7. Putative selective-sweep regions in subgroup jap-S. Table S8. Putative selective-sweep regions in subgroup ind-N. Table S9. Putative selective-sweep regions in subgroup ind-S. Table S10. Cloned genes located on the selection-sweep regions. Table S11. QTLs that overlapped with selection-sweep regions. Table S12. SNPs with absolute value greater than 6 for the first three components of 24 environmental factors. Table S13. SNPs with the top 25 highest |z|-scores among those candidate genes with known functions. Table S14. Summary of SSR markers and primer sequences. Table S15. The detailed information of 24 environmental factors in each population. Table S16. Summary of agronomic traits for rice landraces in each population. The value before the slash shows the data collection from Yunnan, and the value after the slash shows the data collection from Hainan.

附加文件2：表S1。本研究纳入样本清单，包含样本来源与分组信息。表S2。本研究中测序基因及所用引物序列汇总。表S3。核苷酸多态性与中性检验结果汇总。表S4。基于48个简单序列重复（Simple Sequence Repeat，SSR）标记的水稻地方品种遗传多样性分析结果。表S5。各群体水稻地方品种的遗传多样性情况。表S6。粳稻北方亚群（jap-N）推定选择清除区域。表S7。粳稻南方亚群（jap-S）推定选择清除区域。表S8。籼稻北方亚群（ind-N）推定选择清除区域。表S9。籼稻南方亚群（ind-S）推定选择清除区域。表S10。位于选择清除区域的已克隆基因。表S11。与选择清除区域存在重叠的数量性状基因座（Quantitative Trait Locus，QTL）。表S12。24个环境因子前三个主成分中绝对值大于6的单核苷酸多态性（Single Nucleotide Polymorphism，SNP）位点。表S13。在具有已知功能的候选基因中，|z|值排名前25的单核苷酸多态性位点。表S14。SSR标记及引物序列汇总。表S15。各群体24个环境因子的详细信息。表S16。各群体水稻地方品种农艺性状汇总。斜杠前的数据为云南采集所得，斜杠后的数据为海南采集所得。