Additional file 1 of Genetic Diversity and Breeding Signatures for Regional Indica Rice Improvement in Guangdong of Southern China

Additional file 1: Table S1. Information for accessions used in this study. Table S2. Quality assessment of genome sequencing data. Table S3. Genome mapping quality and genome coverage of genome sequencing data. Table S4. Genomic variations for 517 indica rice accessions against the MSU reference genome. Table S5. Number of deleterious variations in subpopulation of landrace and cultivar. Table S6. Genotyping results 319 quantitative trait nucleotidesof the 212 vital gene in rice from RiceNavi database. Table S7. Genomic segments that identified as breeding signatures between Ind IV and Ind II. Table S8. Genomic segments that identified as breeding signatures between Ind I and Ind II. Table S9. QTLs and known genes that identified by GWAS of eleven agronomic traits for Guangdong indica rice. Table S10. Allele combinations of plant heightgenes of Guangdong indica rice germplasm. Table S11. Allele combinations of thousand grain weight, grain length, grain widthand grain length width ratiogenes of Guangdong indica rice germplasm. Table S12. Phenotypic effect assessment of known QTNs that genotyped by RiceNavi. Table S13. Genotyping of 4 eating quality genes.

附加文件1：表S1 本研究使用的供试种质材料信息。表S2 基因组测序数据质量评估结果。表S3 基因组测序数据的基因组比对质量与覆盖度。表S4 517份籼稻种质材料相对于MSU参考基因组的基因组变异信息。表S5 地方品种与栽培品种亚群中的有害变异数量。表S6 来自RiceNavi数据库的水稻212个关键基因的319个数量性状核苷酸（Quantitative Trait Nucleotide, QTN）的基因型分型结果。表S7 印度亚种IV与印度亚种II之间鉴定到的育种选择印记基因组区段。表S8 印度亚种I与印度亚种II之间鉴定到的育种选择印记基因组区段。表S9 广东籼稻11个农艺性状全基因组关联分析（Genome-Wide Association Study, GWAS）鉴定到的数量性状基因座（Quantitative Trait Locus, QTL）与已知功能基因。表S10 广东籼稻种质资源的株高基因等位基因组合。表S11 广东籼稻种质资源的千粒重、粒长、粒宽及粒长宽比基因的等位基因组合。表S12 经RiceNavi数据库分型的已知数量性状核苷酸的表型效应评估结果。表S13 4个稻米食味品质基因的基因型分型结果。