Additional file 2 of Genome-wide association study for resistance in bread wheat (Triticum aestivum L.) to stripe rust (Puccinia striiformis f. sp. tritici) races in Argentina

Additional file 2: Supplementary Figure S1. Structure analysis in the spring wheat association-mapping panel. a) The STRUCTURE analysis showed four hypothetical subpopulations represented by different colors. b) First two components (PC1 and PC2) of a principal component analysis of the spring wheat accessions color coded by breeding program (adapted from Zhang, et al. [45]). c) Neighbor-joining phylogenetic tree showing the subpopulations corresponding to the structure analysis. Supplementary Figure S2. Quantile-quantile (QQ) plots of the observed and the expected p values of the GWAS model. a) QQ-plot for seedling resistance (infection type -IT- for the races Yr19-71 and Yr20-161); b) QQ-plot for Adult plant resistance (Disease Severity and area under disease progress curve –AUDPC-). Supplementary Figure S3. Linkage disequilibrium (LD) decay over physical distance. The scatter plots showing pairwise SNP markers LD r2 value as a function of inter-marker physical distances (Mbp) of (a) 1B chromosome; (b) 2A chromosome; (c) 3A chromosome; (d) 3B chromosome; (e) 5B chromosome; (f) 7A chromosome. The red curve represents the model fit to LD decay. The blue dashed line represents the specific critical r2 value beyond which LD is likely due to linkage. The green dashed line represents the confidence interval for the quantitative trait loci regions in which LD r2 = critical r2 value.附加文件2：补充图S1。春小麦关联作图群体的结构分析。a) STRUCTURE分析显示4个假想亚群，以不同颜色区分。b) 春小麦材料主成分分析的前两个主成分（PC1与PC2），按育种项目着色（改编自Zhang等[45]）。c) 邻接系统发育树，展示与STRUCTURE分析对应的亚群。 补充图S2：全基因组关联分析（Genome-Wide Association Study, GWAS）模型观测p值与预期p值的分位数-分位数（QQ）图。a) 苗期抗性（针对生理小种Yr19-71与Yr20-161的侵染型（Infection Type, IT））的QQ图；b) 成株抗性（病情严重度及病情进展曲线下面积（Area Under Disease Progress Curve, AUDPC））的QQ图。 补充图S3：连锁不平衡（Linkage Disequilibrium, LD）随物理距离的衰减规律。散点图展示成对单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记的LD r²值随标记间物理距离（单位：Mbp）的变化关系，分别为(a) 1B染色体；(b) 2A染色体；(c) 3A染色体；(d) 3B染色体；(e) 5B染色体；(f) 7A染色体。红色曲线为拟合LD衰减的模型曲线；蓝色虚线代表临界r²值，超过该值的LD大概率由连锁导致；绿色虚线代表LD r²等于临界r²值的数量性状位点（Quantitative Trait Loci, QTL）区域的置信区间。