Additional file 2 of Improving genomic prediction of vitamin C content in spinach using GWAS-derived markers

Supplementary Material 2: Figure S1. Distribution of the 147,977 single nucleotide polymorphism (SNP) markers on the 6 chromosomes of spinach. Spinach chromosomes are on the vertical axis. Chromosome length in Mb is on the horizontal axis, and the color represents the number of SNPs per 1 Mb window size, SNP density. Figure S2. |Population structure and phylogeny analysis of 347 spinach accessions. A. Population stratification into three population groups based on ΔK analysis. Two (SQ1 and SQ2) and three (SQ1, SQ2 and SQ3) populations estimated from the admixture model (horizontal axis denotes accessions and vertical axis denotes probability values). B. Phylogenetic tree of two and three sub-populations by neighbor-joining (NJ) method drawn by GAPIT 3 in 347 spinach lines, where PCA = 2 (left) and PCA = 3 (right). Figure S3. The Manhattan and quantile–quantile (QQ) plots of BLINK, FarmCPU, and MLM models for ascorbic acid (AsA) content by GAPIT 3. The x-axis and y-axis in the Manhattan plots denote log10 ( P ) values and identified SNPs on spinach chromosomes. And x-axis and y-axis in the QQ plots denotes observed and expected log10 ( P ) values. Figure S4. The Manhattan and QQ-plot of SMR, GLM, and MLM models for ascorbic acid (AsA) content by TASSEL 5. The x-axis and y-axis in the Manhattan plots denote log10 ( P ) values and identified SNPs on spinach chromosomes. And x-axis and y-axis in the QQ plots denotes observed and expected log10 ( P ) values. Figure S5. Display of LD plots with SNPs on haplotype blocks in different chromosomes of spinach genome. A. Chr. 1, B. Chr. 2, C. Chr. 3, D. Chr. 4, E. Chr. 5, and F. Chr. 6. The triangle (black color) on respective chromosome represents different blocks with VC related SNP markers. Figure S6. Genomic prediction for ascorbic acid (AsA) content in 347 spinach lines, where (top) fourteen different SNP number sets from 12 randomly selected SNPs to 60,000 SNPs and two GWAS SNP marker sets estimated by seven GP models. A. Genomic prediction of Bayes A (BA), Bayes B (BB), Bayes LASSO (BL), and Bayes ridge regression (BRR); B. Genomic prediction of Random forests (RF), ridge-regression best linear unbiased prediction (rrBLUP) and Support vector machines (SVM). C. Genomic prediction of BRR model. Y-axis shows PA (r-value) and X-axis shows GP models in all the plots, and D. Genomic prediction using seven GP models using r1000 and m12 and m62 SNP sets