Additional file 2 of Genome-wide association studies of ionomic and agronomic traits in USDA mini core collection of rice and comparative analyses of different mapping methods
Creators: name: Liu, Shuai
name: Zhong, Hua
name: Meng, Xiaoxi
name: Sun, Tong
name: Li, Yangsheng
name: Pinson, Shannon R. M.
name: Chang, Sam K. C.
name: Peng, Zhaohua
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Supplementary Figure 2. (a). Genome-wide association analysis for As with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). Red arrow indicates published gene, black arrow indicates candidate gene. The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (b) Genome-wide association analysis for Cd with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). Black arrows indicate candidate genes. The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (c) Genome-wide association analysis for Cd with GLM, MLM, MLMM, and FarmCPU methods (left) in unflooded condition. Quantile-quantile plot of each model (right). Black arrows indicate candidate genes. The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (d) Genome-wide association analysis for Cu with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (e) Genome-wide association analysis for Co with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (f) Genome-wide association analysis for Fe with GLM, MLM, MLMM, and FarmCPU methods (left) in unflooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni -corrected significance thresholds and SNPs at −log10(P) = 8.51. (g) Genome-wide association analysis for K with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (h) Genome-wide association analysis for Mo with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (i) Genome-wide association analysis for Mo with GLM, MLM, MLMM, and FarmCPU methods (left) in unflooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (j) Genome-wide association analysis for Ni with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (k) Genome-wide association analysis for Ni with GLM, MLM, MLMM, and FarmCPU methods (left) in unflooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni -corrected significance thresholds and SNPs at −log10(P) = 8.51. (l) Genome-wide association analysis for Rb with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (m) Genome-wide association analysis for Sr with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (n) Genome-wide association analysis for Zn with GLM, MLM, MLMM, and FarmCPU methods (left) in flooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51. (o) Genome-wide association analysis for Zn with GLM, MLM, MLMM, and FarmCPU methods (left) in unflooded condition. Quantile-quantile plot of each model (right). The horizontal dot grey line and green dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 7.81. The horizontal solid grey line and red dots indicate the Bonferroni-corrected significance thresholds and SNPs at −log10(P) = 8.51.