Additional file 3 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 3: Supplementary Figure 3. (a) Genome-wide association analysis for AMYLOSE with GLM, MLM, MLMM, and FarmCPU methods (left). Quantile-quantile plot of each model (right). Red arrows indicate published 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. (b) Genome-wide association analysis for AWNTYPE with GLM, MLM, MLMM, and FarmCPU methods (left). 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. (c) Genome-wide association analysis for DAYSFLOWER with GLM, MLM, MLMM, and FarmCPU methods (left). Quantile-quantile plot of each model (right). 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. (d) Genome-wide association analysis for HULLCOLOR with GLM, MLM, MLMM, and FarmCPU methods (left). 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 HULLCOVER with GLM, MLM, MLMM, and FarmCPU methods (left). 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 KERNELLEN with GLM, MLM, MLMM, and FarmCPU methods (left). Quantile-quantile plot of each model (right). Red arrow indicates published 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. (g) Genome-wide association analysis for KERNELWID with GLM, MLM, MLMM, and FarmCPU methods (left). Quantile-quantile plot of each model (right). Red arrow indicates published 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. (h) Genome-wide association analysis for KERNELRAT with GLM, MLM, MLMM, and FarmCPU methods (left). Quantile-quantile plot of each model (right). Red arrow indicates published 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. (i) Genome-wide association analysis for KERNELWTB with GLM, MLM, MLMM, and FarmCPU methods (left). 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 LODGING with GLM, MLM, MLMM, and FarmCPU methods (left). Quantile-quantile plot of each model (right). 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. (k) Genome-wide association analysis for PLANTHT with GLM, MLM, MLMM, and FarmCPU methods (left). Quantile-quantile plot of each model (right). 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.