Fig. 4: GWAS of important property traits.
a Principal component analysis (PCA) of 12 environmental factors in which the depth of color represents the contribution of the variable. b–j Manhattan plot of marker-trait associations (MTAs) identified using statistical approaches for nine traits, including a clear culm height, node number, ground diameter, density, bending strength (12°), compressive strength, elastic modulus, maximum load, and tensile modulus. The statistical approaches include EMMAX, efficient mixed-model association expedited; FarmCPU, fixed and random model circulating probability unification with high statistical power; Magma, gene-level association; ISI EM-BLASSO: based multi-locus association. The p-value threshold was 2.10 × 10−8, 2.10 × 10−8, and 1.08 × 10−6 for EMMAX, FarmCPU, and Magma by Bonferroni correction method, separately. The log of odds (LOD) threshold for ISIS EM-BLASSO method is 3 as suggested. For simplicity and clarity, only candidate SNPs were plotted. The MTAs are indicated by black triangles in the lower part of the figure. Source data are provided as a Source Data file.
