A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels

Supporting Information

Supporting Information

Supporting Information - Figures S1-S14 and Tables S1-S11 (PDF, 3 MB)
Figure S1 - Genome-wide association study (GWAS) of a binary kernel color trait: white vs. non-white. (PDF, 345 KB)
Figure S2 - Genome-wide association study (GWAS) of 24 carotenoid grain traits. (PDF, 1 MB)
Figure S3 - Genome-wide association study (GWAS) for total β-xanthophylls content in maize grain. (PDF, 360 KB)
Figure S4 - Genome-wide association study (GWAS) for the ratio of total β-xanthophylls to total α-xanthophylls content in maize grain. (PDF, 360 KB)
Figure S5 - Genome-wide association study (GWAS) for the ratio of zeinoxanthin to lutein content in maize grain. (PDF, 356 KB)
Figure S6 - Genome-wide association study (GWAS) for zeinoxanthin content in maize grain. (PDF, 358 KB)
Figure S7 - Genome-wide association study (GWAS) for zeaxanthin content in maize grain. (PDF, 378 KB)
Figure S8 - Genome-wide association study (GWAS) for lutein content in maize grain. (PDF, 381 KB)
Figure S9 - Genome-wide association study (GWAS) for total β-xanthophyll content in maize grain. (PDF, 383 KB)
Figure S10 - Genome-wide association study (GWAS) for total α-xanthophyll content in maize grain. (PDF, 381 KB)
Figure S11 - Genome-wide association study (GWAS) for the ratio of β-carotenoid to α-carotenoid content in maize grain. (PDF, 382 KB)
Figure S12 - Genome-wide association study (GWAS) for zeaxanthin content in maize grain. (PDF, 366 KB)
Figure S13 - Genome-wide association study (GWAS) for zeaxanthin content in maize grain. (PDF, 361 KB)
Figure S14 - Genome-wide association study (GWAS) for total β-xanthophyll content in maize grain. (PDF, 361 KB)
Table S2 - Coordinates for Additional Insertion-Deletion (Indel) and Single-Nucleotide Polymorphism (SNP) Markers. (PDF, 326 KB)
Table S3 - (A) Genomic Information for the 58 a priori Candidate Genes. (B) Genomic Information for the 8 a priori Candidate Genes. (PDF, 447 KB)
Table S4 - Genomic Prediction Model Specifications. (PDF, 314 KB)
Table S5 - BLUPs and Heritabilities for 9 Carotenoid Traits. (PDF, 318 KB)
Table S6 - Correlation Matrix for Untransformed BLUPs of the 24 Carotenoid Traits. (PDF, 455 KB)
Table S7 - Variance Component Estimates from Mixed Linear Models Fitted to 24 Grain Carotenoid Traits. (PDF, 432 KB)
Table S8 - Genome-wide Association Study Results with (A) No Covariates, (B) Covariate from zep1, (C) Covariate from lut1, (D) Covariates for lcyE, (E) S8_171705574 Covariate, (F) Covariate for crtRB1, and (G) Covariates for lut1, zep1, lcyE and crtRB1. (PDF, 808 KB)
Table S9 - (A) Results from the Pathway-level Analysis with (A) No Covariates, (B) S2_44448432 as Covariate Tagging zep1, (C) ss196425306 as Covariate Tagging lut1, (D) S8_138882897 and lcyE SNP216 as Covariates Tagging lcyE, (E) S8_171705574 Covariate, (F) crtRB1_3'TE as Covariate Tagging crtRB1, and (G) Covariates Tagging lut1, zep1, lcyE, and crtRB1. (PDF, 1 MB)
Table S10 - Comparison of Genomic Prediction Methods for 24 Grain Carotenoid Traits using Three Marker Sets as Predictors. (PDF, 443 KB)
Table S11 - Prediction Accuracies for 24 Grain Carotenoid Traits using the Carotenoid QTL-Targeted Prediction Marker Set Relative to Random Marker Sets. (PDF, 323 KB)
Table S1 - Best Linear Unbiased Predictor (BLUP) Values. BLUP values for the 24 carotenoid traits used for the genome-wide association study, pathway-level analysis, and genomic prediction for 201 inbred maize lines. (.xlsx, 53 KB)