Table 3 Mean prediction accuracies and significant marker associations for 15 grain carotenoid traits
Significant marker associations within ±3 kb of a candidate gene
TraitMean prediction accuracySignificant marker associations (10% FDR)Partial r2 of most significant markerP-value of most significant markerTotalPer candidate gene
β-Xanthophylls/α-xanthophylls0.714240.145.05E-1613zep1 (2), lcyE (11)
β-Carotenoids/α-carotenoids0.58740.172.08E-093lcyE (3)
Zeaxanthin0.518110.192.22E-094zep1 (2), lcyE, crtRB1
Lutein0.50930.346.28E-092lcyE (2)
α-Carotene/zeinoxanthin0.50630.193.31E-101lut1
Zeinoxanthin0.48840.148.95E-081lut1
β-Cryptoxanthin0.43910.131.66E-070
Zeinoxanthin/lutein0.43230.154.97E-081lut1
β-Carotene/β-cryptoxanthin0.39500.125.38E-070
α-Carotene0.39000.14.93E-060
Acyclic and monocyclic carotenes0.34500.15.72E-060
Provitamin A0.34200.15.81E-060
β-Cryptoxanthin/zeaxanthin0.33200.13.41E-060
Total carotenoids0.23100.115.80E-060
β-Carotene0.20800.091.46E-050
  • Mean prediction accuracies, significant marker associations, and the partial r2 and P-values of the most significant marker of each trait from a GWAS for the 15 priority grain carotenoid traits. Mean prediction accuracies were obtained by averaging across RR-BLUP, LASSO, and elastic net analysis prediction methods and carotenoid QTL-targeted, pathway-level, and genome-wide marker sets. A 10% FDR threshold was used to determine significance. A full list of significant marker associations detected for each trait in GWAS without covariates, including those located within ±3 kb of a candidate gene, can be found in Table S8A.