Table 3 Statistically significant results from the pathway-level analysis of 20 tocochromanol grain traits when SNPs identified from the MLMM analysis are excluded or included as covariates in the unified mixed model
Significant Associations
CategoryCandidate GeneFunctionNo CovariatesaThree ZmVTE4 SNPs as CovariatesbTwo ZmVTE1 SNPs as CovariatescThree ZmVTE4 SNPs and two ZmVTE1 SNPs as Covariatesd
AHGGRMZM2G5738673-dehydroquinate synthaseαT, δT/αT, αT/γT, γT/(γT + αT)αT, δT/αT
AHGGRMZM2G124365chorismate mutaseαT3, Total T3, αT, δT/αTαT3, Total T3, αT, δT/αT
AHGGRMZM2G138624isochorismatase hydrolaseαT3αT3
AHGGRMZM2G437912prephenate dehydrataseTotal T3Total T3Total T3, γT3Total t3, γT3
AHGGRMZM2G070218shikimate kinaseδT/αT
PGGRMZM2G4933951-deoxy-D-xylulose 5-phosphate synthaseαT/γT, γT/(γT + αT)αT/γT, γT/(γT + αT)
PGAC209374.4_FG0022-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseαT, αT/γT, γT/(γT + αT), δT/αTαT, αT/γT, γT/(γT + αT), δT/αT
PGGRMZM2G1720322-C-methyl-D-erythritol 4-phosphate cytidyltransferaseδT3/(γT3 +αT3), δT3δT3/(γT3 + αT3)
PGGRMZM2G0270594-hydroxy-3-methylbut-2-enyldiphosphate reductaseδT3, αTδT3αT
PGGRMZM2G137409hydroxymethylbutenyl 4-diphosphate synthaseδT3/γT3
PGGRMZM2G133082isopentenyl pyrophosphate isomeraseγT/(γT + αT)γT/(γT+αT)
TPGRMZM2G009785tocopherol cyclase (ZmVTE1)δT/γT, δT3, δT3/(γT3 + αT3), δT3/αT3, δT3/γT3δT/γT, δT3, δT3/(γT3 + αT3), δT3/αT3, δT3/γT3
TPGRMZM2G035213γ-tocopherol methyltransferase (ZmVTE4)αT3, αT3/γT3, γT3/(γT3 + αT3), αT, αT/γT, δT/αT, γT/(γT + αT)αT3, αT3/γT3, γT3/(γT3 + αT3), αT, αT/γT, δT/αT, γT/(γT + αT), δT/(γT + αT)
TPGRMZM2G173358homogentisic acid geranylgeranyl transferase ZmHGGT1)Total T3, Total T/Total T3, γT3, γT3/(γT3 + αT3), αT3Total T3, Total T/Total T3, γT3, γT3/(γT3 + αT3)Total T3, Total T/Total T3, γT3, γT3/(γT3 + αT3), αT3Total T3, total T/total T3, γT3, γT3/(γT3 + αT3)
  • SNP, single-nucleotide polymorphism; MLMM, multilocus mixed model; AHG, aromatic head group; PG, prenyl group synthesis; TP, tocochromanol pathway.

  • a At least one SNP within ±250 kb of the gene open reading frame (ORF) start or stop position is associated with at least one of the indicated traits at a candidate gene-wide 5% false-discovery rate (FDR) using the unified mixed model without covariates.

  • b At least one SNP within ±250 kb of the gene ORF start or stop position is associated with at least one of the indicated traits at a pathway-wide 5% FDR using the unified mixed model with the three ZmVTE4 SNPs identified in the MLMM analysis included as covariates.

  • c At least one SNP within ±250 kb of the gene ORF start or stop position is associated with at least one of the indicated traits at a pathway-wide 5% FDR using the unified mixed model with the two ZmVTE1 SNPs identified in the MLMM analysis included as covariates.

  • d At least one SNP within ±250 kb of the gene ORF start or stop position is associated with at least one of the indicated traits at a pathway-wide 5% FDR using the unified mixed model with the three ZmVTE4 SNPs and two ZmVTE1 SNPs identified in the MLMM analysis included as covariates.