Marker-Assisted Selection at VEQ2 Increases α-Tocopherol Content in Rice Grains Without Yield Penalty

Vitamin E is an essential dietary nutrient, yet deficiency affects large populations, especially in rice-dependent developing countries. To dissect the genetic basis of grain vitamin E content in rice, we performed a genome-wide association study (GWAS) on a diverse panel of 533 rice accessions. A strongly associated locus, VEQ2, was identified on chromosome 2, where the CC genotype significantly increased α-tocopherol content compared with the TT genotype. We developed a kompetitive allele-specific PCR (KASP) marker for VEQ2 and validated its effect in an F₂ population derived from Baikezaohe (TT) and AKITAKOMACHI (CC), consistent with largely additive (incomplete dominance) inheritance. Through marker-assisted backcrossing, we introgressed VEQ2 into an elite indica background, generating near-isogenic lines. The CC introgression lines exhibited α-tocopherol and α-tocotrienol levels that were approximately 1.86- and 5.28-fold those of the control, respectively, accompanied by reduced β-tocopherol, whereas the TT lines displayed the opposite metabolic profile, with no significant penalties in agronomic traits. Analysis of 4726 accessions revealed marked differences in allele frequencies between subspecies: TT was predominant in indica (84.2%), whereas CC was nearly fixed in japonica (99.5%). Collectively, these findings demonstrate that VEQ2 is a key associated locus modulating the rice vitamin E metabolic profile and represents a promising target for biofortification of indica rice without compromising yield.