Genome-wide association mapping and transcriptional analysis uncover genetic determinants of minor tocopherols in rice seeds

Despite the nutritional importance of tocopherols, current knowledge of the genetic architecture underlying the accumulation of minor tocopherols-gamma (γ) and delta (δ)-in rice (Oryza sativa L.) grains remains limited. In this study, we investigated the genetic basis of γ- and δ-tocopherol contents in rice using a genome-wide association study (GWAS) and post-GWAS analysis. Accordingly, 34,323 SNP markers were obtained from 179 genotypically diverse accessions of O. sativa. Minor tocopherol contents had a strong positive correlation (r = 0.76) with each other and varied greatly across the accessions: 0.015-1.74 and 0.005-0.81 (µg/g) for γ and δ, respectively. A total of 18 QTL on nine rice chromosomes were mapped. Eight transcription factor (TF) genes, five lncRNAs, and two transposons were found to be associated with the QTL. Moreover, three intracellular transport proteins were identified as associated genes with γ-tocopherol on chromosomes 1, 2, and 6. Protein kinases seem to have a substantiative function in defining the minor tocopherol contents, as they were associated with all 18 identified QTL. Haplotype analysis revealed that the QTL, namely qDelt2.1, qGam2.1, and qGam6.1, can maintain significant haplogroups. Comparative transcript analysis between high and low-content minor tocopherols demonstrated the possible involvement of ERF71 (Os06g0194000), TOR (Os05g0235300) and NAC70 (Os02g0822400) in defining the minor tocopherol contents in rice. Identified candidate genes in this study could be used in breeding programs to develop rice cultivars with high and beneficial levels of seed tocopherol contents.