Tocopherols, known as members of vitamin E, are the major lipophilic antioxidants in soybean. Since soybean seeds contain a low concentration of α-tocopherol (α-Toc), the tocopherol isoform with the highest vitamin E activity, some breeding efforts have been implemented to increase the α-tocopherol content in the seeds. In the present study, we used F
2 seed and F
2 plant (F
3 seeds) populations derived from a cross between a variety with a high α-tocopherol content, Keszthelyi A.S. (α-Toc 20–30%) and a Japanese cultivar, Ichihime (α-Toc < 10%) for genetic analysis of the high α-tocopherol concentration. There was no significant correlation between the α-tocopherol and total tocopherol contents in the F
2 plant (F
3 seeds) population, suggesting that the α-tocopherol and total tocopherol contents were regulated independently in the seeds. Therefore, it may be possible to increase the α-tocopherol concentration without affecting the total tocopherol content. Broad-sense heritability value for the α-tocopherol concentration trait was estimated to be 0.645 in the F
2 seeds, suggesting that the α-tocopherol concentration trait was highly heritable. Chi-square goodness-of-fit test for evaluating the relationship between genotype of certain SSR markers and the α-tocopherol concentration showed that the Sat_243 and Sat_167 markers (linkage group K) were significantly associated with the α-tocopherol concentration (P < 0.05). These markers could be used for marker-assisted selection to breed soybean cultivars with high α-tocopherol concentrations. Analysis of the F
2 seeds and the F
2 plants (F
3 seeds) for tocopherol composition showed that there was a significantly negative correlation between the α-tocopherol and γ-tocopherol concentrations, suggesting that the activity of γ-tocopherol methyltransferase, the enzyme that converts γ-tocopherol to α-tocopherol, is high in individuals with a high α-tocopherol concentration.
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