A Microsatellite Marker For Analysis of Hilum Color Variation in Soybean [Glycine Max (L.) MERR.] Genotypes​

Soybean varieties with light-colored or yellow seed coat and hilum are most often preferred by soy food processors and thus, have higher marketability. As such, seed hilum color is one of the attributes regarded in the criteria for production of food-grade soybean by plant breeders. Given the moderately complex genetic control of soybean pigmentation, the application of molecular markers is seen to benefit higher precision in selection for soybean breeding in lieu of relying on selection based on phenotype alone. This study utilized the inhibitor (I) locus-based microsatellite marker SM305 in the analysis of 110 soybean genotypes from different collections for variation in hilum color. Initial screening exhibited a presence or absence of heterozygous alleles (between 100-200 bp) wherein 66.36% were found to have a pattern in which SM305 bands were present in genotypes with darker-colored hilum while absent in genotypes with light-colored hilum. To corroborate these observations, 24 genotypes from the pool with the latter marker-trait pattern, with contrary observations, and with inconsistent phenotype among replicates, were used with a more streamlined approach – seed phenotype uniformity was examined, DNA pooling among leaf samples was eliminated, better DNA quality was obtained using root-extracted DNA with the CTAB method, and a color chart was used for phenotyping. Results from screening the 24 genotypes with SM305 consistently yielded the findings wherein the heterozygous alleles were present in soybean genotypes with pigmented (buff, brown, imperfect black and black) hilum while absent in those with non-pigmented (yellow) hilum. No genotype variation was observed among soybeans with pigmented hilum, regardless whether their respective seed coats were yellow or black. Overall, genotyping of the selected soybean population using SM305 was sufficient to distinguish
for the preferred phenotype. Succeeding breeding plans must be measured to consider results from F2 generations. Elucidating structural variations between DNA of non-pigmented and pigmented hilum soybean genotypes is also another aspect to explore. This preliminary screening fundamentally aspires to forward a verified marker for marker-assisted selection in soybean breeding.