Cloning of the Pleiotropic T Locus in Soybean and Two Recessive Alleles That Differentially Affect Structure and Expression of the Encoded Flavonoid 3 Hydroxylase

Three loci (I, R, and T) control pigmentation of the seed coats in Glycine max and are genetically distinct from those controlling flower color. The T locus also controls color of the trichome hairs. We report the identification and isolation of a flavonoid 3ʹ hydroxylase gene from G. max (GmF3ʹH) and the linkage of this gene to the T locus. This GmF3ʹH gene was highly expressed in early stages of seed coat development and was expressed at very low levels or not at all in other tissues. Evidence that the GmF3ʹH gene is linked to the T locus came from the occurrence of multiple RFLPs in lines with varying alleles of the T locus, as well as in a population of plants segregating at that locus. GmF3ʹH genomic and cDNA sequence analysis of color mutant lines with varying t alleles revealed a frameshift mutation in one of the alleles. In another line derived from a mutable genetic stock, the abundance of the mRNAs for GmF3ʹH was dramatically reduced. Isolation of the GmF3ʹH gene and its identification as the T locus will enable investigation of the pleiotropic effects of the T locus on cell wall integrity and its involvement in the regulation of the multiple branches of the flavonoid pathway in soybean.