Seed coat color in soybean is determined by four alleles of the classically defined I (inhibitor) locus that controls the presence or absence as well as the spatial distribution of anthocyanin pigments in the seed coat. By analyzing spontaneous mutations of the I locus, we demonstrated that the I locus is a region of chalcone synthase (CHS) gene dupllcations. Paradoxically, deletions of CHS gene sequences allow higher levels of CHS mRNAs and restore pigmentation to the seed coat. The unusual nature of the I locus suggests that its dominant alleles may represent naturally occurring examples of homology-dependent gene silenclng and that the spontaneous deletions erase the gene-silencing phenomena. Specifically, mutations from the dominant i ‘ allele (yellow seed coats wlth pigmented hila) to the recessive i allele (fully pigmented) can be associated wlth the absence of a 2.3-W Hindlll fragment that carries CHS4, a member of the multigene CHS family. Seven independent mutatlons exhibit deletions in the CHS4 promoter mgion. The dominant I allele (yellow seed coats) exhibits an extra 12.1-kb Hindlll fragment that hybridlzes with both the CHS coding region and CHSí promoter-specific probes. Mutatlons of the dominant I allele to the mcessive i allele (pigmented seed coats) give rise to 10.4- or 9.6-kb Hindlll CHS fragments that have lost the duplicated CHSí promoter. Finally, gene expression analysis demonstrated that heterozygous plants (//i) wlth yellow seed coats have reduced mRNA levels, indlcatlng that the 12.1-kb Hindlll CHS fragment associated with the dominant I allele inhibits pigmentation in a trans-dominant manner. Moreover, CHS gene-specific expression in seed coats shows that multiple CHS genes are expressed ln seed coats
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