Duplications That Suppress and Deletions That Restore Expression from a Chalcone Synthase Multigene Family.

Abstract

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.

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

“…3d and Supplementary Fig. 11b), respectively 21 .We also detected a GWAS signal responsible for purple or white flower color at the W1 locus 22 and a GWAS signal corresponding to seed coat color variation at the I locus [23][24][25] . We found that these two signals underwent selection during domestication and improvement, respectively (Supplementary Fig.…”

Repression of seed coat pigmentation in Ethiopian mustard

“…The inhibition of seed coat pigment synthesis, or the dominance of the absence of pigment over its presence, has been demonstrated in a recent study in soybean (Todd and Vodkin 1996). In that study, the absence of the pigment in the seed coat was controlled by a dominant allele, l, which inhibited pigment synthesis whereas the recessive allele, i, conferred a pigmented seed coat phenotype.…”

“…In genotypes homozygous for the l allele (yellow seeds) and l i (yellow seeds with pigmented hilum), the chalcone synthase enzyme activity was seven to ten fold lower as compared with genotypes homozygous for i alleles (pigmented seed coat). Todd and Vodkin (1996) also indicated that chalcone synthase was coded by a family of seven duplicated genes, and their partial deletion restored pigment synthesis. This observation of soybean seed colour inheritance is the first publication that provides molecular evidence for the existence of a repressor locus that controls seed coat pigment synthesis, and we believe that our segregation data in B. carinata could be interpreted on the same basis, even though we have no molecular evidence for the presence of a repressor locus.…”

A deletion mutation at the ep locus causes low seed coat peroxidase activity in soybean

“…Structural gene rearrangements may also have unpredictable consequences on gene expression. The I locus controlling soybean seed coat coloration comprises several chalcone synthase genes that interact to produce a variety of pigmentation phenotypes (Todd and Vodkin, 1996). Allelic variation at the Ep locus of soybean is naturally occurring and commercially important since this affects the amount of peroxidase enzyme contained in the seed coat.…”