Organization of soybean chalcone synthase gene clusters and characterization of a new member of the family

Akada, Shinji; Dube, Shyam K.

doi:10.1007/bf00043645

Cited by 68 publications

(75 citation statements)

References 33 publications

(36 reference statements)

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“…Williams (i') DNA is used as the reference restriction fragment length polymorphism (RFLP) pattern because all CHS sequence data are based on this cultivar (Akada et al, 1990;Akada and Dube, 1995). The CHS multigene family contains three genes that constitute a 10-kb duplication region (diagrammed in Figure 28) in the cultivar Williams (Akada and Dube, 1995).…”

Section: Many Spontaneous Mutations Of the Dominant I' Allele To The mentioning

confidence: 99%

“…The CHS multigene family contains three genes that constitute a 10-kb duplication region (diagrammed in Figure 28) in the cultivar Williams (Akada and Dube, 1995). CHSl and CHS3 are in head-to-head orientation; CHS3 and CHS4 are in tail-to-tail orientation.…”

Section: Many Spontaneous Mutations Of the Dominant I' Allele To The mentioning

confidence: 99%

“…(B) Schematic representation of the 10-kb duplication region shows the relative orientations of CHSJ, CHS3, and CHS4, as marked by the directional arrows. Triangles indicate the regions of sequence data as entered in GenBank (Akada and Dube, 1995). The black box in the enlargement of CHS4 shows the promoter region that was amplified by two primers, CHCODE and CHS4A2, which are denoted by the small arrows.…”

Section: Many Spontaneous Mutations Of the Dominant I' Allele To The mentioning

confidence: 99%

“…The relative orientations of CHS1, CHS3, and CHS4 are marked by the directional arrows. Triangles indicate the regions of sequence data as entered in GenBank (Akada and Dube, 1995). The six PCR products that could be amplified from;' genotypes are shown in relation to the CHS4 gene.…”

Section: Pcr Analysis Confirms Deletion Of the Chs4 Promoter In /' -~mentioning

confidence: 99%

“…Three of the w e n members (CHSI, CHS3, and CHS4) are located in tandem within a 10-kb duplication region (Akada and Dube, 1995). There is a high degree of amino acid identity among the members of the CHS family, with CHS proteins 1 to 5 showing >98% amino acid identity.…”

Section: Introductionmentioning

confidence: 99%

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

1996

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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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Section: Many Spontaneous Mutations Of the Dominant I' Allele To The mentioning

confidence: 99%

Section: Many Spontaneous Mutations Of the Dominant I' Allele To The mentioning

confidence: 99%

Section: Many Spontaneous Mutations Of the Dominant I' Allele To The mentioning

confidence: 99%

Section: Pcr Analysis Confirms Deletion Of the Chs4 Promoter In /' -~mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

1996

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Nonallelic homologous recombination events responsible for copy number variation within an RNA silencing locus

2019

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The structure of chalcone synthase ( CHS ) gene repeats in different alleles of the I (inhibitor) locus in soybean spawns endogenous RNA interference (RNAi) that leads to phenotypic change in seed coat color of this major agronomic crop. Here, we examined CHS gene copy number by digital PCR and single nucleotide polymorphisms (SNPs) through whole genome resequencing of 15 cultivars that varied in alleles of the I locus ( I , i i , i k , and i ) that control the pattern distribution of pigments in the seed coats. Lines homozygous for the i i allele had the highest copy number followed by the I and i k cultivars which were more related to each other than to the lines with i i alleles. Some of the recessive i alleles were spontaneous mutations, and each revealed a loss of copy number by digital PCR relative to the parent varieties. Amplicon sequencing and whole genome resequencing determined that the breakpoints of several i i to i mutations resulted from nonallelic homologous recombination (NAHR) events between CHS genes located in segmental duplications leading to large 138‐kilobase deletions that erase the structure generating the CHS siRNAs along with eight other non‐ CHS genes. Functional hybrid CHS genes (designated CHS5:1 ) were formed in the process and represent rare examples of NAHR in higher plants that have been captured by examining spontaneous mutational events in isogenic mutant lines.

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Molecular characterization and in silico expression analysis of a chalcone synthase gene family in Sorghum bicolor

Coolbaugh

Nicholson

2002

Physiological and Molecular Plant Pathology

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Recent use of Sorghum bicolor as a target for grass genomics has presented new resources for gene discovery in novel metabolic pathways in Poaceae. Sorghum synthesizes a unique class of flavonoid phytoalexins, the 3-deoxyanthocyanidins, in response to fungal infection. The biosynthetic pathways for 3-deoxyflavonoids are largely uncharacterized but are known to involve transcriptional activation of chalcone synthase (CHS). CHS, or naringenin CHS, catalyzes the formation of naringenin, the precursor for different flavonoids. We have isolated seven sorghum CHS genes, CHS1 to 7, from a genomic library on high-density filters. CHS1 to 7 are highly conserved and closely related to the maize C2 and Whp genes. Several of them are also linked in the genome. These findings suggest that they are the result of recent gene duplication events. Expression of the individual CHS genes was studied in silico by examination of expressed sequence tag (EST) data available in the public domain. Our analyses suggested that CHS1-7 were not differentially expressed in the various growth and developmental conditions represented by the cDNA libraries used to generate the EST data. However, we identified a CHS-like gene, CHS8, with significantly higher EST abundance in the pathogen-induced library. CHS8 shows only 81-82% identity to CHS1 to 7 and forms a distinct subgroup in our phylogenetic analysis. In addition, the active site region contains substitutions that distinguish CHS8 from naringenin CHS. We propose that CHS8 has evolved new enzymatic functions that are involved in the synthesis of defense-related flavonoids, such as the 3-deoxyanthocyanidins, during fungal infection.

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Organization of soybean chalcone synthase gene clusters and characterization of a new member of the family

Cited by 68 publications

References 33 publications

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

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

Nonallelic homologous recombination events responsible for copy number variation within an RNA silencing locus

Molecular characterization and in silico expression analysis of a chalcone synthase gene family in Sorghum bicolor

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