Analysis of the duplicated CHS1 gene related to the suppression of the seed coat pigmentation in yellow soybeans

Novel Seed Size: A Novel Seed-Developing Gene in Glycine max

Soybean-seed development is controlled in multiple ways, as in many known regulating genes. Here, we identify a novel gene, Novel Seed Size (NSS), involved in seed development, by analyzing a T-DNA mutant (S006). The S006 mutant is a random mutant of the GmFTL4pro:GUS transgenic line, with phenotypes with small and brown seed coats. An analysis of the metabolomics and transcriptome combined with RT-qPCR in the S006 seeds revealed that the brown coat may result from the increased expression of chalcone synthase 7/8 genes, while the down-regulated expression of NSS leads to small seed size. The seed phenotypes and a microscopic observation of the seed-coat integument cells in a CRISPR/Cas9-edited mutant nss1 confirmed that the NSS gene conferred small phenotypes of the S006 seeds. As mentioned in an annotation on the Phytozome website, NSS encodes a potential DNA helicase RuvA subunit, and no such genes were previously reported to be involved in seed development. Therefore, we identify a novel gene in a new pathway controlling seed development in soybeans.

Identification of genetic loci conferring seed coat color based on a high-density map in soybean

Seed coat color is a typical evolutionary trait. Identification of the genetic loci that control seed coat color during the domestication of wild soybean could clarify the genetic variations between cultivated and wild soybean. We used 276 F₁₀ recombinant inbred lines (RILs) from the cross between a cultivated soybean (JY47) and a wild soybean (ZYD00321) as the materials to identify the quantitative trait loci (QTLs) for seed coat color. We constructed a high-density genetic map using re-sequencing technology. The average distance between adjacent markers was 0.31 cM on this map, comprising 9,083 bin markers. We identified two stable QTLs (qSC08 and qSC11) for seed coat color using this map, which, respectively, explained 21.933 and 26.934% of the phenotypic variation. Two candidate genes (CHS3C and CHS4A) in qSC08 were identified according to the parental re-sequencing data and gene function annotations. Five genes (LOC100786658, LOC100801691, LOC100806824, LOC100795475, and LOC100787559) were predicted in the novel QTL qSC11, which, according to gene function annotations, might control seed coat color. This result could facilitate the identification of beneficial genes from wild soybean and provide useful information to clarify the genetic variations for seed coat color in cultivated and wild soybean.

MYB transcription factors GmMYBA2 and GmMYBR function in a feedback loop to control pigmentation of seed coat in soybean

Soybean has undergone extensive selection pressures for seed nutrient composition and seed color during domestication, but the major genetic loci controlling seed coat color have not been completely understood, and the transcriptional regulation relationship among the loci remains elusive. Here, two major regulators, GmMYBA2 and GmMYBR, were functionally characterized as an anthocyanin activator and repressor, respectively. Ectopic expression of GmMYBA2 in soybean hairy roots conferred the enhanced accumulation of delphinidin and cyanidin types of anthocyanins in W1t and w1T backgrounds, respectively, through activating anthocyanin biosynthetic genes in the reported loci. The seed coat pigmentation of GmMYBA2-overexpressing transgenic plants in the W1 background mimicked the imperfect black phenotype (W1/w1, i, R, t), suggesting that GmMYBA2 was responsible for the R locus. Molecular and biochemical analysis showed that GmMYBA2 interacted with GmTT8a to directly activate anthocyanin biosynthetic genes. GmMYBA2 and GmMYBR might form a feedback loop to fine-tune seed coat coloration, which was confirmed in transgenic soybeans. Both GmTT8a and GmMYBR that were activated by GmMYBA2 in turn enhanced and obstructed the formation of the GmMYBA2-GmTT8a module, respectively. The results revealed the sophisticated regulatory network underlying the soybean seed coat pigmentation loci and shed light on the understanding of the seed coat coloration and other seed inclusions.

Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections

We performed whole-genome Illumina resequencing of 198 accessions to examine the genetic diversity and facilitate the use of soybean genetic resources and identified 10 million single nucleotide polymorphisms and 2.8 million small indels. Furthermore, PacBio resequencing of 10 accessions was performed, and a total of 2,033 structure variants were identified. Genetic diversity and structure analysis congregated the 198 accessions into three subgroups (Primitive, World, and Japan) and showed the possibility of a long and relatively isolated history of cultivated soybean in Japan. Additionally, the skewed regional distribution of variants in the genome, such as higher structural variations on the R gene clusters in the Japan group, suggested the possibility of selective sweeps during domestication or breeding. A genome-wide association study identified both known and novel causal variants on the genes controlling the flowering period. Novel candidate causal variants were also found on genes related to the seed coat colour by aligning together with Illumina and PacBio reads. The genomic sequences and variants obtained in this study have immense potential to provide information for soybean breeding and genetic studies that may uncover novel alleles or genes involved in agronomically important traits.

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

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, ii , ik , and i) that control the pattern distribution of pigments in the seed coats. Lines homozygous for the ii allele had the highest copy number followed by the I and ik cultivars which were more related to each other than to the lines with ii 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 ii 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.

Comparative analysis of the inverted repeat of a chalcone synthase pseudogene between yellow soybean and seed coat pigmented mutants

In soybean, the I gene inhibits pigmentation over the entire seed coat, resulting in yellow seeds. It is thought that this suppression of seed coat pigmentation is due to naturally occurring RNA silencing of chalcone synthase genes (CHS silencing). Fully pigmented seeds can be found among harvested yellow seeds at a very low percentage. These seed coat pigmented (scp) mutants are generated from yellow soybeans by spontaneous recessive mutation of the I gene. A candidate for the I gene, GmIRCHS, contains a perfect inverted repeat (IR) of a CHS pseudogene (pseudoCHS3) and transcripts of GmIRCHS form a double-stranded CHS RNA that potentially triggers CHS silencing. One CHS gene, ICHS1, is located 680 bp downstream of GmIRCHS. Here, the GmIRCHS-ICHS1 cluster was compared in scp mutants of various origins. In these mutants, sequence divergence in the cluster resulted in complete or partial loss of GmIRCHS in at least the pseudoCHS3 region. This result is consistent with the notion that the IR of pseudoCHS3 is sufficient to induce CHS silencing, and further supports that GmIRCHS is the I gene.

A novel gene IBF1 is required for the inhibition of brown pigment deposition in rice hull furrows

The role of flavonoids as the major red, blue, purple and brown pigments in plants has gained these secondary products a great deal of attention over the years. In this study, we characterized a rice inhibitor for brown furrows1 (ibf1) mutant. In the ibf1 mutant, brown pigments specifically accumulate in hull furrows during seed maturation and reach a maximum level in dry seeds. Higher amounts of total flavonoids and anthocyanin in hull may be responsible for the brown pigmentation of ibf1. The IBF1 gene, which encodes a similar kelch repeat-containing F-box protein, was isolated by map-based cloning approach. Real-time RT-PCR and GUS activity assays revealed that IBF1 specifically expressed in reproductive tissues. GFP-IBF1 fusion protein mainly localized in cytoplasm. The expression of some major structural enzymatic genes involved in flavonoids biosynthesis could be up- or down-regulated to some different extent in ibf1 mutant. Our data suggested that IBF1 as a suppressor could inhibit the brown pigmentation of rice hull furrows.

[Progress in genes related to seed-coat color in soybean]

Seed-coat color has changed from black to yellow during natural and artificial selection of cultivated soybean from wild soybean, and it is also an important morphological marker. Therefore, discovering genes related to the soybean seed-coat color will play a very important role in breeding and evolutionary study. Different seed-coat colors caused by deposition of various anthocyanin pigments. Although pigmentation has been well dissected at molecular level in several plant species, the genes controlling natural variation of seed-coat color in soybean remain to be unknown. Genes related to seed-coat color in soybean were discussed in this paper, including 5 genetic loci (I, T, W1, R and O). Locus I is located in a region that riches in chalcone synthase (CHS) genes on chromosome 8. Gene CHS is a multi-gene family with highly conserved sequences in soybean. Locus T located on chromosome 6 has been cloned and verified, which encodes a flavon-oid-3'-hydroxylase. Mutant of F3'H can not interact with the heme-binding domain due to lack of conservative domain GGEK caused by a nucleotide deletion in the coding region of F3'H. Locus R is located between A668-1 and K387-1 on chromosome 9 (linkage group K). This locus may encode a R2R3 MYB transcription factor or a UDP flavonoid 3-O glyco-syltransferase. Locus O is located between Satt207 and Satt493 on chromosome 8 (linkage group A2) and its molecular characteristics has not been characterized. Locus W1 may be a homology of F3'5'H gene.

The β-conglycinin deficiency in wild soybean is associated with the tail-to-tail inverted repeat of the α-subunit genes

β-conglycinin, a major seed protein in soybean, is composed of α, α', and β subunits sharing a high homology among them. Despite its many health benefits, β-conglycinin has a lower amino acid score and lower functional gelling properties compared to glycinin, another major soybean seed protein. In addition, the α, α', and β subunits also contain major allergens. A wild soybean (Glycine soja Sieb et Zucc.) line, 'QT2', lacks all of the β-conglycinin subunits, and the deficiency is controlled by a single dominant gene, Scg-1 (Suppressor of β-conglycinin). This gene was characterized using a soybean cultivar 'Fukuyutaka', 'QY7-25', (its near-isogenic line carrying the Scg-1 gene), and the F₂ population derived from them. The physical map of the Scg-1 region covered by lambda phage genomic clones revealed that the two α-subunit genes, a β-subunit gene, and a pseudo α-subunit gene were closely organized. The two α-subunit genes were arranged in a tail-to-tail orientation, and the genes were separated by 197 bp in Scg-1 compared to 3.3 kb in the normal allele (scg-1). In addition, small RNA was detected in immature seeds of the mutants by northern blot analysis using an RNA probe of the α subunit. These results strongly suggest that β-conglycinin deficiency in QT2 is controlled by post-transcriptional gene silencing through the inverted repeat of the α subunits.

Suppressive mechanism of seed coat pigmentation in yellow soybean

In soybean seeds, numerous variations in colors and pigmentation patterns exist, most of which are observed in the seed coat. Patterns of seed coat pigmentation are determined by four alleles (I, i(i), i(k) and i) of the classically defined I locus, which controls the spatial distribution of anthocyanins and proanthocyanidins in the seed coat. Most commercial soybean cultivars produce yellow seeds with yellow cotyledons and nonpigmented seed coats, which are important traits of high-quality seeds. Plants carrying the I or i(i) allele show complete inhibition of pigmentation in the seed coat or pigmentation only in the hilum, respectively, resulting in a yellow seed phenotype. Classical genetic analyses of the I locus were performed in the 1920s and 1930s but, until recently, the molecular mechanism by which the I locus regulated seed coat pigmentation remained unclear. In this review, we provide an overview of the molecular suppressive mechanism of seed coat pigmentation in yellow soybean, with the main focus on the effect of the I allele. In addition, we discuss seed coat pigmentation phenomena in yellow soybean and their relationship to inhibition of I allele action.

Simultaneous post-transcriptional gene silencing of two different chalcone synthase genes resulting in pure white flowers in the octoploid dahlia

Garden dahlias (Dahlia variabilis) are autoallooctoploids with redundant genes producing wide color variations in flowers. There are no pure white dahlia cultivars, despite its long breeding history. However, the white areas of bicolor flower petals appear to be pure white. The objective of this experiment was to elucidate the mechanism by which the pure white color is expressed in the petals of some bicolor cultivars. A pigment analysis showed that no flavonoid derivatives were detected in the white areas of petals in a star-type cultivar 'Yuino' and the two seedling cultivars 'OriW1' and 'OriW2' borne from a red-white bicolor cultivar, 'Orihime', indicating that their white areas are pure white. Semi-quantitative RT-PCR showed that in the pure white areas, transcripts of two chalcone synthases (CHS), DvCHS1 and DvCHS2 which share 69% nucleotide similarity with each other, were barely detected. Premature mRNA of DvCHS1 and DvCHS2 were detected, indicating that these two CHS genes are silenced post-transcriptionally. RNA gel blot analysis revealed that small interfering RNAs (siRNAs) derived from CHSs were produced in these pure white areas. By high-throughput sequence analysis of small RNAs in the pure white areas with no mismatch acceptance, small RNAs were mapped to two alleles of DvCHS1 and two alleles of DvCHS2 expressed in 'Yuino' petals. Therefore, we concluded that simultaneous siRNA-mediated post-transcriptional gene silencing of redundant CHS genes results in the appearance of pure white color in dahlias.

QTL underlying resistance to two HG types of Heterodera glycines found in soybean cultivar 'L-10'

BACKGROUND

Resistance of soybean (Glycine max L. Merr.) cultivars to populations of cyst nematode (SCN; Heterodera glycines I.) was complicated by the diversity of HG Types (biotypes), the multigenic nature of resistance and the temperature dependence of resistance to biotypes. The objective here was to identify QTL for broad-spectrum resistance to SCN and examine the transcript abundances of some genes within the QTL.

RESULTS

A Total of 140 F(5) derived F(7) recombinant inbred lines (RILs) were advanced by single-seed-descent from a cross between 'L-10' (a soybean cultivar broadly resistant to SCN) and 'Heinong 37' (a SCN susceptible cultivar). Associated QTL were identified by WinQTL2.1. QTL Qscn3-1 on linkage group (LG) E, Qscn3-2 on LG G, Qscn3-3 on LG J and Qscn14-1 on LG O were associated with SCN resistance in both year data (2007 and 2008). Qscn14-2 on LG O was identified to be associated with SCN resistance in 2007. Qscn14-3 on LG D2 was identified to be associated with SCN resistance in 2008. Qscn14-4 on LG J was identified to be associated with SCN resistance in 2008. The Qscn3-2 on LG G was linked to Satt309 (less than 4 cM), and explained 19.7% and 23.4% of the phenotypic variation in 2007 and 2008 respectively. Qscn3-3 was less than 5 cM from Satt244 on LG J, and explained 19.3% and 17.95% of the phenotypic variations in 2007 and 2008 respectively. Qscn14-4 could explain 12.6% of the phenotypic variation for the SCN race 14 resistance in 2008 and was located in the same region as Qscn3-3. The total phenotypic variation explained by Qscn3-2 and Qscn3-3 together was 39.0% and 41.3% in 2007 and 2008, respectively. Further, the flanking markers Satt275, Satt309, Sat_350 and Satt244 were used for the selection of resistant lines to SCN race 3, and the accuracy of selection was about 73% in this RIL population. Four genes in the predicted resistance gene cluster of LG J (chromosome 16) were successfully cloned by RT-PCR. The transcript encoded by the gene Glyma16g30760.1 was abundant in the SCN resistant cultivar 'L-10' but absent in susceptible cultivar 'Heinong 37'. Further, the abundance was higher in root than in leaf for 'L-10'. Therefore, the gene was a strong candidate to underlie part of the resistance to SCN.

CONCLUSIONS

Satt275, Satt309, Sat_305 and Satt244, which were tightly linked to the major QTL for resistance to SCN on LG G and J, would be candidates for marker-assisted selection of lines resistant to the SCN race 3. Among the six RLK genes, Glyma16g30760.1 was found to accumulate transcripts in the SCN resistance cultivar 'L-10' but not in 'Heinong 37'. The transcript abundance was higher in root than in leaf for L-10.

Variation of GmIRCHS (Glycine max inverted-repeat CHS pseudogene) is related to tolerance of low temperature-induced seed coat discoloration in yellow soybean

In yellow soybean, seed coat pigmentation is inhibited by post-transcriptional gene silencing (PTGS) of chalcone synthase (CHS) genes. A CHS cluster named GmIRCHS (Glycine max inverted-repeat CHS pseudogene) is suggested to cause PTGS in yellow-hilum cultivars. Cold-induced seed coat discoloration (CD), a commercially serious deterioration of seed appearance, is caused by an inhibition of this PTGS upon exposure to low temperatures. In the highly CD-tolerant cultivar Toyoharuka, the GmIRCHS structure differs from that of other cultivars. The aim of this study was to determine whether the variation of GmIRCHS structure among cultivars is related to variations in CD tolerance. Using two sets of recombinant inbred lines between Toyoharuka and CD-susceptible cultivars, we compared the GmIRCHS genotype and CD tolerance phenotype during low temperature treatment. The GmIRCHS genotype was related to the phenotype of CD tolerance. A QTL analysis around GmIRCHS showed that GmIRCHS itself or a region located very close to it was responsible for CD tolerance. The variation in GmIRCHS can serve as a useful DNA marker for marker-assisted selection for breeding CD tolerance. In addition, QTL analysis of the whole genome revealed a minor QTL that also affected CD tolerance.

Molecular mechanism of seed coat discoloration induced by low temperature in yellow soybean

Seed coat pigmentation is inhibited in yellow soybean. The I gene inhibits pigmentation over the entire seed coat. In yellow soybean, seed coat discoloration occurs when plants are exposed to low temperatures after the onset of flowering, a phenomenon named 'cold-induced discoloration (CD)'. Inhibition of seed coat pigmentation results from post-transcriptional gene silencing (PTGS) of the chalcone synthase (CHS) genes. PTGS is a sequence-specific RNA degradation mechanism in plants and occurs via short interfering RNAs (siRNAs). Similar post-transcriptional suppression is called RNAi (RNA interference) in animals. Recently, we identified a candidate of the I gene designated GmIRCHS. In this study, to elucidate the molecular mechanism of CD, CHS mRNA and siRNA levels in the seed coat were compared between CD-sensitive and CD-tolerant cultivars (Toyomusume and Toyoharuka, respectively). In Toyomusume, the CHS siRNA level was reduced markedly by low temperature treatment, and subsequently the CHS mRNA level increased rapidly after treatment. In contrast, low temperature treatment did not result in severe reduction of the CHS siRNA level in Toyoharuka, and the CHS mRNA level did not increase after the treatment. These results suggest that the rapid increase in CHS mRNA level after low temperature treatment may lead to enhanced pigmentation in some of the seed coat cells and finally in seed coat discoloration. Interestingly, we found a Toyoharuka-specific difference in the GmIRCHS region, which may be involved in CD tolerance.

Perfusion reversed-phase high-performance liquid chromatography/mass spectrometry analysis of intact soybean proteins for the characterization of soybean cultivars

Perfusion reversed-phase HPLC (RP-HPLC)-electrospray mass spectrometry (ESI-MS) was employed for the characterization of soybean cultivars through the analysis of intact soybean proteins. The similarities and differences between yellow soybeans (the most usual soybeans) and other beans with different pigmentation (green, red, and black) commercialized as soybean were investigated. Red beans commercialized as azuki that are frequently sold as red soybean were also analyzed. Separation was carried out using a perfusion column at a flow-rate of 0.5 mL/min and a gradient elution. A step-by-step procedure was used for the optimization of the mass spectrometry parameters enabling the most sensitive detection. The method was applied to the analysis of the above-mentioned beans and the main soybean proteins (11S and 7S globulins) obtained by a fractionation procedure. MS spectra obtained from every peak in the beans and in their fractions were compared observing clear differences between yellow soybeans and the other beans with different pigmentation. The identification of some soybean proteins in yellow soybeans was also possible.

Structural features of GmIRCHS, candidate of the I gene inhibiting seed coat pigmentation in soybean: implications for inducing endogenous RNA silencing of chalcone synthase genes

Most commercial soybean varieties have yellow seeds due to loss of pigmentation in the seed coat. The I gene inhibits pigmentation over the entire seed coat, resulting in a uniform yellow color of mature harvested seeds. We previously demonstrated that the inhibition of seed coat pigmentation by the I gene results from post-transcriptional gene silencing (PTGS) of chalcone synthase (CHS) genes. Little is known about the structure of the I gene and the mechanism by which it induces PTGS of CHS genes. Here, we report a candidate of the I gene, GmIRCHS, which consists of a 5'-portion of a DnaJ-like gene containing a promoter region and a perfect inverted repeat (IR) of 1.1-kb truncated CHS3 sequences (5'-DeltaCHS3 and 3'-DeltaCHS3). RT-PCRs and RNase protection assay indicated the existence of the read-through product from 5'-DeltaCHS3 to 3'-DeltaCHS3 and the dsRNA region of DeltaCHS3, suggesting that dsRNA of DeltaCHS3 could be transcribed from GmIRCHS and could induce PTGS of CHS genes. Moreover, the IR structure of DeltaCHS3 in GmIRCHS was lost in the soybean mutants in which I was changed to i, supporting the conclusion that GmIRCHS is the I gene.

Molecular linkage mapping and phylogeny of the chalcone synthase multigene family in soybean

Chalcone synthase (CHS), the key enzyme in the flavonoid biosynthesis pathway, is encoded by a multigene family, CHS1-CHS8 and dCHS1 in soybean. A tandem repeat of CHS1, CHS3 and CHS4, and dCHS1 that is believed to be located in the vicinity comprises the I locus that suppresses coloration of the seed coat. This study was conducted to determine the location of all CHS members by using PCR-based DNA markers. Primers were constructed based on varietal differences in either the nucleotide sequence of the 5'-upstream region or the first intron of two cultivars, Misuzudaizu, with a yellow seed coat (II), and Moshidou Gong 503, with a brown seed coat (ii). One hundred and fifty recombinant inbred lines that originated from a cross between these two cultivars were used for linkage mapping together with 360 markers. Linkage mapping confirmed that CHS1, CHS3, CHS4, dCHS1, and the I locus are located at the same position in molecular linkage group (MLG) A2. CHS5 was mapped at a distance of 0.3 cM from the gene cluster. CHS2 and CHS6 were located in the middle region of MLGs A1 and K, respectively, while CHS7 and CHS8 were found at the distal end of MLGs D1a and B1, respectively. Phylogenetic analysis indicated that CHS1, CHS3, CHS4, and CHS5 are closely related, suggesting that gene duplication may have occurred repeatedly to form the I locus. In addition, CHS7 and CHS8 located at the distal end and CHS2, CHS6, and CHS members around the I locus located around the middle of the MLG are also related. Ancient tetraploidization and repeated duplication may be responsible for the evolution of the complex genetic loci of the CHS multigene family in soybean.

Features of a 103-kb gene-rich region in soybean include an inverted perfect repeat cluster of CHS genes comprising the I locus

The I locus in soybean (Glycine max) corresponds to a region of chalcone synthase (CHS) gene duplications affecting seed pigmentation. We sequenced and annotated BAC clone 104J7, which harbors a dominant i(i) allele from Glycine max 'Williams 82', to gain insight into the genetic structure of this multigenic region in addition to examining its flanking regions. The 103-kb BAC encompasses a gene-rich region with 11 putatively expressed genes. In addition to six copies of CHS, these genes include: a geranylgeranyltransferase type II beta subunit (E.C.2.5.1.60), a beta-galactosidase, a putative spermine and (or) spermidine synthase (E.C.2.5.1.16), and an unknown expressed gene. Strikingly, sequencing data revealed that the 10.91-kb CHS1, CHS3, CHS4 cluster is present as a perfect inverted repeat separated by 5.87 kb. Contiguous arrangement of CHS paralogs could lead to folding into multiple secondary structures, hypothesized to induce deletions that have previously been shown to effect CHS expression. BAC104J7 also contains several gene fragments representing a cation/hydrogen exchanger, a 40S ribosomal protein, a CBL-interacting protein kinase, and the amino terminus of a subtilisin. Chimeric ESTs were identified that may represent read-through transcription from a flanking truncated gene into a CHS cluster, generating aberrant CHS RNA molecules that could play a role in CHS gene silencing.

Tissue-specific gene silencing mediated by a naturally occurring chalcone synthase gene cluster in Glycine max

Chalcone synthase, a key regulatory enzyme in the flavonoid pathway, constitutes an eight-member gene family in Glycine max (soybean). Three of the chalcone synthase (CHS) gene family members are arranged as inverted repeats in a 10-kb region, corresponding to the I locus (inhibitor). Spontaneous mutations of a dominant allele (I or i(i)) to a recessive allele (i) have been shown to delete promoter sequences, paradoxically increasing total CHS transcript levels and resulting in black seed coats. However, it is not known which of the gene family members contribute toward pigmentation and how this locus affects CHS expression in other tissues. We investigated the unusual nature of the I locus using four pairs of isogenic lines differing with respect to alleles of the I locus. RNA gel blots using a generic open reading frame CHS probe detected similar CHS transcript levels in stems, roots, leaves, young pods, and cotyledons of the yellow and black isolines but not in the seed coats, which is consistent with the dominant I and i(i) alleles mediating CHS gene silencing in a tissue-specific manner. Using real-time RT-PCR, a variable pattern of expression of CHS genes in different tissues was demonstrated. However, increase in pigmentation in the black seed coats was associated with release of the silencing effect specifically on CHS7/CHS8, which occurred at all stages of seed coat development. These expression changes were linked to structural changes taking place at the I locus, shown to encompass a much wider region of at least 27 kb, comprising two identical 10.91-kb stretches of CHS gene duplications. The suppressive effect of this 27-kb I locus in a specific tissue of the G. max plant represents a unique endogenous gene silencing mechanism.

Sequence divergence at chalcone synthase gene in pigmented seed coat soybean mutants of the Inhibitor locus

Seed coat color in soybeans is determined by the I (Inhibitor) locus. The dominant I allele inhibits seed coat pigmentation, and it has been suggested that there is a correlation between the inhibition of pigmentation by the I allele and chalcone synthase (CHS) gene silencing in the seed coat. Analysis of spontaneous mutations from I to i has shown that these mutations are closely related to the deletion of one of the CHS genes (designated ICHS1). In soybeans with the I/I genotype (cv. Miyagi shirome), a truncated form of the CHS gene (CHS3) is located in an inverse orientation 680 bp upstream of ICHS1, and it was previously suggested that the truncated CHS3- ICHS1 cluster might be involved in CHS gene silencing in the seed coat. In the current study, the truncated CHS3- ICHS1 cluster was compared with the corresponding region of pigmented seed coat mutants in which I had changed to i in Miyagi shirome and in the strain Karikei 584. In the Karikei 584 mutant, the truncated CHS3-ICHS1 cluster was retained and the sequence diverged at a point immediately upstream (32 bp) of this cluster. The sequences upstream of the points of divergence in both mutants almost perfectly matched a part of the registered sequence in a soybean BAC clone containing the soybean cyst nematode resistance-associated gene, and inspection of the sequences suggested that the sequence divergence of the CHS gene in the Karikei 584 and Miyagi shirome mutants was due to an unequal crossing-over via 4-bp or 5-bp short repeats, respectively.