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Determination of the phamacophore of penclomedine, a clinically-evaluated antitumor pyridine derivative.

The main objective of this investigation was to identify the reactive pharmacophore in penclomedine (PEN, 3,5-dichloro-4,6-dimethoxy-2-(trichloromethyl) pyridine) for in vivo antitumor activity and also to discover related ring structures and sulfur analogues that might exhibit superior antitumor activity in vivo. Several new analogues of PEN and related structural variants have been synthesized and evaluated in vivo against MX-1 human breast tumor xenograft implanted subcutaneously (sc), although none of them demonstrated significant activity.

Animals↗

Substrate specificity of and product formation by muconate cycloisomerases: an analysis of wild-type enzymes and engineered variants.

Muconate cycloisomerases play a crucial role in the bacterial degradation of aromatic compounds by converting cis,cis-muconate, the product of catechol ring cleavage, to (4S)-muconolactone. Chloromuconate cycloisomerases catalyze both the corresponding reaction and a dehalogenation reaction in the transformation of chloroaromatic compounds. This study reports the first thorough examination of the substrate specificity of the muconate cycloisomerases from Pseudomonas putida PRS2000 and Acinetobacter "calcoaceticus" ADP1. We show that they transform, in addition to cis,cis-muconate, 3-fluoro-, 2-methyl-, and 3-methyl-cis, cis-muconate with high specificity constants but not 2-fluoro-, 2-chloro-, 3-chloro-, or 2,4-dichloro-cis,cis-muconate. Based on known three-dimensional structures, variants of P. putida muconate cycloisomerase were constructed by site-directed mutagenesis to contain amino acids found in equivalent positions in chloromuconate cycloisomerases. Some of the variants had significantly increased specificity constants for 3-chloro- or 2,4-dichloromuconate (e.g., A271S and I54V showed 27- and 22-fold increases, respectively, for the former substrate). These kinetic improvements were not accompanied by a change from protoanemonin to cis,cis-dienelactone as the product of 3-chloro-cis,cis-muconate conversion. The rate of 2-chloro-cis,cis-muconate turnover was not significantly improved, nor was this compound dehalogenated to any significant extent. However, the direction of 2-chloro-cis,cis-muconate cycloisomerization could be influenced by amino acid exchange. While the wild-type enzyme discriminated only slightly between the two possible cycloisomerization directions, some of the enzyme variants showed a strong preference for either (+)-2-chloro- or (+)-5-chloromuconolactone formation. These results show that the different catalytic characteristics of muconate and chloromuconate cycloisomerases are due to a number of features that can be changed independently of each other.

Acinetobacter calcoaceticus↗

Specificity of S fimbriae on recombinant Escherichia coli: preferential binding to gangliosides expressing NeuGc alpha (2-3)Gal and NeuAc alpha (2-8)NeuAc.

The adhesins of Escherichia coli strains HB101(pANN801-13) and HB101(pAZZ50), which express S fimbriae encoded by a recombinant plasmid containing the sfaI and sfaII gene clusters, respectively, were characterized with regard to the detailed structural requirements of their binding to sialyloligosaccharides on (neo)glycoproteins and (neo)glycolipids. From binding and binding inhibition studies in solid-phase enzyme immunoassays with isolated S fimbriae, several major conclusions can be drawn. S fimbriae bind specifically to sialic acid on gangliosides. The most active structural variant of sialic acid on GM3 ganglioside is N-glycolylneuraminic acid (NeuGc). In contrast to previous reports, high binding activities were measured also for b-series gangliosides expressing NeuAc alpha (2-8)NeuAc. In agreement with earlier studies, the site of sialic acid substitution to subterminal sugars strongly influences the binding to sialyloligosaccharides, i.e., alpha-6-linked sialic acid is only poorly recognized by the adhesin compared with alpha-3-linked sialic acid. C-8 and C-9 hydroxyl groups form essential structural elements of sialic acid in the binding event.

Animals↗

Long-Read Haplotype Phasing Resolves Allelic Configuration as a Missing Layer of Precision Oncology.

Short-read sequencing cannot determine whether co-occurring variants within a cancer gene lie on the same allele (cis) or opposing alleles (trans), a distinction with direct therapeutic consequences: trans configurations confirm biallelic tumor suppressor inactivation, whereas cis configurations generate compound oncogenic alleles with enhanced activity. Among 768 patients with prostate, breast, or ovarian cancers, we used mutational signatures to nominate cryptic genomic instability cases lacking a causative biallelic event on short-read sequencing. Long-read nanopore sequencing resolved 32 of 46 cryptic cases (69.6%) through methylation detection, long insertion resolution, and structural variant characterization, confirming trans inactivation in every resolved tumor suppressor case. Analysis of 4,496 MiOncoSeq samples identified 17,519 multi-hit gene pairs, 78.7% of which exceeded the 500 bp short-read phasing limit, and long-read phasing revealed recurrent compound cis alleles in NOTCH1, PIK3CA, PDGFRB, and KIT. Haplotype phasing addresses an overlooked gap in cancer variant interpretation and warrants integration into precision oncology.

Journal Article↗

Human red cell aquaporin CHIP. I. Molecular characterization of ABH and Colton blood group antigens.

Blood group antigens are structural variants in surface carbohydrate or amino acid polymorphisms on extracellular domains of membrane proteins. The red cell water channel-forming integral protein (Aquaporin CHIP) is a homotetramer with only one N-glycosylated subunit, however no CHIP-associated blood group antigens have yet been identified. Immunoblotting, monosaccharide composition analysis, and selective glycosidase digestions revealed that the CHIP-associated oligosaccharide contains ABH determinants and resembles a band 3-type glycan that cannot be cleaved from intact membranes by Peptide:N-glycosidase F. The molecular structure of the Colton antigens was previously unknown, but CHIP was selectively immunoprecipitated with anti-Coa or anti-Co(b). The DNA sequence from Colton-typed individuals predicted that residue 45 is alanine in the Co(a+b-) phenotype and valine in the Co(a-b+) phenotype. The nucleotide polymorphism corresponds to a PflMI endonuclease digestion site in the DNA from Co(a-b+) individuals. These studies have defined antigens within two blood group systems on CHIP: (a) an ABH-bearing polylactosaminoglycan attached to a poorly accessible site in the native membrane; and (b) the Colton antigen polymorphism which may permit the identification of rare individuals with defective water channel expression.

ABO Blood-Group System↗

Alternative splicing in the cytoplasmic II-III loop of the N-type Ca channel alpha 1B subunit: functional differences are beta subunit-specific.

Structural diversity of voltage-gated Ca channels underlies much of the functional diversity in Ca signaling in neurons. Alternative splicing is an important mechanism for generating structural variants within a single gene family. In this paper, we show the expression pattern of an alternatively spliced 21 amino acid encoding exon in the II-III cytoplasmic loop region of the N-type Ca channel alpha(1B) subunit and assess its functional impact. Exon-containing alpha(1B) mRNA dominated in sympathetic ganglia and was present in approximately 50% of alpha(1B) mRNA in spinal cord and caudal regions of the brain and in the minority of alpha(1B) mRNA in neocortex, hippocampus, and cerebellum (<20%). The II-III loop exon affected voltage-dependent inactivation of the N-type Ca channel. Steady-state inactivation curves were shifted to more depolarized potentials without affects on either the rate or voltage dependence of channel opening. Differences in voltage-dependent inactivation between alpha(1B) splice variants were most clearly manifested in the presence of Ca channel beta(1b) or beta(4), rather than beta(2a) or beta(3), subunits. Our results suggest that exon-lacking alpha(1B) splice variants that associate with beta(1b) and beta(4) subunits will be susceptible to voltage-dependent inactivation at voltages in the range of neuronal resting membrane potentials (-60 to -80 mV). In contrast, alpha(1B) splice variants that associate with either beta(2a) or beta(3) subunits will be relatively resistant to inactivation at these voltages. The potential to mix and match multiple alpha(1B) splice variants and beta subunits probably represents a mechanism for controlling the plasticity of excitation-secretion coupling at different synapses.

Alternative Splicing↗

[Effect of laminin on numerical karyotype variability of kangaroo rat kidney cell lines].

The numerical karyotypic variability has been investigated in "markerless" epithelial-like Rat kangaroo kidney cell lines NBL-3-11 and NBL-3-17 on cultivation on a laminin-2/4 coated surface. In cell line NBL-3-17, cultivated on the laminin-coated surface for 2, 4 and 12 days, the character of numerical karyotypic variability has changed. In 2 days the general character of cell distribution for the chromosome number did not change, but the frequency of cells with modal number of chromosomes decreases significantly, while that of cells with lower chromosome number show a tendency to increase. At a prolongation of cultivation time to 4 and 12 days, the numerical karyotypic heterogeneity in cell population increases due to a significant change in the general character of cell distribution for the chromosome number, which is caused by a significant decrease in the frequency of cells with the modal number of chromosomes, and by an increase in the frequency of cells with lower chromosome number. The analysis of distribution of individual chromosomes showed that the number of types of additional structural variants of the karyotype (SVK) increases significantly on cultivation on laminin for 2-12 days. In cell line NBL-3-11, cultivated on the laminin-coated surface for 2 and 4 days, the character of numerical karyotypic variability did not change compared to control variants. Possible reasons of the observed changes of numerical karyotypic variability in cell line NBL-3-17 is discussed. The reason of differences in the character of numerical karyotypic variability between cell lines NBL-3-11 and NBL-3-17 possibly consists in the change of gene expression, namely in a dose of certain functioning genes. The polymerase chain reaction with arbitrary primers revealed no differences between DNA patterns of cell lines NBL-3-17 and NBL-3-11. This can reflect a similarity in the primary DNA structure of both cell lines. Hence, these lines differ only in the number of homologous chromosomes (hypotriploid and hypodiploid).

Animals↗

Three classes of ubiquinone analogs regulate the mitochondrial permeability transition pore through a common site.

To identify the structural features required for regulation of the mitochondrial permeability transition pore (PTP) by ubiquinone analogs (Fontaine, E., Ichas, F., and Bernardi, P. (1998) J. Biol. Chem. 40, 25734-25740), we have carried out an analysis with quinone structural variants. We show that three functional classes can be defined: (i) PTP inhibitors (ubiquinone 0, decylubiquinone, ubiquinone 10, 2,3-dimethyl-6-decyl-1,4-benzoquinone, and 2,3,5-trimethyl-6-geranyl-1,4-benzoquinone); (ii) PTP inducers (2,3-dimethoxy-5-methyl-6-(10-hydroxydecyl)-1,4-benzoquinone and 2,5-dihydroxy-6-undecyl-1,4-benzoquinone); and (iii) PTP-inactive quinones that counteract the effects of both inhibitors and inducers (ubiquinone 5 and 2,3,5-trimethyl-6-(3-hydroxyisoamyl)-1,4-benzoquinone) . The structure-function correlation indicates that minor modifications in the isoprenoid side chain can turn an inhibitor into an activator, and that the methoxy groups are not essential for the effects of quinones on the PTP. Since the ubiquinone analogs used in this study have a similar midpoint potential and decrease mitochondrial production of reactive oxygen species to the same extent, these results support the hypothesis that quinones modulate the PTP through a common binding site rather than through oxidation-reduction reactions. Occupancy of this site can modulate the PTP open-closed transitions, possibly through secondary changes of the PTP Ca(2+) binding affinity.

Animals↗

Detection and characterization of variant and modified structures of proteins in blood and tissues by mass spectrometry.

Some variant proteins cause diseases, and some diseases result in increases of proteins with abnormally modified structures. The detection, characterization, and estimation of the relative amounts of protein variants and abnormally modified proteins are important for clinical diagnosis and for elucidation of the mechanisms of the pathogenesis of diseases. Analysis of the covalent structures of proteins using matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography-electrospray ionization MS (LC-ESI-MS), which had been developed by the early 1990s, have largely replaced analyses by conventional protein chemistry. Here, we review the detection and characterization of hemoglobin variants, HbA1c measurement, detection of carbohydrate-deficient transferrin, and identification of variants of transthyretin (TTR) and Cu/Zn-superoxide dismutase (SOD-1) using soft ionization MS. We also propose the diagnostic application of the signals of modified forms of TTR, that is, S-sulfonated TTR and S-homocysteinyl TTR. The relative peak height ratio of the abnormal/normal components gives valuable information about the instability of variants and enables the detection of unstable Hb subunits or thalassemia heterozygotes. We found unique modified structures of TTR that suggested changes in amyloid fibrils.

Amino Acid Sequence↗

Apolipoprotein genetic variation and human disease.

Atherosclerosis is the major public health problem in much of the world today. The information summarized in this review, based on the recognized apolipoprotein structural variants appreciated at both the protein and gene levels, indicates that apolipoprotein genetic variation plays a major role in determining human genetic susceptibility to this disease. With the use of cloned apolipoprotein genes, it should, in the near future, be possible to determine how their expression is regulated; this should provide insight into other classes of mutations of a regulatory nature that might have clinical significance. In addition, the many association and linkage studies currently being undertaken will provide the rationale for cloning defective alleles and determining specific causative mutations. Both structural and regulatory mutations can then be described either with restriction enzymes and Southern blotting or by direct oligonucleotide hybridization techniques in the general population. This will allow the identification of presymptomatic atherosclerosis-susceptible individuals who would be targets for primary preventative therapy.

Apolipoproteins↗

Genome-wide variation analysis of two Salvia hispanica L. genotypes and implication for associations with metabolic and adaptive traits.

BACKGROUND: Advances in next-generation sequencing have accelerated genome-wide exploration of genetic diversity in underutilized oilseed crops. Salvia hispanica L. (chia), a high-nutrient pseudocereal rich in omega-3 fatty acids, is increasingly valued for its health benefits and commercial potential, yet it remains poorly characterized at the genomic level. Understanding the scale and nature of genomic variation is essential for improving complex traits such as oil yield, stress tolerance, and seed quality. METHODS: Two contrasting chia genotypes, Black-chia (CACH-B) and White- chia (CACH-W), were resequenced using the Bio-Resequencing Toolkit (BRT) pipeline. High-coverage sequencing, with a mapping rate exceeding 99% and an average depth of approximately 28&#xd7;, facilitated the detection and annotation of single-nucleotide polymorphisms (SNPs), insertions and deletions (InDels), copy-number variations (CNVs), and structural variants (SVs). The functional classification of variant impacts enabled the identification of genes potentially linked to metabolic and adaptive traits. RESULTS: A total of 1.97 million SNPs, 401,493 InDels, 836 CNVs, and 15,288 SVs were identified across the chia genome. Notably, approximately 53% of exonic SNPs were non-synonymous (dN/dS&#xa0;&#x2248;&#xa0;1.28), predominantly affecting lipid metabolism, transcriptional regulation, and stress response pathways, potentially altering key agronomic traits. In addition, CNV hotspots were concentrated in chromosomes 3 and 6, overlapping MYB, WRKY, and bZIP transcription factor loci, may potentially be involved in stress tolerance and yield. Furthermore, structural rearrangements, including inversions and duplications within the FAD2, FAD3, and CYP450 gene clusters, were potentially associated with seed pigmentation and omega-3 biosynthesis, pointing to their potential breeding relevance. Observed heterozygosity (H&#x2092;&#xa0;&#x2248;&#xa0;0.71) and nucleotide diversity (&#x3c0;&#xa0;&#x2248;&#xa0;7&#xa0;&#xd7;&#xa0;10-3) indicated moderate to high allelic richness. In addition, the low FST value (0.038) indicates substantial genomic similarity between the two genotypes. CONCLUSION: This study presents the first comprehensive map integrating SNPs, CNVs, and SVs in S. hispanica L. The results reveal a structurally dynamic genome characterized by substantial sequence and structural variation, providing valuable insights into genomic diversity and potential adaptive mechanisms in chia. The coexistence of high SNP diversity and abundant structural variation underpins chia's nutritional specialization and environmental resilience. These results deliver a foundational genomic resource for marker-assisted breeding, genome-wide association studies, and the development of climate-resilient chia cultivars.

Copy-number variation, structural variation↗

Synthesis of an inhibitor-tethered resin for detection of active matrix metalloproteinases involved in disease.

Matrix metalloproteinases (MMPs), of which 26 members are known in humans, are implicated in a number of diseases. Their activity is strictly controlled, but when the biological control over the activity is lost, disease processes set in. In an attempt to delineate what MMP activity has gone awry in what diseases, including metastatic cancers that are of special interest to our laboratories, we conceived and synthesized two chromatographic resins incorporated with a multifunctional broad-spectrum inhibitor for MMPs. The broad-spectrum inhibitor contains three sterogentic centers and was synthesized in 13 steps. Two structural variants of the inhibitors were linked to the polymer support via disulfide moieties. These resins are intended for use in cellular systems to selectively fish out from a complex mixture of all cellular proteins the active MMP forms important for the specific disease for identification.

Disease↗

Elucidation of a polychlorinated bipyrrole structure using enantioselective GC.

A hexachloro congener (Q1-hex) of the natural heptachloro-1'-methyl-1,2'-bipyrrole Q1 was recently observed as a byproduct of the Q1 synthesis. NMR investigation confirmed that Q1-hex has a proton on a carbon in beta-position to a nitrogen. Three isomers are possible that fulfill this prerequisite; unfortunately, however, the NMR data were not sufficient to distinguish among the three structural variants. Because only one isomer of Q1-hex is expected to be chiral, we utilized enantioselective gas chromatography and two chiral stationary phases to separate the atropisomers. Baseline separation of the Q1-hex atropisomers was obtained on 10% chemically bonded permethyl-beta-cyclodextrin. In the full-scan mode, it was found that Q1-hex was racemic and that both atropisomers had identical mass fragmentation patterns. Partial resolution of the Q1-hex atropisomers was obtained on 25% tert-butyldimethylsilylated beta-cyclodextrin diluted in PS086. In concert with previous NMR data, these enantioseparations prove that the structure of Q1-hex is 2,3,3',4',5,5'-hexachloro-1'-methyl-1,2'-bipyrrole (5). To our knowledge, this is the first gas chromatographic separation of atropisomers of an axially chiral 1,2'-bipyrrole derivative.

Chromatography, Gas↗

Potent low molecular weight substrates for protein-tyrosine phosphatase.

The ability of protein-tyrosine phosphatases (PTPases) to catalyze the hydrolysis of simple aromatic phosphates has been recognized for some time. However, these compounds are significantly poorer substrates than their peptide-based counterparts containing phosphotyrosine. Consequently, the effort to create potent PTPase substrates has predominantly focused on the use of peptidic carriers to deliver the phosphotyrosine moiety to the enzyme active site. We now report the synthesis and evaluation of several low molecular weight aromatic phosphates that serve as robust substrates for the rat PTPase, PTP1. We initially surveyed the ability of PTP1 to catalyze the hydrolysis of a variety of phenyl phosphate structural variants. Sterically demanding substituents positioned ortho and (to a lesser extent) meta to the phosphate group severely compromise the ability of these species to serve as phosphatase substrates. However, both benzylic and negatively charged substituents para to the hydrolyzable phosphate dramatically promote hydrolytic efficiency, which appears to be augmented through a dramatic enhancement in the affinity of the substrate for PTP1. The best substrate examined in this study exhibits a Km of 16 +/- 3 microM. In addition, it serves as an inhibitor of the PTP1-catalyzed hydrolysis of p-nitrophenyl phosphate with a Ki of 4.9 +/- 0.7 microM. The extraordinary structural simplicity of this compound, as well as those of several others described herein, provides a promising starting point for the design of potent PTPase inhibitors.

Animals↗

Antigenic sites of human growth hormone and related molecules detected by monoclonal antibodies to human growth hormone.

Four major antigenic sites for human growth hormone (hGH) were identified by 27 mouse monoclonal antibodies to hGH. Sites 1 and 2 are spatially close whereas sites 3 and 4 are located in other parts of the molecule. There also appears to be a subdivision of antigenic sites. A panel of 10 monoclonal antibodies, which included representatives from each antigenic site group, were used to determine cross-reactivities between hGH and human placental lactogen (hPL), human prolactin (hPRL), the 20,000 mol. wt variant of hGH (hGH20K) and a disulfide-linked dimer of hGH (diS-dimer). The data suggest a high conformational dependence of antigenic sites in hGH. DiS-dimer retains all four antigenic sites of hGH, although all have been altered. hGH20K retains sites 2-4 but site 1 has been dramatically altered. hPL retains site 3, whereas sites 1 and 4 have been dramatically altered and site 2 may be lacking. The extremely low cross-reactivity observed for hPRL is consistent with the dissimilarity between hGH and hPRL. Antigenic site 3 is the most conserved of all sites. The lack of structural similarity compared with hGH of site 1 in hGH20K and of a portion of site 3 in diS-dimer suggests that it may be possible to develop specific radioimmunoassays for these structural variants of hGH.

Antibodies, Monoclonal↗

The effect of synthetic fragment 31-44 of human growth hormone on glucose uptake by isolated adipose tissue.

Synthetic tetradecapeptide corresponding to amino acid sequence 31-44 of human growth hormone molecule and possessing a lipotropic activity was tested for the ability to stimulate glucose uptake by isolated epididymal fat pads of fed rats. Tetradecapeptide 31-44 (1 microgram/ml), growth hormone (1 microgram/ml) and insulin (50 microU/ml) stimulated in about equal degree the uptake of [U-14C]glucose by adipose tissue. Tissue samples were preliminary incubated for 3-4 hours in the absence of hormones to eliminate the refractoriness to the insulin-like effects of growth hormone. Without preincubation the tissue was refractory to the action of growth hormone and tetradecapeptide 31-44, but was sensitive to insulin. The data obtained together with the findings of Lewis et al., which showed that 20K structural variant of human growth hormone having the deletion of residues 32-46 cannot stimulate glucose uptake and lipolysis in rats, make it possible to suggest that both activities are associated with fragment 31-44.

Adipose Tissue↗

Long-Read Haplotype Phasing Resolves Allelic Configuration as a Missing Layer of Precision Oncology.

Conventional short-read sequencing cannot determine whether co-occurring variants within a cancer gene reside on the same allele (cis) or on opposing alleles (trans), a distinction with direct biological and therapeutic consequences. Trans configurations confirm biallelic tumor suppressor inactivation and inform therapy selection, while cis configurations generate compound oncogenic alleles with enhanced activity. We analyzed 768 patients with prostate, breast, or ovarian cancers in the PROBLEM cohort, using mutational signatures to nominate cryptic genomic instability cases where the causative biallelic event was not apparent from short-read sequencing. Long-read nanopore sequencing resolved 32 of 46 cryptic cases (69.6%), leveraging its unique advantages in direct methylation detection, long insertion resolution, and complex structural variant characterization, confirming trans biallelic inactivation in all resolved tumor suppressor cases. Systematic analysis of 4,496 MiOncoSeq samples identified 17,519 multi-hit gene pairs, of which 78.7% exceeded the 500 bp short-read phasing limit. Long-read phasing further revealed recurrent compound cis oncogenic alleles in NOTCH1, PIK3CA, PDGFRB, and KIT with functionally synergistic activity. Haplotype phasing resolves a systematically overlooked gap in cancer variant interpretation and warrants broader integration into precision oncology workflows.

Journal Article↗

Allelic variation and light-responsive regulation of FaMYB10-2 underlie tissue-specific anthocyanin accumulation in strawberry.

Anthocyanins critically determine fruit color, nutrition, and stress resilience in cultivated strawberry (Fragaria &#xd7; ananassa), directly influencing consumer preference. Despite complex genetic and environmental regulation of their biosynthesis, the basis for tissue-specific pigmentation, notably the widespread occurrence of red skin and pale flesh, remains poorly understood. We integrated genomic, transcriptomic, and functional analyses across 200 cultivars to dissect receptacle pigmentation regulation. Approaches included FaMYB10-2 allele mining, promoter structural variant (SV) identification, expression profiling, regulatory interaction assays, and characterization of upstream light-responsive factors. FaMYB10-2 was identified as the key R2R3-MYB regulator of fruit anthocyanin biosynthesis. Alleles FaMYB10-2.2 and FaMYB10-2.3 encode truncated proteins retaining bHLH-binding capacity but lacking activation domains, functioning as dominant-negative repressors. A promoter SV 986&#x2005;bp upstream of FaMYB10-2 was associated with reduced pale fruit due to cis-regulatory divergence. The SV (Alt) allele is prevalent in Asian cultivars, while the Ref allele is enriched in Western germplasm. Crucially, a light-responsive FaHYH-FaWRKY71 cascade activates FaMYB10-2 and structural genes haplotype-dependently, compensating for weak MYB activity in the skin. Our findings reveal a multilayered regulatory system integrating allelic variation, cis-regulatory divergence, and environmental signals, advancing anthocyanin understanding and providing engineering targets for polyploid crop color improvement.

Fragaria↗