--- scientific_name: Phaseolus vulgaris gene_symbols: - PvSYMRK gene_symbol_long: Symbiosis Receptor-like Kinase gene_model_pub_name: Phvul.002G143400 gene_model_full_id: phavu.G19833.gnm2.ann1.Phvul.002G143400 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - PvSYMRK is activated in root hairs by phosphorylation of the T589 residue in response to the perception of NOD factors produced by rhizobia. - SYMRK labeled with EGFP (enhanced green fluorescence protein) is endocytosed from the plasma membrane to intracellular puncta in response to Rhizobium etli inoculation. The consequent redistribution affects the SYMRK signaling pathway. - Deletion of the SYMRK endocytic sorting motif YKTL and application of endocytosis inhibitors reduced the prevalence of SYMRK-EGFP intracellular puncta. Endocytosis was also negatively impacted in phosphorylation-deficient (T589A) and kinase-inactivated (K618E) mutants of SYMRK. phenotype_synopsis: The PvSYMRK protein undergoes rhizobia-induced endocytosis and regulates a dependent kinase signal transduction cascade leading to rhizobial infection and nodule organogenesis. traits: - entity_name: biological process involved in symbiotic interaction entity: GO:0044403 - entity_name: kinase activity entity: GO:0016301 - entity_name: positive regulation of receptor-mediated endocytosis entity: GO:0048260 - entity_name: nodulation entity: GO:0009877 references: - citation: Davila-Delgado, Flores-Canul et al., 2023 doi: 10.1007/s00425-023-04116-0 pmid: 36928335 --- scientific_name: Phaseolus vulgaris classical_locus: Sd gene_symbols: - PvP gene_symbol_long: Pigment gene_model_pub_name: Phvul.007G171333 gene_model_full_id: phavu.G19833.gnm2.ann1.Phvul.007G171333 confidence: 5 curators: - Scott Kalberer comments: - Postharvest seed coat darkening results in decreased consumer preference and lower economic value for the Common bean market class of Pintos. Rapid and saturated darkening after harvest of dry beans results from heavy accumulation of proanthocyanidins (PAs) and PA monomers (epicatechin and catechin) in developing seed coat tissues. - Psd is a recessive allele of the Pigment (P) candidate gene responsible for the slow darkening seed coat in Pinto beans (Phaseolus vulgaris). Evidence provided in Islam, Bett et al. (2020) that shows Pigment (allele Psd) is the SLOW DARKENING (Sd) gene included genetic complementation, transcript abundance, metabolite analysis, and an inheritance study. - The P gene encodes a basic helix-loop-helix transcription factor. One of its two transcript variants (P-1) is involved in proanthocyanidin (PA) biosynthesis and the other truncated variant (P-2) has either no or unknown function. Two mutations in the Psd allele- supplemental glutamate residue in the activation domain; arginine to histidine substitution in the bHLH domain- are likely responsible for reduced protein activity and PA accumulation in the slow-darkening (SD) cultivar. Flavonoid biosynthesis leading to PAs is regulated by an MBW complex consisting of members of the myeloblastosis (MYB), bHLH transcription factor, and WD40 repeat protein (WDR) families. - The P gene is a functional ortholog of the bHLH transcription factor AtTT8 that regulates testa pigment biosynthesis in Arabidopsis thaliana. In genetic complementation tests, ectopic expression among Arabidopsis tt8 mutants of the P-1 allele from regular darkening (RD) bean cultivar CDC Pintium completely restored both the activity of Dihydroflavonol 4-Reductase (AtDFR) and Anthocyanidin Reductase (AtANR) as well as the wild-type testa phenotype with expected PA levels. Transgenic expression of the Psd-1 allele from SD cultivar 1533-15 only partially redeemed the mutant phenotype, whereas transformation with constructs containing P-2 (CDC Pintium) failed to recover the wild-type phenotype. Loss-of-function alleles of the P gene were shown to cause white seed coat color in common bean (McClean, Bett et al., 2018). - The gene model Phvul.007G171333 corresponds to the P gene and was previously annotated as a transcription factor known as TRANSPARENT TESTA 8 (TT8). Evidence that P is Sd includes its gene expression being highest in seed coat tissue among the six candidate genes on chromosome 7 near markers Pvsd-1158 and Pvsd-1157 in both cultivars CDC Pintium and 1533-15. phenotype_synopsis: Pinto bean cultivars carrying the Psd allele of the Pigment gene have seed coats that darken more slowly following harvest. traits: - entity_name: seed coat color entity: TO:0000190 - quality_name: brown quality: PATO:0000952 - relation_name: positively regulates relation: RO:0002213 - entity_name: regulation of proanthocyanidin biosynthetic process entity: GO:2000029 - entity_name: bHLH transcription factor binding entity: GO:0043425 references: - citation: Islam, Bett et al., 2020 doi: 10.1002/ppp3.10132 pmid: 34268482 - citation: McClean, Bett et al., 2018 doi: 10.1111/nph.15259 pmid: 29897103 --- scientific_name: Phaseolus vulgaris classical_locus: V gene_symbols: - PvV - PvPUR gene_symbol_long: Violet gene_model_pub_name: Phvul.006G018800 gene_model_full_id: phavu.G19833.gnm2.ann1.Phvul.006G018800 confidence: 5 curators: - Scott Kalberer comments: - The classical V (Violet, Purple) locus of Phaseolus vulgaris affects the colors of seed coats and flowers. Plants with the dominant V allele are purple-flowered whereas homozygous recessive plants exhibit white (v) or pink (v-lae) flowers. The dominant V allele is associated with black-seeded beans, even as recessive v alleles produce seeds without dihydromyricetin-derived flavonoids (McClean, Lee et al., 2022). - Solely genotypes carrying the dominant V allele produced the anthocyanin named delphinidin 3-O-glucoside in seed coats. The colors of these lines ranged from blue to black (Beninger and Hosfield, 2003). - Phytochemical analysis showed that dihydromyricetin-related compounds (e.g.,delphinidin 3-glucoside, myricetin 3-glucoside) were absent in flowers from introgression lines with recessive v alleles, greatly reduced in seed coats of pink-flowered v-lae lines, and absent in the seed coats of white-flowered v lines. The purple-flowered V dominant-allele lines had flowers and seeds containing these compounds (McClean, Lee et al., 2022). - McClean, Lee et al. (2022) physically mapped the V locus to a narrow interval surrounding a Flavonoid 3′5’Hydroxylase (F3′5′H) candidate gene model (Phvul.006G018800) on chromosome Pv06. This low recombination heterochromoatic region resisted fine-mapping and the RAPD marker OD12-800 and 15 indels all co-segregated with V. Knowing the V locus to be associated with F3′5′H, a search for gene models including the F3′5′H KEGG identifier K13083 within the suspected Pv06 region of the reference genome G19833 revealed the gene model Phvul.006G018800. - Garcia-Fernandez, Campa et al. (2021) mapped a ‘TU’ × ‘Musica’ RIL population and showed that one of two genes responsible for a black seed coat phenotype was localized to a Pv06 region associated with locus V. They also proposed Phvul.006G018800 as the candidate V gene. Yet another study found Phvul.006G018800, the candidate gene for a Purple Mutation (PvPUR), was localized to the 243.9-kb region of Pv06 (Liu, Yang et al., 2023). - Protein and domain modeling determined the V gene encodes the enzyme Flavonoid 3′,5′-Hydroxylase (F3′5′H), a member of the Cytochrome P450 family (McClean, Lee et al., 2022). Sequence analysis of Phvul.006G018800 protein identified six conserved substrate recognition sites (SRS) and four functional motifs typical of Cytochrome P enzymes. Almost all these domain sequences were nearly the same as the functional F3′5′H domains of other legumes. - Active F3'5'H is required for biosynthesis of dihydromyricetin-derived flavonoids (McClean, Lee et al., 2022). Specifically, F3’5’H converts the dihydroflavonols named dihydrokaempferol (DHK) and dihydroquercetin (DHQ) to dihydromyricetin (DHM), a precursor of the blue-to-red pH-sensitive plant pigment delphinidin, its methylated derivatives such as petunidin and malvidin, and its glycoside-containing anthocyanin derivatives such as delphinidin 3-O-glucoside (Liu, Yang et al., 2023). - Nine total F3′5′H CDS haplotypes were discovered among the screened genotypes. Eight recessive haplotypes that control pink or white flower color, defined by mutations of functional domains required for P450 activities, evolved independently in the two bean gene pools from a common ancestral haplotype V-[5-593]. Dominant V-[5-593] expression was connected to purple flowers in Mesoamerican and Andean gene pools. The white v-[Mex235] haplotype was discovered in both gene pools indicating its early emergence. Other haplotypes were gene pool-specific, including the v-lae pink-flowered haplotypes in the Andean gene pool (McClean, Lee et al., 2022). - Definitive evidence that V encodes F3′5′H was provided by discovery of the v-[M0056] white-flowering haplotype. This v-[M0056] was produced by a natural intragenic crossover event between the v-lae[MDRK] (pink flower) and v-[Mex235] (white flower) haplotypes. The 14-nt deletion within the v-[Mex235] chromosome resulted in a frame-shift stop codon that eliminated the heme-binding domain and SRS6 functional regions of F3'5'H. The v-[M0056] recombinant haplotype contains the 5′-end of v-lae[MDRK] alongside the 3′-end of v-[Mex235]. Experimentally, if a section of a candidate gene were to be deleted and a phenotypic change observed, one would conclude the candidate gene was validated. This recombination event is a natural equivalent to gene editing in a species, P. vulgaris, in which complementation technologies have yet to be developed (McClean, Lee et al., 2022). - Purple mutants of P. vulgaris exhibited purple cotyledons, hypocotyls, stems, leaf veins, flower and pod tissues (Liu, Yang et al., 2023). Levels of total anthocyanins, delphinidins, and malvidins in purple-mutant pods were significantly higher than in wild-type plants (Liu, Yang et al., 2023). Six single-base mutations within the coding region of PvPUR altered the protein structure of F3’5’H resulting in the purple phenotype (Liu, Yang et al., 2023). - To validate the candidate gene's function, Arabidopsis thaliana were transformed using wild-type and purple-mutant common bean alleles. Compared with the wild-type Arabidopsis, the leaf bases and internodes of plants receiving the purple-mutant allele were purple, whereas the phenotypes of Arabidopsis transformed with the wild-type allele remained unaffected (Liu, Yang et al., 2023). phenotype_synopsis: The Violet (V) gene in Phaseolus vulgaris encodes the cytochrome P450 enzyme Flavonoid 3′,5′-Hydroxylase (F3′5′H). Functional V expression is needed for the biosynthesis of dihydromyricetin-derived flavonoids and affects the coloration of flowers, seed coats, and many other tissues. traits: - entity_name: flavonoid content entity: TO:0000290 - entity_name: anthocyanin content entity: TO:0000071 - entity_name: seed coat color entity: TO:0000190 - entity_name: flower color entity: TO:0000537 - entity_name: pericarp color entity: TO:0000707 references: - citation: McClean, Lee et al., 2022 doi: 10.3389/fpls.2022.869582 pmid: 35432409 - citation: Liu, Yang et al., 2023 doi: 10.1007/s11032-023-01362-8 pmid: 37313298 - citation: Garcia-Fernandez, Campa et al., 2021 doi: 10.1007/s00122-021-03922-y pmid: 34328529 - citation: Beninger, Hosfield, 2003 doi: 10.1021/jf0304324 pmid: 14690368 - citation: McClean, Lee et al., 2002 doi: 10.1093/jhered/93.2.148 pmid: 12140276