The Common Bean V Gene Encodes Flavonoid 3′5′ Hydroxylase: A Major Mutational Target for Flavonoid Diversity in Angiosperms

Abstract

The classic V (violet, purple) gene of common bean (Phaseolus vulgaris) functions in a complex genetic network that controls seed coat and flower color and flavonoid content. V was cloned to understand its role in the network and the evolution of its orthologs in the Viridiplantae. V mapped genetically to a narrow interval on chromosome Pv06. A candidate gene was selected based on flavonoid analysis and confirmed by recombinational mapping. Protein and domain modeling determined V encodes flavonoid 3′5′ hydroxylase (F3′5′H), a P450 enzyme required for the expression of dihydromyricetin-derived flavonoids in the flavonoid pathway. Eight recessive haplotypes, defined by mutations of key functional domains required for P450 activities, evolved independently in the two bean gene pools from a common ancestral gene. V homologs were identified in Viridiplantae orders by functional domain searches. A phylogenetic analysis determined F3′5′H first appeared in the Streptophyta and is present in only 41% of Angiosperm reference genomes. The evolutionarily related flavonoid pathway gene flavonoid 3′ hydroxylase (F3′H) is found nearly universally in all Angiosperms. F3′H may be conserved because of its role in abiotic stress, while F3′5′H evolved as a major target gene for the evolution of flower and seed coat color in plants.

Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance

“…The most significant SNP for seed coat color in tepary bean is SNP S06_11037669 which was statistically significant for L* and b* . This SNP was located 56 kbp from tepary gene Phacu.CVR.006G029800, which is a homolog of the recently characterized Flavonoid 3′5' Hydroxylase (F3′5′H) gene (Phvul.006G018800) (McClean et al., 2022) at the classical V locus. The master regulator of seed coat color in common bean is the P gene which is located on chromosome Pv07 (McClean et al., 2018).…”

Genome-wide association study for the extractable phenolic profile and coat color of common bean seeds (Phaseolus vulgaris L.)

“…The gene Phvul.006G018800 located in this region encodes a F3’,5’H and was previously proposed as the gene controlling the black seed coat color in the cultivar TU [ 26 ]. Later, McClean et al [ 27 ] confirmed that V encodes an F3’,5’H required for the expression of dihydromyricetin-derived metabolites. Beninger et al [ 6 , 24 ] affirmed that anthocyanin production is dependent on the V gene, since the presence of dominant genotypes V leads to anthocyanin accumulation, whereas recessive genotypes v results in flavonol accumulation.…”

“…Later, the P gene was confirmed to be a basic helix-loop-helix ( bHLH ) MYB transcription factor, with two candidate genes, Phvul.007G171333 and Phvul.007G 171466, that allows or blocks the expression of other color genes [ 21 ]. García-Fernandez et al [ 26 ] using a RIL population derived from the cross TUxMUSICA identified two candidate genes controlling black seed coat color, Phvul.006G018800 encoding an F3´5´H on Pv06 that correspond to V color gene [ 27 ], and Phvul.008G038400 encoding a MyB113 transcription factor on Pv08 that could correspond to the C color locus.…”

TandZ, Partial Seed Coat Patterning Genes in Common Bean, Provide Insight into the Structure and Protein Interactions of a Plant MBW Complex

“…The sequence of recessive zz donors lines V0869 (PI527806), V0919 (PI527820), and Earliwax (PI549618) used to develop multiple introgression lines, was extracted from a 40X resequencing data set (McClean et al 2022). Relative to 5-593, all three lines share the 12 nt in-frame deletion with G19833.…”