Dissecting the genetic control of seed coat color in a RIL population of common bean (Phaseolus vulgaris L.)

García-Fernández, Carmen; Čampa, Ana; Fernández, Juan José Ferreira

doi:10.1007/s00122-021-03922-y

Cited by 21 publications

(32 citation statements)

References 47 publications

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“…Here, we describe biochemical analysis of introgression lines, with a shared background and different recessive v alleles, and found that dihydromyricetin-related compounds, including delphinidin, were greatly reduced in seeds and flowers with recessive v alleles. We physically mapped V near a F3′5′H gene model, a result also reported recently using RIL mapping by García-Fernández et al (2021) . Our sequencing of natural variants and a haplotype reconstruction conclusively shows that V indeed encodes F3′5′H.…”

Section: Introductionsupporting

confidence: 54%

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

et al. 2022

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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.

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Section: Introductionsupporting

confidence: 54%

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

et al. 2022

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“…These regulatory genes include a MYB transcription factor that forms part of the MBW (MYB-βHLH-WD40) ternary complex, which activates the late biosynthetic proteins required for the anthocyanin and proanthocyanidin synthesis in other species [ 41 ]. One of these genes encoding a MYB113- related factor, Phvul.008G038400 , has been proposed as a gene responsible for the black seed coat color expression in the cultivar TU [ 26 ]. Another wide QTL for phenolic metabolites, Phe_Pv08(62.5), was located at the end position of chromosome Pv08, between 62.58–63.28 Mbp, associated with the synthesis of the anthocyanin Pel_G.…”

Section: Discussionmentioning

confidence: 99%

“…The other QTL including the black_NB seed trait, C_Pv06(4.2), corresponds with the V color gene. 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.…”

Section: Discussionmentioning

confidence: 99%

“…Genotyping-by-sequencing (GBS), as described by [ 59 ], was carried out at BGI-Tech (Copenhagen, Denmark) using the ApeKI restriction enzyme. The sequencing reads from different genotypes were aligned [ 26 ] using the reference genome v2.1 [ 60 , 61 ]. Data were filtered in Tassel v5.2 software [ 62 ] for missing values (< 10%) and minor allele frequency (MAF > 0.05), and a total of 11,763 SNPs were considered for GWAS (Additional file 1 ).…”

Section: Methodsmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2023

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Background A large variation in seed coat colors and seed phenolic metabolites is present in common bean (Phaseolus vulgaris L.). The study of the relationships between seed coat color phenotype and the phenolic profile is an important step in the elucidation of the gene network involved in the phenylpropanoid biosynthetic pathway. However, this relationship is still poorly understood in this species. Results A genome-wide association study (GWAS) was used to investigate the genomic regions associated with the synthesis of 10 flavonoids (5 anthocyanins and 5 flavonols) and with 10 seed coat color traits using a set of 308 common bean lines of the Spanish Diversity Panel (SDP) which have been genotyped with 11,763 SNP markers.. A total of 31 significant SNP-trait associations (QTNs) were identified, grouped in 20 chromosome regions: 6 for phenolic metabolites on chromosomes Pv01, Pv02, Pv04, Pv08, and Pv09, 13 for seed coat color on chromosomes Pv01, Pv02, Pv06, Pv07, and Pv10, and 1 including both types of traits located on chromosome Pv08. In all, 58 candidate genes underlying these regions have been proposed, 31 of them previously described in the phenylpropanoid pathway in common bean, and 27 of them newly proposed in this work based on the association study and their homology with Arabidopsis anthocyanin genes. Conclusions Chromosome Pv08 was identified as the main chromosome involved in the phenylpropanoid pathway and in consequence in the common bean seed pigmentation, with three independent chromosome regions identified, Phe/C_Pv08(2.7) (expanding from 2.71 to 4.04 Mbp), C_Pv08(5.8) (5.89–6.59 Mbp), and Phe_Pv08(62.5) (62.58 to 63.28 Mbp). Candidate genes previously proposed by other authors for the color genes V and P were validated in this GWAS. Candidate genes have been tentatively proposed from this study for color genes B and Rk on Pv02, Asp on Pv07, and complex C on Pv08. These results help to clarify the complex network of genes involved in the genetic control of phenolic compounds and seed color in common bean and provide the opportunity for future validation studies.

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Genetic control of pod morphological traits and pod edibility in a common bean RIL population

García-Fernández,

Jurado,

Campa

et al. 2023

Theor Appl Genet

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Key message QTL mapping, association analysis, and colocation study with previously reported QTL revealed three main regions controlling pod morphological traits and two loci for edible pod characteristics on the common bean chromosomes Pv01 and Pv06. Abstract Bean pod phenotype is a complex characteristic defined by the combination of different traits that determine the potential use of a genotype as a snap bean. In this study, the TUM RIL population derived from a cross between ‘TU’ (dry) and ‘Musica’ (snap) was used to investigate the genetic control of pod phenotype. The character was dissected into pod morphological traits (PMTs) and edible pod characteristics (EPC). The results revealed 35 QTL for PMTs located on seven chromosomes, suggesting a strong QTL colocation on chromosomes Pv01 and Pv06. Some QTL were colocated with previously reported QTL, leading to the mapping of 15 consensus regions associated with bean PMTs. Analysis of EPC of cooked beans revealed that two major loci with epistatic effect, located on chromosomes Pv01 and Pv06, are involved in the genetic control of this trait. An association study using a subset of the Spanish Diversity Panel (snap vs. non-snap) detected 23 genomic regions, with three regions being mapped at a position similar to those of two loci identified in the TUM population. The results demonstrated the relevant roles of Pv01 and Pv06 in the modulation of bean pod phenotype. Gene ontology enrichment analysis revealed a significant overrepresentation of genes regulating the phenylpropanoid metabolic process and auxin response in regions associated with PMTs and EPC, respectively. Both biological functions converged in the lignin biosynthetic pathway, suggesting the key role of the pathway in the genetic control of bean pod phenotype.

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Dissecting the genetic control of seed coat color in a RIL population of common bean (Phaseolus vulgaris L.)

Cited by 21 publications

References 47 publications

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

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

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

Genetic control of pod morphological traits and pod edibility in a common bean RIL population

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