A dominant gene for garnet brown seed coats at the Rk locus in ‘Dorado’ common bean and mapping Rk to linkage group 1

Bassett, Mark J.; Miklas, Phillip N.; Caldas, Gina V.; Blair, Matthew W.

doi:10.1007/s10681-010-0247-3

Cited by 6 publications

(5 citation statements)

References 17 publications

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“…5 Length in base pairs refers to the length of the candidate gene (as in the case of p ) or the length of a marker sequence linked to a color/patterning gene. 6 Not shown is Rk (recessive red seed testa), whose location is controversial; it has been located to both Pv01 [34] and Pv02 [35].…”

Section: Figurementioning

confidence: 99%

Improving the Health Benefits of Snap Bean: Genome-Wide Association Studies of Total Phenolic Content

et al. 2019

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Snap beans are a significant source of micronutrients in the human diet. Among the micronutrients present in snap beans are phenolic compounds with known beneficial effects on human health, potentially via their metabolism by the gut-associated microbiome. The genetic pathways leading to the production of phenolics in snap bean pods remain uncertain. In this study, we quantified the level of total phenolic content (TPC) in the Bean Coordinated Agriculture Program (CAP) snap bean diversity panel of 149 accessions. The panel was characterized spectrophotometrically for phenolic content with a Folin–Ciocalteu colorimetric assay. Flower, seed and pod color were also quantified, as red, purple, yellow and brown colors are associated with anthocyanins and flavonols in common bean. Genotyping was performed through an Illumina Infinium Genechip BARCBEAN6K_3 single nucleotide polymorphism (SNP) array. Genome-Wide Association Studies (GWAS) analysis identified 11 quantitative trait nucleotides (QTN) associated with TPC. An SNP was identified for TPC on Pv07 located near the P gene, which is a major switch in the flavonoid biosynthetic pathway. Candidate genes were identified for seven of the 11 TPC QTN. Five regulatory genes were identified and represent novel sources of variation for exploitation in developing snap beans with higher phenolic levels for greater health benefits to the consumer.

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Section: Figurementioning

confidence: 99%

Improving the Health Benefits of Snap Bean: Genome-Wide Association Studies of Total Phenolic Content

et al. 2019

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“…The P gene (chromosome Pv07) is a primary basic gene considered as the control factor for the presence or absence of color, whose dominant genotypes show a colored seed coat while recessive genotypes prevent color expression and produce a white coat [ 20 , 21 ]. Other color genes described are J (= L gene, mature color development on Pv10), G (yellow–brown, Pv04), B (gray-brown, Pv02), V (violet factor, Pv06), complex C locus (complete color; Pv08), Rk (red kidney) whose location is controversially being located on both Pv01 [ 22 ], and Pv02 [ 11 , 17 ], Z (= D , zonal pattern color, Pv03), T (totally pattern color, Pv09), Gy (Grenish-yellow pattern, Pv08), and Bip (coat patterns based on the hilum, Pv10) [ 11 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

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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“…Color‐modifying genes do not confer a color by themselves but intensify color expression of the color genes. Color‐modifying genes include G for yellow‐brown, B for greenish yellow‐brown, V for purple to black, Rk for recessive red, R for dark red, and Gy for greenish‐yellow (Bassett, 2002; Bassett et al., 2010; Beninger & Hosfield, 1999). The mechanism of color expression is complicated; some of the genes are multiallelic, and they interact with each other to collectively determine the colors and patterns of seed coat, hilum ring, corona, pods, and flowers (Bassett, 2007).…”

Section: Introductionmentioning

confidence: 99%

Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association

et al. 2021

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Common bean (Phaseolus vulgaris L.) is consumed worldwide, with strong regional preferences for seed appearance characteristics. Colors of the seed coat, hilum ring, and corona are all important, along with susceptibility to postharvest darkening, which decreases seed value. This study aimed to characterize a collection of 295 yellow bean genotypes for seed appearance and postharvest darkening, evaluate genotype × environment (G × E) effects and map those traits via genome‐wide association analysis. Yellow bean germplasm were grown for 2 yr in Michigan and Nebraska and seed were evaluated for L*a*b* color values, postharvest darkening, and hilum ring and corona colors. A model to exclude the hilum ring and corona of the seeds, black background, and light reflection was developed by using machine learning, allowing for targeted and efficient L*a*b* value extraction from the seed coat. The G × E effects were significant for the color values, and Michigan‐grown seeds were darker than Nebraska‐grown seeds. Single‐nucleotide polymorphisms (SNPs) were associated with L* and hilum ring color on Pv10 near the J gene involved in mature seed coat color and hilum ring color. A SNP on Pv07 associated with L*, a*, postharvest darkening, and hilum ring and corona colors was near the P gene, the ground factor gene for seed coat color expression. The machine‐learning‐aided model used to extract color values from the seed coat, the wide variability in seed morphology traits, and the associated SNPs provide tools for future breeding and research efforts to meet consumers’ expectations for bean seed appearance.

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A dominant gene for garnet brown seed coats at the Rk locus in ‘Dorado’ common bean and mapping Rk to linkage group 1

Cited by 6 publications

References 17 publications

Improving the Health Benefits of Snap Bean: Genome-Wide Association Studies of Total Phenolic Content

Improving the Health Benefits of Snap Bean: Genome-Wide Association Studies of Total Phenolic Content

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

Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association

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