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Postharvest seed coat darkening effects in pinto bean. Pictures were taken for pinto bean lines CDC Pintium (RD), 1533‐15 (SD), and cranberry‐like Wit‐rood boontje (ND) on the same day of harvest (non‐aged) and after 6 months of storage at room temperature (aged)
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Pinto bean (Phaseolus vulgaris) is one of the leading market classes of dry beans that is most affected by postharvest seed coat darkening. The process of seed darkening poses a challenge for bean producers and vendors as they encounter significant losses in crop value due to decreased consumer preference for darker beans. Here, we identified a nov...
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Proanthocyanidins (PAs) are polyphenolic compounds present widely in the plant kingdom. These specialized metabolites are derived from the phenylpropanoid pathway and are known for producing brown pigments in different plant organs. PAs accumulate in the seed coat tissues of flowering plants and play a determinant role in seed germination and viabi...
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... Seeds with light background such as pinto, cranberry, and light red kidney bean are affected by postharvest darkening. Seed darkening is strongly dependent on the interaction between genotype and environment [6,84,85]. Genetically, it is determined by the J gene (beans with the genotype jj do not darken) and the sd gene, which determine how quickly the seeds darken. Slow darkening is determined by the sd gene (recessive inheritance). ...
... Regular darkening is associated with a higher content of proanthocyanidins in the seed coat than in the coat of slowly darkening beans. Storage conditions such as high temperatures, humidity and light lead to the oxidation of proanthocyanidins to visible pigments, which are reflected in a darker or browner seed coat [6,85,86]. The above-mentioned genes, such as T, P, V, Rk, Sal, Am, and Bic, show a high level of pleiotropic gene expression and control the colour of seed coats and flowers. ...
The common bean is an important legume valued for its protein-rich seeds and its ability to fix nitrogen, making it a key element of crop rotation. In conventional agriculture, the emphasis is on uniformity and genetic purity to optimize crop performance and maximize yields. This is due to both the legal obligations to register varieties and the challenges of implementing breeding programs to create genetically diverse varieties. This paper focuses on the factors that influence the occurrence of heterogeneous common bean populations. The main factors contributing to this diversity have been described, including local adaptations, variable weather conditions, different pollinator species, and intricate interactions between genes controlling seed coat colour. We also discuss the benefits of intercropping common beans for organic farming systems, highlighting the improvement in resistance to diseases, and adverse environmental conditions. This paper contributes to a better understanding of common bean seed heterogeneity and the legal obligation to use heterogeneous populations.
... The seed coat darkening trait is determined by epistatic interactions between the J locus and the P sd allele (McClean et al., 2002;Elsadr et al., 2011;Erfatpour et al., 2018;Islam et al., 2020). The P sd allele determines how quickly a seed coat will darken in the presence of a dominant allele at J (Elsadr et al., 2011). ...
... The P sd allele is related to the gene model Phvul.007G171333 encoding a bHLH transcription factor affecting the PA pathways (Islam et al., 2020). ...
ND Rodeo’ (PVP no. 202300270; Reg. no. CV‐356, PI 703020) is a new slow‐darkening (SD) pinto bean (Phaseolus vulgaris L.) cultivar developed by the Dry Edible Bean Breeding Program at North Dakota State University and released by the North Dakota Agricultural Experiment Station. Pinto bean is the largest market class grown in the United States, representing over 47% of the total US production for dry beans, and more than 70% is produced in North Dakota. SD pinto beans offer a good alternative to commercial cultivars of regular darkening (RD) pinto beans, which are typically subject to the risk of economic losses due to seed coat darkening. However, reaching seed yields comparable to RD pintos has been challenging. Between 2017 and 2022, ND Rodeo was tested across 25 environments in North Dakota, where seed yield was significantly higher than the SD pinto cultivars ‘ND Palomino’ and ‘Vibrant’ (18% and 22%, respectively), and comparable with RD pinto cultivars ‘La Paz’ and ‘Monterrey’. ND Rodeo is resistant to Bean common mosaic virus and has intermediate resistance to common bacterial blight, but similar to the commercial checks, it is susceptible to local races/strains of white mold, anthracnose, and rust pathogens. ND Rodeo has an average height of 56 cm which is significantly higher than the average of ND Palomino, Vibrant, and La Paz, and exhibits a desirable upright architecture to facilitate direct harvest. It has a 100‐seed weight of 36.2 g and matures in 102 days. Canning quality was rated as acceptable.
... The early-generation pinto bean cultivars were plagued by lodging, small seed size, and low yields (Miklas et al., 2020). Briefly, slow seed coat darkening in pinto beans is conferred by the P sd allele (Islam et al., 2020), an allele at the P (pigment) locus (McClean et al., 2018). The P sd allele reduces seed pigmentation and phytoalexin accumulation in the seed coat, which results in slower darkening of pinto bean seeds in storage (Duwadi et al., 2018). ...
The pinto bean (Phaseolus vulgaris L.) cultivar ‘USDA Diamondback’ (Reg. no. CV‐353, PI 698822) was released by the USDA‐ARS in 2022 as a high‐yielding cultivar with an upright architecture and the slow‐darkening seed coat trait. It was bred for tolerance to multiple abiotic stresses in a “purgatory” plot purposely managed to have compacted soil, low soil fertility, and intermittent drought conditions. Conversely, selection for high yield potential was conducted in non‐stress trials with tillage, irrigations, and fertilizers applied for optimal production. USDA Diamondback exhibits wide adaption to production regions across the United States, as evidenced by an average seed yield of 3808 kg ha⁻¹ across 14 location‐years in the Cooperative Dry Bean Nursery. Virus testing and resistance gene–linked markers indicate USDA Diamondback has a three‐gene combination (bc‐ud, bc‐1, and bc‐3) that confers durable resistance to all known strains of Bean common mosaic virus and Bean common mosaic necrosis virus. A similar combination of pathogen and marker testing indicated that USDA Diamondback possesses the Ur‐3 and Ur‐6 genes for resistance to bean rust. The seed size, appearance, and canning quality characteristics of USDA Diamondback meets the industry standards for packaging and processing.
... Non aged (freshly harvested) and aged (after 6 months of storage at room temperature) pictures of three different pinto cultivars: CDC Pintium (RD), 1533-15 (SD) and cranberry like Wit-rood boontje (ND). (adapted from Islam et al. 2020). b Area specific PA-level variation in a seed of pinto bean cultivar CDC Pintium biosynthetic genes were upregulated in darker cranberry beans at early and intermediate stages of seed development leading to higher levels of PAs compared to non-darkening beans (Freixas Coutin et al. 2017). ...
... These genes follow either the dominance, epistasis, multi-, or co-dominance rules of genetics to produce different seed phenotypes (Bassett 2007). From the nine color coding loci only, P, J, and V are identified in the common bean genome by molecular characterization (Erfatpour and Pauls 2020; Islam et al. 2020;McClean et al. 2022). Among them, P (P sd allele) and J control PA levels and postharvest seed coat darkening, while V determines flower color. ...
... The Pigment (P) gene is called the ''ground factor'' for determining the seed coat and flower color and patterns in beans, first described by Emerson (1909). Later, during the search for the gene determining the SD trait in pinto beans, Islam et al. (2020) identified the P sd allele of P. P is a basic helix loop helix (bHLH) transcription factor that regulates DFR and ANR expression and PA biosynthesis. A recessive P allele (pp) produces white seeds and flowers (McClean et al. 2018). ...
Proanthocyanidins (PAs) are polyphenolic compounds present widely in the plant kingdom. These specialized metabolites are derived from the phenylpropanoid pathway and are known for producing brown pigments in different plant organs. PAs accumulate in the seed coat tissues of flowering plants and play a determinant role in seed germination and viability, protect seeds from biotic and abiotic stresses, and thus ensure the long-term storage potential of seeds. In addition, PAs are a rich source of antioxidants for the health of both human and livestock. Many of the commercially relevant dry beans (Phaseolus vulgaris) contain high levels of PAs, which when oxidized cause the beans to overdarken, a phenomenon known as postharvest darkening. These darker beans give the impression of oldness, and consumers tend to avoid buying them which, in turn, affects their market value. Pinto beans, one of the leading market classes of dry beans, are affected the most by the postharvest darkening. Therefore, exploring the regulation of PA biosynthesis and accumulation in bean seed coat tissues will help to develop strategy to manage the postharvest darkening effect in pintos. In this review, we discuss the PA biosynthesis and its regulation, connecting it to seed coat color genetics for a better understanding of the mechanism of seed coat darkening.
... The J locus (Pv10) controls whether a genotype will darken (Elsadr et al. 2011). The P sd allele (slow darkening) of the P gene on Pv07 influences the rate of darkening; slow darkening is recessive to regular darkening (Junk-Knievel et al. 2008;Felicetti et al. 2012;Islam et al. 2020). Slow darkening has been deployed in commercial pinto cultivars, including "ND-Palomino" . ...
Genetic vulnerability refers to (sometimes catastrophic) actual or potential losses in the production of a crop (in quantity and/or quality), attributable to spatial or temporal reduction in the crop's biodiversity. Conversely, genetic resilience refers to the natural and anthropic capabilities of this biodiversity to mitigate these reductions in crop production. Here, an assessment is provided of genetic vulnerability and resilience of Phaseolus beans, which provide an abundant and sustainable source of protein and micronutrients for populations around the world. We provide an overview of the economic, nutritional, and cultural role of Phaseolus beans and phylogenetic and diversity analyses of the genus, its five domesticated species, and seven domestications, which provide key foundational information for this appraisal. We then assess the uniformity of the crop in the United States and the main drivers of genetic erosion in the centers of origin of the genus in the Americas. Next, the current and emerging breeding constraints are discussed for biotic and abiotic stresses, morphological and phenological traits, and dietary and cooking needs. To address these vulnerabilities, several resources have been developed and, which have been applied to increase the genetic resilience of Phaseolus beans. The resilience resources include genetic resources collections such as the global collection at the Centro Internacional de Agricultura Tropical (CIAT, Colombia), national collections in the United States, Brazil, the European Union, and elsewhere, which include wild and domesticated types across the genus but focus primarily on domesticated species. Resilience resources also include genome‐wide reference DNA sequences for three of the five domesticated species, multiple diversity panels and recombinant inbred populations, and large sets of whole‐genome diversity data based on single‐nucleotide polymorphism (SNP) arrays, genotyping by sequencing, and whole‐genome sequencing of germplasm sets. Numerous marker–trait associations and genes affecting agronomic traits have also been characterized in the genus. In turn, these resources have been successfully utilized to make Phaseolus beans more resistant against biotic and abiotic stresses (including those incurred by climate change) and to improve dietary and culinary quality through significant breeding efforts in the United States, at CIAT (mainly Latin America and Africa) and in national programs in Latin America and Eastern Africa. Future challenges remain, however, which include (1) a continued need for ex situ and in situ conservation of diversity, with agroecologically informed germplasm explorations and integration of farmers into conservation and breeding activities; (2) increased pre‐breeding efforts involving gene bank curators and bean improvement scientists; (3) expansion of breeding of domesticated species other than common bean, where appropriate based on their potential adaptation to global climate change and consumer preferences; (4) an increased focus on culinary and dietary improvement; and (5) inclusion of microorganisms (both pathogenic and beneficial) in genetic conservation. We conclude that in the short term (~5 years), Phaseolus beans have limited genetic vulnerability. However, over the longer term, vulnerability due to several factors will increase, which can be addressed by a wide range of the resilience resources presented here.
... Most recessive p alleles eliminate flavonoids rendering seeds and flowers white. One allele, P SD (Islam et al., 2020), is unique. It allows normal seed FIGURE 1 | The flavonoid biosynthetic pathway. ...
... color development, but the typical post-harvest seed darkening observed with the P allele is greatly delayed when P SD is present. The delayed darkening is associated with a significant reduction in the expression of dihydroflavonol reductase and anthocyanin reductase (Islam et al., 2020) and the synthesis of procyanidins (Wiesinger et al., 2021) that are precursors of proanthocyanins whose oxidation darkens the seed. Since procyanidins are inhibitors of iron uptake (Hart et al., 2015(Hart et al., , 2017, iron is more readily available from seeds of P SD . ...
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.
... P sd is the Sd gene. P sd is another allele of the P (Pigment) gene, whose loss-of-function alleles result in a white seed coat (Islam et al., 2020). Several sources of slowdarkening pinto beans have been developed, including 'Pinto Saltillo' (Sanchez-Valdez et al., 2004), 'CDC Pintium' (Junk-Knievel et al., 2008), and SDIP-1 (Singh et al., 2006). ...
Slow‐darkening pinto common bean (Phaseolus vulgaris L.) cultivar ‘Wildcat’ (Reg. no. CV‐345, PI 698190) was released by the University of Nebraska dry bean breeding program in 2018. It was bred for adaptation to western Nebraska growing conditions and enhanced resistance to bean rust, common bacterial blight (CBB), and Bean common mosaic virus (BCMV). The yield of Wildcat was comparable to conventional and slow‐darkening pinto bean cultivars grown in Nebraska from 2015 to 2020. During the 2017 Western Regional Bean Trial, 2017 Midwest Regional Performance Nursery, and 2018 Cooperative Dry Bean Nursery, Wildcat had a higher seed yield than ‘Twin Falls’, ‘Nez Perce’, ‘Black Foot’, ‘Montrose’, ‘Buster’, ‘ND‐Palomino’, and ‘La Paz’ at some locations. Wildcat has the Ur‐11 gene that confers resistance to all but one known bean rust race and carries the Indel NDSU_IND_11_48.459.896 marker tagging the Ur‐11 locus. Wildcat also has the SAP6 sequence characterized amplified region (SCAR) marker linked to a major CBB resistance quantitative trait locus, with an intermediate CBB rating (5.0) under field conditions at western Nebraska in 2020. Wildcat also carries the single dominant I gene that confers resistance to all non‐necrotic strains of BCMV and the SW13 SCAR marker linked to the I gene for resistance to BCMV. Wildcat has white flowers, blooms 46 d after planting, and is a full‐season bean, maturing 93 d after planting. The seed size of Wildcat, 43.3 g 100 seeds–1 on average, was significantly larger than current conventional and slow‐darkening pinto beans.
... Previous studies have shown that two unlinked interacting genes control postharvest darkening, J and sd, with the J genotype presenting postharvest darkening, jj genotype showing no darkening, and recessive sdsd paired with J showing slow darkening (Elsadr et al., 2011;Junk-Knievel et al., 2008). Gene sd has been confirmed to be an allele of the ground factor P and is denoted as p sd (Islam et al., 2020). Color-modifying genes do not confer a color by themselves but intensify color expression of the color genes. ...
... The gray dotted lines are false discovery rate-adjusted threshold at α = 0.05. P is the ground factor gene for seed coat color, of which p sd allele confers slow darkening trait (Islam et al., 2020;McClean et al., 2018). Sb*.4.1,Sa*.3.1,Sb*.3.1,SL*.3.1, quantitative trait loci reported by Bassett et al. (2021). ...
... This SNP was also significant for postharvest darkening, and 36 out of the 45 Mayocoba genotypes in the minor allele group at this SNP were non-or slow-darkening genotypes. Allele p sd , an allele of P, is involved in slow darkening in the presence of J; genotypes with homozygous recessive p sd shows a slower rate of darkening than regulardarkening genotypes (Elsadr et al., 2011;Islam et al., 2020;Junk-Knievel et al., 2008). The postharvest darkening genotype at Chr07pos29169848, background information, hilum ring color, corona color, and BLUE of the L*a*b* values of the YBC genotypes are summarized in Supplemental Table S6. ...
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.
... Similarly, Spitti et al. (2019) described that this characteristic is oligogenic or even polygenic from significant results obtained by the genotype and environment interaction. Islam et al. (2020) demonstrated yet another allele in the P gene (Psd) responsible for the SD trait in common beans, "P" is a transcription factor that restores the seed coat color. The sequence comparison of this gene in several beans differing in the seed coat postharvest darkening provided insights into the molecular mechanism that governs this characteristic and the development of new specific gene markers for potential use in bean breeding programs. ...
... The latter do not show any darkening pattern among different grain types and do not strongly affect the environment (Alvares et al., 2019;Spitti et al., 2019). Seed coat postharvest darkening depends on beans genotype (Islam et al., 2020). ...
The culinary quality of carioca beans is related to their market value and consumer acceptability. The depreciation of the cooking/technological quality of the product occurs mainly because of the integument browning and the longer cooking time of the grains, which are influenced by the storage time and conditions. The loss of culinary quality reduces the market value of carioca beans because consumers reject darkened grains that are attributed to a longer cooking time. As a result, cooking time (resistance to cooking), the color of the integument, and the texture of the cooked beans are determinant factors in the acceptance of carioca bean cultivars. The browning of the grain integument and the cooking time mainly depends on the environmental conditions, storage time, the tegument of each genotype, and the chemical and physical properties of the cotyledons. Therefore, this review aims to survey the scientific literature on the extrinsic and intrinsic factors that affect the culinary quality of carioca beans.
... Even though the flavonoid biosynthesis pathway has been widely elucidated in different species, such as Arabidopsis thaliana and Glycine max, information available in common bean is more limited (Caldas and Blair 2009;Reinprecht et al. 2013;Myers et al. 2019), since to date few candidate genes have been physically positioned in the genome and the implication of nucleotide allelic variations in determining seed coat color has been poorly evaluated (Reinprecht et al. 2013;McClean et al. 2018;Islam et al. 2020). Although certain species-specific differences have been described, the flavonoid biosynthesis pathway presents a high degree of conservation among species at both the structural and functional genetic levels (Chaves-Silva et al. 2018;Petroni and Tonelli 2011). ...
Key message
Three genes associated with the seed coat color in a TU/Musica RIL population were located on a genetic map, and two candidate genes proposed to control black seed coat in the TU genotype were characterized.
Abstract
Seed coat color is an important characteristic of common bean (Phaseolus vulgaris L.) associated with the marketability of dry bean cultivars, quality and nutritional characteristics of seed, as well as response to pathogens. In this study, the genetic control of seed coat color in a recombinant inbred line population (175 lines) obtained from the cross ‘TU’ × ‘Musica’ was investigated. Phenotypic segregation fitted 1:1 for white vs. nonwhite, and 3:1 for brown versus black, indicating the involvement of three independent genes, one controlling white color and two (with epistatic interaction) controlling black color. Using a genetic map built with 842 SNPs, the gene responsible for the white seed coat was mapped on the linkage group Pv07, in the position previously described for the P gene. For the black seed coat phenotype, two genes were mapped to the beginning of chromosomes Pv06 and Pv08, in the positions estimated for the V gene and the complex C locus, respectively, by classical studies. The involvement of these two genomic regions was verified through two crosses between three selected RILs exhibiting complementary and dominant inheritance, in which the TU alleles for both genes resulted in a black phenotype. Two genes involved in the anthocyanin biosynthesis pathway were proposed as candidate genes: Phvul.006G018800 encoding a flavonoid 3′5’hydroxylase and Phvul.008G038400 encoding MYB113 transcription factor. These findings add knowledge to the complex network of genes controlling seed coat color in common bean as well as providing genetic markers to be used in future genetic analysis or plant breeding.
