Mark A. Brick

A reference genome for common bean and genome-wide analysis of dual domestications

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.

Mechanisms Associated with Dose-Dependent Inhibition of Rat Mammary Carcinogenesis by Dry Bean (Phaseolus vulgaris, L.)

The purpose of this study was to determine whether a dry bean (Phaseolus vulgaris, L.) containing diet exerts an inhibitory effect on mammary carcinogenesis in a well-characterized rodent model for breast cancer. Twenty-one-d-old female Sprague Dawley rats were given an intraperitoneal injection of 1-methyl-1-nitrosourea and 7 d after carcinogen injection were randomized to 1 of 5 groups fed a modification of the AIN-93G diet formulation containing 0, 7.5, 15, 30, or 60% (wt:wt) small red dry bean incorporated as cooked, freeze-dried, and milled powder. All experimental diets had the same macronutrient content based on proximate analysis. Compared with the control group, dry bean consumption resulted in dose-dependent reductions in mammary cancer incidence (P = 0.046), cancer multiplicity (P = 0.001), and tumor burden (P = 0.01). Dry bean consumption was associated with dose-dependent reductions in plasma concentrations of glucose, insulin, insulin-like growth factor-1, C-reactive protein, and interleukin-6 in food-deprived rats. Analysis of mammary adenocarcinomas indicated that a dominant mechanism accounting for reduced tumor burden was the induction of apoptosis. B cell lymphoma 2 and X-linked inhibitor of apoptosis protein levels decreased and BCL-2-associated X protein increased with increasing dry bean consumption, findings consistent with the induction of apoptosis via the mitochondrial pathway. These data demonstrate that a legume without noteworthy content of isoflavones inhibits the development of mammary carcinogenesis and are consistent with a recent report from the Nurses Health Study that bean or lentil intake is associated with a lower risk for breast cancer.

Metabolomic and Functional Genomic Analyses Reveal Varietal Differences in Bioactive Compounds of Cooked Rice

Emerging evidence supports that cooked rice (Oryza sativa L.) contains metabolites with biomedical activities, yet little is known about the genetic diversity that is responsible for metabolite variation and differences in health traits. Metabolites from ten diverse varieties of cooked rice were detected using ultra performance liquid chromatography coupled to mass spectrometry. A total of 3,097 compounds were detected, of which 25% differed among the ten varieties. Multivariate analyses of the metabolite profiles showed that the chemical diversity among the varieties cluster according to their defined subspecies classifications: indica, japonica, and aus. Metabolite-specific genetic diversity in rice was investigated by analyzing a collection of single nucleotide polymorphisms (SNPs) in genes from biochemical pathways of nutritional importance. Two classes of bioactive compounds, phenolics and vitamin E, contained nonsynonymous SNPs and SNPs in the 5′ and 3′ untranslated regions for genes in their biosynthesis pathways. Total phenolics and tocopherol concentrations were determined to examine the effect of the genetic diversity among the ten varieties. Per gram of cooked rice, total phenolics ranged from 113.7 to 392.6 µg (gallic acid equivalents), and total tocopherols ranged between 7.2 and 20.9 µg. The variation in the cooked rice metabolome and quantities of bioactive components supports that the SNP-based genetic diversity influenced nutritional components in rice, and that this approach may guide rice improvement strategies for plant and human health.

Traits associated with dry edible bean (Phaseolus vulgaris L.) productivity under diverse soil moisture environments

Two experiments were conducted in the Rift Valley, Ethiopia (8°N and 39°E) to determine associations between eight plant traits and seed yield, and to obtain estimates of narrow sense heritability for the traits. Experiment I evaluated seven dry edible bean cultivars/lines at two locations to simulate different soil moisture stress, including, Debre Zeit(non-stress) and Dera (moderate-stress). Experiment II evaluated 25 cultivars/lines in three environments including, Melkassa early planted (non-stress), Melkassa late planted (high-stress), and Dera (moderate-stress). A randomized-complete-block design with three replicates was used in both experiments. Plant traits evaluated were seed yield, pods plant-1, seeds pod-1, 100 seed weight, root dry weight, hypocotyl diameter, plant biomass, plant height and days to flowering. Plant traits that were significantly associated with seed yield were included in a stepwise-regression model to determine which trait or combination of traits provided the best model to estimate seed yield in each environment. An analysis of variance was conducted to test main effects and interactions between plant traits and environments. Significant variation among lines occurred for seed yield and all plant traits in both experiments. Strong positive correlations were observed between plant biomass and seed yield in all environments. Seed yield and pods plant-1 were also highly associated in four of the five environments. Stepwise regression models indicated that the combination of pods plant-1 and plant biomass consistently contributed to seed yield prediction, while other traits did not. Because both plant biomass and pods plant-1 had moderate to high narrow sense heritability estimates and low GE interactions, they should be useful as indirect selection criteria to improve and stabilize seed yield in a breeding program.

Inheritance of resistance to a Colorado race of Fusarium oxysporum f. sp. phaseoli in common beans

Fusarium wilt of common bean Phaseolus vulgaris caused by Fusarium oxysporum f. sp. phaseoli (FOP) is a serious disease in many production areas of the world. Inheritance of resistance in common bean to a pathogenic race of FOP isolated from pinto bean, U.I. 114, in Colorado was investigated. Resistant (R) and susceptible (S) common bean lines and cultivars from diverse sources were used as parents. The parental material, and F 2 and F 3 progeny derived from crosses between R and S lines were evaluated for reaction to FOP using a seedling root-clip inoculation technique under controlled greenhouse conditions. Inheritance of resistance to FOP differed among the parental lines and cultivars. Three segregation patterns were observed in the F 2 progeny of crosses between R and S parents. In one group, segregation patterns fit a single completely-dominant gene model (3R:1S), whereas segregation in the other group fit a more complex inheritance pattern in which recessive gene action controlled resistance to FOP. Other resistance patterns were more indicative of a quantitative pattern. Resistant lines that possessed single dominant genes for resistance originated from the Durango race, while resistant lines having recessive genetic resistance were from the Mesoamerican race of the Middle American Center of Diversity

Relationships between productivity and carbon isotope discrimination among dry bean lines and F2 progeny

Common bean (Phaseolus vulgaris L.) and tepary bean (P. acutifolius Gray) are grown for their edible seed and production is limited by insufficient soil moisture in many parts of the world. Carbon isotope discrimination (Δ) against 13CO_2 during photosynthesis has been suggested as a useful selection criterion to improve crop productivity in water-limited environments, however, there is a need to first understand relationships between productivity and Δ in common bean. The objectives of this study were to: 1) evaluate relationships between productivity (as measured by seed yield and biomass) and Δ among diverse dry bean lines and F2 progeny, 2) evaluate associations for Δ, seed yield and biomass among lines grown in different field environments and 3) estimate narrow sense heritability for Δ, seed yield and yield components. One hundred dry bean lines were evaluated at Yellow Jacket, CO in irrigated and non-irrigated field plots during 1988 and 1989. All significant relationships between seed yield or biomass and Δ were positive. In general, relationship between seed yield and Δ among lines were weak and R2 ranged from near zero to 0.29 across years and environments. The correlations for Δ, seed yield and biomass production among lines grown in different environments were all significant and positive (0.76 > r > 0.36). Narrow-sense heritability estimates for Δ and seed yield were 0.78 and 0.75, respectively. These results support the positive relationship between productivity and Δ in bean, however, the weak relationships between Δ and seed yield do not suggest that Δ would be a useful sole selection criterion to improve productivity.

Cell signaling pathways associated with a reduction in mammary cancer burden by dietary common bean (Phaseolus vulgaris L.)

Emerging evidence indicates that common bean (Phaseolus vulgaris L.) is associated with reduced cancer risk in human populations and rodent carcinogenesis models. This study sought to identify cancer-associated molecular targets that mediate the effects of bean on cancer burden in a chemically induced rat model for breast cancer. Initial experiments were conducted using a high dietary concentration of bean (60% wt/wt) where carcinoma burden in bean-fed rats was reduced 62.2% (P < 0.001) and histological and western blot analyses revealed that the dominant cellular process associated with reduced burden was induction of apoptosis. Further analysis of mammary carcinomas revealed changes in the phosphorylation states of mammalian target of rapamycin (mTOR) substrates (4E-binding protein 1 and p70S6 kinase) and mTOR regulators adenosine monophosphate-activated protein kinase and protein kinase B (Akt) (P < 0.001). Effects on mTOR signaling in carcinomas were also found at lower dietary concentrations of bean (7.5-30% wt/wt). Liquid chromatography-time of flight-mass spectrometry analysis of plasma provided evidence of altered lipid metabolism consistent with reduced mTOR network activity in the liver (P < 0.001). Plasma concentrations of insulin and insulin-like growth factor-1 were reduced by 36.3 and 38.9%, respectively, (P < 0.001), identifying a link to Akt regulation. Plasma C-reactive protein, a prognostic marker for long-term survival in breast cancer patients, was reduced by 23% (P < 0.001) in bean-fed rats. Identification of a role for the mTOR signaling network in the reduction of cancer burden by dietary bean is highly relevant given that this pathway is deregulated in the majority of human breast cancers.

Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean

Common bean (Phaseolus vulgaris L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome‐wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single‐nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits. The degree of inter‐ and intrachromosomal linkage disequilibrium (LD) was estimated after accounting for population structure and relatedness. The LD varied between chromosomes for the entire MDP and among race Mesoamerica and Durango–Jalisco genotypes within the panel. The LD patterns reflected the breeding history of common bean. Genome‐wide association studies led to the discovery of new and known genomic regions affecting the agronomic traits at the entire population, race, and location levels. We observed strong colocalized signals in a narrow genomic interval for three interrelated traits: growth habit, lodging, and canopy height. Overall, this study detected ∼30 candidate genes based on a priori and candidate gene search strategies centered on the 100‐kb region surrounding a significant SNP. These results provide a framework from which further research can begin to understand the actual genes controlling important agronomic production traits in common bean.

Resistance to Fusarium oxysporum f.sp. phaseoli in tepary beans (Phaseolus acutifolius)

More than 60 accessions of tepary bean (Phaseolus acutifolius) and five cultivars of common bean (P. vulgaris) were evaluated for disease reactions to different races of wilt-causing Fusarium (F. oxysporum f. sp. phaseoli under glasshouse conditions; 95% of the tepary accessions were resistant. Resistant sources included both cultivars and wild accessions. We propose that a systematic screening of diverse germ plasm sources such as tepary beans be conducted to complement Fusarium wilt and multiple disease resistance information currently available for common beans

Characterization and density of trichomes on three common bean cultivars

Trichomes have been implicated as a mechanism which can confer resistance to both plant pests and drought. A study was conducted to provide information regarding genetic variability for trichome distribution and density among three diverse dry bean (Phaseolus vulgaris L.) cultivars, and to characterize the types of trichomes present among the cultivars. Trichomes on the leaf surfaces were micrographed with a scanning electron microscope (SEM) and counted using a stereomicroscope on both the abaxial and adaxial leaf surfaces of the cultivars ‘Bill Z’, ‘Pompadour Checa’ and ‘Diacol Calima’. Straight, hooked, and glandular trichomes were observed on the leaf surfaces of each cultivar. SEM micrographs are presented for the leaf surfaces of each cultivar and trichome type. The abaxial leaf surface had more straight trichomes than the adaxial leaf surface for ‘Pompadour Checa’ and ‘Diacol Calima’, however ‘Bill Z’ had more on the adaxial surface. The opposite relationship existed among the cultivars and leaf surfaces for the hooked trichomes.ResumenTricomas han sido implicado como un mechanismo el cual puede conferir resistencia a sequía y pestes. Un estudiofue conducido para obtener información acerca de la variabilidad genética de la distribución y densidad de tricomas entre tres diversos cultivares de frijol para grano seco, y caracterizar los tipos de tricomas presente entre los cultivares. Los tricomas de la superficie de la hojas fueron micrografiados con un scanning microscopio electronico (SEM) y contados empleando un stereo microscopio en ambas superficies abaxial y adaxial de hojas de los cultivares ‘Bill Z’, ‘Pompadour Checa’ y ‘Diacol Calima’. Tricomas rectos, unciforme, y glandulares fueron observados sobre la superficie de las hojas en coda cultivar. SEM micrografias son presentados para la superficie de las hojas de cada cultivar y tipo de tricoma. La superficie abaxial de la hoja tuvo más tricomas rectos que la superficie adaxial de la hoja para ’Pompadour Checa ’y ’Diacol Calima ’, sin embargo ‘Bill Z’ tuvo mas en la superficie adaxial. Una relaciôn opuesta existe entre los cultivares y superficie de las hojas para los tricomas unciformes.