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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Research Project #425227

Research Project: Genetic Enhancement of Dry Bean Nutritional and Processing Qualities

Location: Sugarbeet and Bean Research

2017 Annual Report

Objective 1: Breed dry bean germplasm for increased nutrient density and for decreased phytic acid in dry bean seeds, and identify the genes involved in these traits. Objective 2: Determine the genetic control of, and develop molecular markers for, dry bean germplasm with decreased cooking time, improved canning quality and color retention traits.

Identify QTL for seed iron (Fe) and zinc (Zn) in a black bean RIL population. Conduct Meta QTL analysis using the results of six QTL studies for seed Fe and Zn content. The consensus QTL identified through the meta analysis will be validated by developing near isogenic lines for the consensus QTL using the closest markers. Inbred backcross will be used to introduce high seed Fe and Zn content into U.S. adapted black beans. Develop low phytic acid U.S. adapted black bean germplasm via backcrossing the single gene trait into a U.S. black bean background. Identify and validate markers for canning quality in black beans. Identify the Rk and C seed coat color in light red kidney and dark red kidney colors via RNA sequencing. Develop improved cranberry bean germplasm. A diversity analysis and strategic crossing with other seed types will be used as an approach to increase the genetic diversity in the market class. Assessment of cooking time and canning quality will be conducted in a panel of P. vulgaris genotypes from the Andean gene pool. Multivariate clustering analyses will be performed for traits such as cooking time, water uptake, canning appearance, texture, and color for determining similarity and grouping of lines. Genotypes with superior quality traits and combinations of traits will be identified for use as parents for crossing. Association mapping will be conducted to identify genomic regions influencing cooking time and canning quality.

Progress Report
QTL analysis for seed iron and zinc concentration: A meta-analysis from seven QTL studies in Andean and Middle American intra and inter genepool populations was conducted to identify the regions in the genome that control the Fe and Zn levels in seeds. In total, 4 Meta QTL specific to Fe and 3 Meta QTL specific to Zn were identified. Additionally, eight Meta QTL that co-localized for Fe and Zn concentration were identified across 8 chromosomes. Individually 10 to 27% of the phenotypic variation was explained by the shared Meta QTL. The physical positions for 15 individual Meta-QTL were identified across six recombinant inbred bi-parental and one advanced backcross population. In the 15 Meta-QTLs we identified 38 candidate genes that belong to six gene families that have been related with transport of iron and zinc in plants. In addition, previously identified Meta QTL for seed Fe and Zn concentrations on two bean chromosomes, Pv02 and 11 were further supported with genome wide association analysis results for seed Zn concentration in the Andean Diversity Panel. Markers in these regions were tested for utility as molecular markers in black bean breeding lines. These particular markers were not good candidates for marker assisted selection. We will evaluate an alternative approach of using genomic selection methodology for future breeding populations. Breeding high iron and zinc bean germplasm: A total of 33 black bean F2 populations and 45 advanced black bean breeding lines are in advanced yield trials at the Saginaw Valley Research Farm in Richville, Michigan. Breeding low phytic acid black bean lines: Low phytic acid (LPA) black breeding lines were evaluated for phytic acid levels and end use quality. In the F2 generation single plant selections were made for plant architecture, adaptation and seed type. In the F2 through F4 generation, the LPA genotype was classified through high resolution melting curve analysis. F4 selections were field grown and harvested seed was analysed for seed yield, phytic acid concentration, cooking, canning and nutritional quality. The LPA black bean lines had 37 to 74% less phytic acid than the wild type siblings. We found that the LPA lines had exceptionally long cooking times, after three hours in boiling water most were not cooked. The LPA lines had higher levels of Zn in raw seeds as compared to wild type siblings, however when cooked, the LPA lines lost much more Zn than the WT lines and ended up with less actual Zn than wild types. On the basis of yield performance, canning and cooking qualities, two LPA lines (B14-4 and B14-49) were identified as best germplasm for further breeding improvements. We have developed near isogenic LPA lines and they are currently planted at the Saginaw Valley Research Farm. Evaluation of bean germplasm for cooking time and canning quality: A yellow dry bean recombinant inbred line population (ADP0468 x ADP0512) of 227 genotypes were assessed for cooking time, flavor characteristics, and texture. Cooking times ranged from approximately 20 to 40 minutes. A trained sensory panel determined flavor and texture profiles of each genotype using 5-point hedonic scales. A texture analyzer with a 2mm cylindrical probe was used to determine work to bite for each genotype and to support the texture data obtained from the panel. Dry bean genotypes from six market classes were evaluated for their use as a milled flour ingredient. Michigan grown dry beans seeds were treated then milled using a commercial mill. The resulting flours were used to produce single-variety bean pastas. Formulations were optimized using a bench top fresh pasta maker. Consumer sensory panels were conducted for six single variety dry bean pastas with wheat pasta as the point of comparison. The pastas were evaluated for nutritional attributes and compared to boiled whole beans of the same varieties and wheat pasta. Dry bean pastas retained the nutritional profile of boiled whole seeds with respect to protein, starch as well as iron concentrations. They are also nutritionally superior to wheat pasta. Resistant starch (a component of dietary fiber) concentrations in bean pastas were comparable to their boiled whole seed counterparts. Varietal and genotypic differences were observed in the colors and texture of dry bean pastas. No statistically significant differences were observed among the bean pastas for the attributes of appearance, aroma, flavor, texture and overall. However, the wheat control was significantly different from both light and dark colored bean pastas for most attributes. Develop improved cranberry bean germplasm: We currently have 30 cranberry bean breeding lines in advanced yield trials, some of which have combined acceptable plant architecture with superior seed and canning quality. We have materials under evaluations at the F2 to F6 generations, including 45 lines in preliminary yield trial and 14 F2 populations. We also have one line that we are considering for a germplasm release and is currently being evaluated in six field locations in Michigan. In addition to cranberry beans, we have early generation yellow, dark and white kidney, and purple speckled bean populations under development. Identify and validate markers for canning quality in black beans: Genetic variability for color retention was evaluated on black bean breeding lines and cultivars from the major U.S. public bean breeding programs. Color retention as determined by a trained sensory panel on a scale of 1 to 5 was highly variable and ranged from 1.4 to 4.5. Genome wide association analysis was conducted to determine genomic regions responsible for color retention and canning quality in black beans that were genotyped with 5398 SNP markers. A region on Pv05 at 39Mb was associated with color retention and was polymorphic candidates for MAS.Delphinidin-3-glucoside was identified as the dominant anthocyanin with the highest concentration among black bean genotypes. The anthocyanin malvidin-3-glucoside was found to be retained after canning more than the other two anthocyanins. These results are in preparation for a peer reviewed publication. An experimental technique for scanning dry bean seeds using Vis/NIR spectroscopy (over the range of 400–2,498 nm) and hyperspectral imaging (over the range of 400–1,000 nm) was developed and optimized. This involved the spectral and spatial calibration of the optical sensors, selection of the best setting conditions for the spectral fiber sensor or camera and source of light, the sample holder design; as well as, the development of various image processing algorithms for hyperspectral imaging written in MATLAB software including: (i) image reading and preprocessing, (ii) segmentation of seeds from the background, (iii) separation of touching seeds, and (iv) image analysis for computing mean intensity of individual seeds at each spectral wavelength, data transformation using various spectral preprocessing methods, and regression analysis using multivariate methods such as partial least squares, feature selection and multiple regression analysis. All these methods have been intensively tested with a wide range of bean genotypes and different sensorial characteristics in appearance, color retention and firmness. The major noteworthy findings using both Vis/NIR spectroscopy and hyperspectral imaging include: First, the accuracy and robustness of end-use quality models for predicting appearance, color and texture (i.e., firmness/softness) in canned black beans were successfully optimized by applying the appropriate spectral preprocessing method. Second, the accuracy of the models was significantly affected by the genetic variability of the data set. Third, in spite of the sensitivity of the sensing techniques to the genetic variability, the implemented techniques (Vis/NIR or hyperspectral) have confirmed their great potential for predicting from intact dry bean seeds the canned bean texture and color retention.

1. Genetic control of Fusarium root rot resistance. Fusarium root rot (FRR) is the most serious soil borne disease in the U.S. FRR causes major yield losses especially in large seeded Andean beans, such as kidney beans that have little genetic resistance. USDA-ARS scientists, East Lansing, Michigan, in collaboration with Michigan State University and the International Center for Tropical Agriculture in Uganda identified sources of FRR resistance of value to U.S. Andean bean breeding programs. Genomic regions associated with FRR resistance in both greenhouse screening to a specific virulent strain and under natural field FRR disease pressure were identified on three bean chromosome Pv02, Pv07 and Pv11. The identified quantitative trait loci are candidates for marker-assisted selection. It is challenging to select for Fusarium root rot resistance visually because of the strong influence of the environment of this trait, therefore molecular markers are very useful.

Review Publications
Wiesinger, J.A., Cichy, K.A., Glahn, R.P., Grusak, M.A., Brick, M., Thompson, H., Tako, E.N. 2016. Demonstrating a nutritional advantage to the fast cooking dry bean (Phaseolus vulgaris L.). Journal of Agricultural and Food Chemistry. 64(45):8592-8603.
Wiesinger, J.A., Cichy, K.A., Hooper, S., Moreno, D.E., Brick, M., Thompson, H. 2016. Carbohydrate profile of a dry bean (Phaseolus vulgaris L.) panel encompassing broad genetic variability for cooking time. Cereal Chemistry. 94(1):135-141.
Mendoza, F., Kelly, J., Cichy, K.A. 2017. Automated prediction of sensory scores for color and appearance in canned black beans (Phaseolus vulgaris L.) using a color imaging technique. International Journal of Food Properties. 20(1):83-99.
Kelly, J.D., Varner, G., Hooper, S., Cichy, K.A., Wright, E. 2016. Registration of ‘Samurai’ Otebo Bean. Journal of Plant Registrations. 10(2):109-114.