Location: Sugarbeet and Bean Research
2023 Annual Report
Objectives
Objective 1: Develop U.S. adapted fast cooking dry bean cultivars and germplasm
across multiple market classes using phenotypic evaluations combined with
molecular tools and marker-assisted breeding methods.
Sub-objective 1: To identify, evaluate, and screen the food ingredient and nutritional quality of pea, chickpea, lentil and beans to enable development of new varieties suited for use as an ingredient.
Objective 2: Understand genetic variability for anthocyanin composition and color
retention in black beans to expand uses for black beans and processing byproducts.
Sub-objective 2: To develop pre and post milling treatments to improve the food ingredient quality of pea, chickpea, lentil and beans.
Approach
Objective 1: Fast cooking U.S. adapted dry bean germplasm will be developed within yellow, cranberry, kidney and black bean market classes. Fast cooking germplasm will be crossed to U.S. adapted germplasm within each market class. Plant selection during the breeding cycle will be based on plant architecture, seed type, pod load, maturity, disease resistance, and cooking time and nutritional quality characteristics. QTL associated with cooking time will be identified and validated by conducting QTL analyses and compiling results from three recombinant inbred populations and three diversity panels grown in multiple locations and across multiple years. Mechanisms and shelf life of fast cooking bean genotypes will be evaluated. Components to be measured include: seed coat weight, seed hardness, water uptake during soaking, seed germination, soluble and insoluble dietary fiber, cell wall components, including water soluble pectin, cellulose, total protein, total starch, and resistant starch. Beans will be evaluated for use as a flour ingredient. Genetic diversity for flour milling quality will be assessed in a diversity panel of two sets of germplasm, the first will be commercial bean varieties grown in Michigan. The second will a panel lines previously identified to have unique cooking, canning or nutritional characteristics. The following flour attributes will be measured: particle size distribution, water holding capacity, gelatinization temperature, and pasting properties.
Objective 2: Develop improved black bean germplasm with superior end use quality, especially canning quality and color retention. New uses of black beans will be evaluated, especially for anthocyanins that can be extracted for use as a colorant. The specific anthocyanins profile of black bean seed coats of select genotypes will be measured and the best anthocyanin profile for colorants will be determined.
Progress Report
In support of Objective 1 the following progress has been made in the development of fast cooking, U.S. adapted dry bean germplasm. Phenotypic selection for reduced cooking times was implemented in the yellow, cranberry, kidney, and black bean market classes breeding pipeline in preliminary and advanced inbred line evaluations. Within the yellow market class, one line that cooks within 18 min, which is 8 to 25 min faster than current cultivars, is being considered for cultivar release under the name USDA-Honeycomb. Within the cranberry market class the cooking time screening has been used to cull materials that are susceptible to developing hardshell, which prevents them from imbibing water during soaking and results in very long cooking time. Unfortunately, hardshell was prevalent in many of the highest yielding breeding lines. Within the kidney and black bean market classes, selections have been made for germplasm that cooks within 20-30 minutes. Additional characteristics that have been considered in breeding for each of these market classes included plant architecture, seed yield, bean common mosaic virus resistance, canning quality, and seed iron concentration and bioavailability.
The cooking time trait has been studied to understand its inheritance, identify genomic regions associated with shorter cooking times, and develop molecular markers that can be implemented in breeding programs. Genetic mapping studies for cooking time were conducted on two diversity panels and two recombinant inbred line populations grown in locations in Africa and the United States. Based on these studies, 15 genomic regions related to water uptake and cooking time were found and the most robust locations were used to develop DNA markers. Thus far, two of these markers appear to have potential usefulness for breeding. They are currently being screened and validated across all breeding lines to determine where they can be most useful. Additional marker development and testing is also underway.
The genetic mechanisms underlying shorter cooking times has been studied through seed composition and RNA studies. The cotyledon cell wall was identified as an important location determining cooking time, with differences in thickness and genes expressed related to cell wall integrity and intracellular calcium content found. Shelf life of germplasm with short cooking times was evaluated by storing beans in temperate (room temperature and low humidity) and tropical (high temperature and high humidity) conditions. The rate of increase in cooking time from temperate to tropical conditions was similar for beans with shorter and longer cooking time, and therefore the shorter cooking beans were found to maintain their advantage across these conditions.
Beans were evaluated for use as a flour ingredient. Beans with mild flavor and thin seed coats produced flours that worked well in fresh and dry pasta products. One breeding line with favorable flour functionality and nutritional characteristics is being considered for cultivar release under the name USDA-Yellowjacket. Seed protein content was identified as an important characteristic for bean flour quality. Pasta made from bean flour with higher protein content is firmer than pasta made from bean flour with lower protein content. The firmer pasta is more favorable, therefore increased protein content screening will be included in breeding traits in the upcoming project.
In support of Objective 2, the following progress has been made in the development of improved black bean germplasm with superior end use quality and alternative uses. Advanced breeding lines have been developed with excellent canning quality and canned bean color retention. Genomic prediction models have been developed for seed yield, canning quality, and color retention. Prediction accuracies were very high for color retention indicating that genomic selection has a good probability of success for this trait. Dehulling black beans was tested at the pilot scale to develop alternative uses. The seed coat tightly adheres to the cotyledon, so it was difficult to remove. Alternative dehulling methods will be explored in the upcoming project.
Accomplishments
1. Identification of breeding tools for dry bean yield and canning quality assessment. A major end use of dry beans in the U.S. is the canning market and new bean cultivars should be high yielding and have canning quality that meets industry standards. Simultaneously improving yield and canning quality is challenging due to antagonism of the two traits and specialized methodology needs for evaluating canning quality. ARS researchers in East Lansing, Michigan, investigated the usefulness of genomic prediction which uses genomic sequence pattern information to improve genetic gain for seed yield and canning quality. Genomic prediction accuracies were moderate for yield and canning appearance, and high for canned bean color retention. As genotypes from the new breeding cycle were included in the models, prediction accuracy tended to increase. The researchers found that the use of these multi-trait models increased the prediction ability of complex traits, suggesting the feasibility of genomic prediction in early generations to increase selection intensity and lead to higher genetic gain for seed yield and canning quality.
Review Publications
Parker, T.A., Gallegos, J.A., Beaver, J., Brick, M., Brown, J.K., Cichy, K.A., Debouck, D., Delgado-Salinas, A., Dohle, S., Ernest, E., Estevez de Jensen, C., Gomez, F., Hellier, B.C., Karasev, A.V., Kelly, J.D., McClean, P., Miklas, P.N., Myers, J.R., Osorno, J., Pasche, J.S., Pastor-Corrales, M.A., Porch, T.G., Steadman, J.R., Urrea, C., Wallace, L.T., Diepenbrock, C.H., Gepts, P. 2022. Genetic resources and breeding priorities in Phaseolus beans: Vulnerability, resilience, and future challenges. Plant Breeding Reviews. Volume 46. Somerset, New Jersey: John Wiley & Sons, Inc. p. 289-420. https://doi.org/10.1002/9781119874157.ch6.
Mukankusi, C., Amongi, W., Kabwama, A., Buendia, H., Raatz, B., Kasule, F., Kayaga, H., Mughu, H., Cichy, K.A., Balasubramanian, P. 2022. Canning quality of popular common bean germplasm in eastern and central Africa. African Journal of Food, Agriculture, Nutrition and Development. 22(8):21269-21307. https://doi.org/10.18697/ajfand.113.21630.
Izquierdo, P., Kelly, J.D., Beebe, S., Cichy, K.A. 2023. Combination of meta-analysis of QTL and GWAS to uncover the genetic architecture of seed yield and seed yield components in common bean. The Plant Genome. 16(2). Article e20328. https://doi.org/10.1002/tpg2.20328.
Sadohara, R., Winham, D., Cichy, K.A. 2022. Food industry views on pulse flour – perceived intrinsic and extrinsic challenges for product utilization. Foods. 11(4). Article 2146. https://doi.org/10.3390/foods11142146.
Amongi, W., Nkalubo, S., Ochwo-Ssemakula, M., Arfang, B., Dramadri Onziga, I., Odongo Lapaka, T., Nuwamanya, E., Tukamuhabwe, P., Izquierdo, P., Cichy, K.A., Kelly, J., Mukankusi, C. 2023. Phenotype based clustering, and diversity of common bean genotypes in seed iron concentration and cooking time. PLOS ONE. 18(5). Article e0248976. https://doi.org/10.1371/journal.pone.0284976.
Amongi, W., Nkalubo, S., Ochwo-Ssemakula, M., Badji, A., Dramadri Onziga, I., Odongo Lapaka, T., Nuwamanya, E., Tukamuhhabwe, P., Izquierdo, P., Cichy, K.A., Kelly, J., Mukankusi, C. 2023. Genetic clustering, and diversity of African panel of released common bean genotypes and breeding lines. Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-023-01559-y.
Jeffery, H.R., Mudukuti, N., Buell, C., Childs, K.L., Cichy, K.A. 2023. Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time. The Plant Genome. 16(3). Article e20364. https://doi.org/10.1002/tpg2.20364.
