Research Project: Utilizing Genetic Diversity within Phaseolus vulgaris to Develop Dry Beans with Enhanced Functional Properties

Location: Sugarbeet and Bean Research

2022 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 FY2022 the following progress has been made in the development of fast cooking, U.S. adapted dry bean germplasm (1a) and to develop improved black bean germplasm with superior end use quality (2a): 101 yellow, 113 kidney, 93 cranberry, and 55 black bean early generation (F3 to F6) breeding lines were field selected in Fall 2021. These lines were sent to a winter nursery in Puerto Rico for advancement. The early generation breeding lines were also screened for Fusarium root rot resistance, seed non-darkening and evaluated with SNP markers for the I gene (bean common mosaic virus resistance). Phenotypic evaluation of cooking time, seed iron and zinc concentration, and iron bioavailability, and canning quality were conducted on preliminary and advanced breeding lines to select best breeding lines to advance. In 2022, the following breeding nurseries were field planted: Advanced yield trials- 36 cranberry, 36 yellow, 36 kidney, 24 black beans. Preliminary yield trials: 42 yellow, 52 cranberry, 92 kidney and 55 black beans. In addition, one black, one white kidney, one cranberry and three yellow breeding lines were sent for Michigan regional testing, and two yellow, two cranberry and one black bean lines were sent to Idaho for disease free seed production. In winter of 2022 new crosses were made in the yellow, kidney, black, nuna, otebo, and cranberry market classes. In total 66 different crosses were made using diverse germplasm sources as the parental materials. Identification and validation of QTL associated with cooking time (1b): A review of all published quantitative trait loci (QTL) for cooking time was initiated and is underway. Genome sequence data has been received for four genotypes. These four are the parental lines of our two published cooking time QTL studies. The genome sequence and QTL information is being used to identify single nucleotide polymorphisms (SNP) for molecular marker development. Elucidate mechanisms and longevity (shelf life) of fast cooking beans (1c): A gene expression study for fast and slow cooking germplasm stored under ideal and adverse conditions is underway. The storage experiment, RNA extraction, and sequencing have been completed and the data analysis is underway. Evaluate beans for use as an ingredient (1d): Lectin activity has been evaluated on bean flours of different pulses and multiple market classes. Various processing treatments including dry heat, soaking, and microwaving were evaluated for their ability to reduce lectin activity. Regular and slow darkening pinto beans from ARS, Prosser and North Dakota State University were evaluated for flour quality and pasta and cookie product quality. The seed compositional characteristics associated with processing quality, including protein and starch, were also evaluated. Evaluate new uses for black beans (2b): Black bean breeding lines were assessed for their ability to produce food safe blue color. Food safe extracts were produced at various pH levels.

Accomplishments
1. Identification of genomic regions most important for increasing dry bean seed yield across diverse germplasm and environments. Like most grain legumes, seed yield is a universally important trait in dry bean breeding programs and a major factor of varietal adoption and success. Genetic characterization of seed yield in dry beans has been studied in numerous populations and in various temperate and tropical bean growing regions of the world. ARS scientists in East Lansing, Michigan, in collaboration with Michigan State University compiled 20 plus years of genetic results for seed yield and factors associated with yield including days to maturity and seed weight consisting of 743 measurements from 21 independent studies to identify which regions of the bean genome most contribute to increasing seed yields. The scientists identified 58 key genomic regions associated with seed yield, 51 of which were important in drought stress as well as non-drought conditions, and 14 of which were similar to seed yield related regions in other legume crops including soybean and pea. The integration of genomic region and comparative genomics used in this study will be applicable to breeding for increased yields.

Review Publications
Cichy, K.A., Chiu, C., Isaacs, K., Glahn, R.P. 2022. Dry bean biofortification with iron and zinc. In: Kumar, Shiv, Dikshit, Harsh Kumar, Mishra, Gyan Prakash, Singh, Akanksha, editors. Biofortification of Staple Crops. Singapore. Springer. p. 225-270. https://doi.org/10.1007/978-981-16-3280-8_10.
Sadohara, R., Long, Y., Izquierdo, P., Urrea, C., Morris, D., Cichy, K.A. 2021. Seed coat color genetics and genotype x environment effects in yellow beans via machine-learning and genome-wide association. The Plant Genome. 15(1). Article e20173. https://doi.org/10.1002/tpg2.20173.
Uebersax, M., Cichy, K.A., Gomez, F., Porch, T.G., Heitholt, J., Osorno, J., Kamfwa, K., Snapp, S., Bales, S. 2022. Dry beans (Phaseolus vulgaris L.) as a vital component of sustainable agriculture and food security – A review. Legume Science. Article e155. https://doi.org/10.1002/leg3.155.
Kelly, J.D., Varner, G., Chilvers, M., Cichy, K.A., Wright, E. 2020. Registration of 'Coho' light red kidney bean. Journal of Plant Registrations. 14(2):134-138. https://doi.org/10.1002/plr2.20051.
Winham, D.M., Thompson, S.V., Heer, M.M., Davitt, E.E., Hooper, S.D., Cichy, K.A., Knoblauch, S.T. 2022. Black bean pasta meals with varying protein concentrations reduce postprandial glycemia and insulinemia similarly compared to white bread control in adults. Foods. 11(11): Article 1652. https://doi.org/10.3390/foods11111652.
Sadohara, R., Izquierdo, P., Alves, F.C., Porch, T.G., Beaver, J., Urrea, C., Cichy, K.A. 2022. The Phaseolus vulgaris Yellow Bean Collection: Genetic diversity and characterization for cooking time. Genetic Resources and Crop Evolution. 69:1627-1648. https://doi.org/10.1007/s10722-021-01323-0.
Geng, P., Hooper, S., Sun, J., Chen, P., Cichy, K.A., Harnly, J.M. 2022. Contrast study on secondary metabolite profile between pastas made from three single varietal common bean (Phaseolus vulgaris L.) and durum wheat (Triticum durum). ACS Food Science and Technology. 2(5):895–904. https://doi.org/10.1021/acsfoodscitech.2c00050.
Wang, W., Wright, E.M., Uebersax, M., Cichy, K.A. 2021. A pilot-scale dry bean canning and evaluation protocol. Journal of Food Processing and Preservation. Article e16171. https://doi.org/10.1111/jfpp.16171.