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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

2015 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
Quantitative Trait Locus (QTL) analysis for seed iron and zinc concentration: We identified Meta QTL for seed Fe and Zn concentrations on three bean chromosomes, focusing on two of them for characterization of the genomic region underlying the QTL and molecular marker identification and validation. The physical distance of these Meta QTL were determined and single nucleotide polymorphism (SNP) and insertion deletion markers are being used to pare down the effective QTL region. Breeding high iron and zinc bean germplasm: We made hybridizations between high mineral lines and high yielding, Michigan adapted black beans in 2013. In 2013, we evaluated F2 lines in Michigan and F3 seed of selected lines were sent to Puerto Rico for advancement. In 2014, we planted seed of thirty F4 lines in Michigan and upon harvest we evaluated yield, iron, zinc, and protein concentration and canning quality. The highest seed Zn concentration was 35 ppm, which is about 25% higher than the Zn concentration of the commercial checks. The highest seed Fe concentration was 72 ppm, which is also about 25% higher than the Fe concentration of the commercial checks. Protein levels ranged from 18 to 23% and averaged 21%. Canning quality was evaluated on these lines and two lines were identified that had both high seed Fe and superior canning quality. Two CIAT lines, MIB801 and MIB748, with carioca seed types and high seed Fe and Zn derived from P. dumosus were crossed with Michigan adapted bean lines. These two were chosen because they have good adaptation to Michigan growing conditions. Breeding low phytic acid black bean lines: With the assistance of our ARS collaborators, four low phytic acid x MI adapted black bean F2 population were increased in Puerto Rico. F3 seed was bulk harvested and planted in Michigan in June of 2015. Single plant selections will be conducted in the field based on plant architecture and adaptation. We also adapted a molecular marker assay to test for the presence of the low phytic acid trait in the populations. This assay was developed with support from scientists at CIAT, Colombia. It is a DNA based melting curve analysis used to detect the single nucleotide polymorphism responsible for the low phytic acid phenotype. It can also identify heterozygote lines. Evaluation of bean germplasm for cooking time and canning quality: We evaluated dry bean germplasm for cooking time. We have received seed from numerous locations around the world, including Michigan, Washington, Puerto Rico, South Africa and Tanzania. Different cooking protocols were used to assess genetic variability for cooking time. These methods include 1) soaking/cooking in distilled water, 2) cooking in distilled water without a pre-soak, and 3) soaking/cooking in hard water. The germplasm screening with the three different cooking protocols serves as a means to classify different genetic mechanisms. We also evaluated canning quality on diverse bean germplasm and observed a negative correlation between cooking time and canning quality. We used two methods to assess canning quality: 1) via a trained sensory panel of ~20 individuals and 2) via machine vision. Comparative analysis of the two methods suggest that machine vision system has potential to be applied to canning evaluations and may reduce the need for a trained sensory panel. Developing improved cranberry bean germplasm: We have developed over 30 cranberry bean breeding populations at the F2 to F6 generations. Some are being screened for root rot resistance in field research plots with high root rot disease pressure. Cranberry beans are highly susceptible to root rot, and resistant or tolerant lines are needed by the bean industry. Identifying and validating markers for canning quality in black beans: We completed the evaluation of canning quality and color retention in 71 black bean breeding lines, which were received from the seven public bean breeding programs in the U.S. The lines were genotyped with 5,300 SNP markers in collaboration with an ARS program in Beltsville, MD. Genomic regions associated with canning quality and color retention were identified. Anthocyanins in raw and canned seed were also measured. This data will be used for genome wide association analysis and to determine if there is a relationship between color retention and anthocyanin level or type. Characterizing seed coat color gene expression: The appropriate germplasm has been identified for RNA extraction. Progress was made on adapting a protocol to extract RNA from seeds.

1. Identification of genomic regions associated with seed protein and zinc in bean seeds. Dry beans are a dietary staple in regions of Africa and Latin America. They are rich in protein and minerals such as zinc essential in the human diet, but not all bean varieties have the same nutritional profile. ARS scientists in East Lansing, MI characterized the genetic diversity for seed protein and zinc in a panel of over 200 diverse bean lines, including many from Africa. These lines represented nine market classes of beans of economic importance, including kidney, yellow, and red mottled seed types. Genetic variability for seed protein ranged from 16 to 31 percent and for seed zinc from 19 to 54 µg g-1. Protein and zinc levels were positively correlated, suggesting that by selecting for one in a breeding program the other will increase as well. These findings will be used to breed more nutritious bean varieties that are adapted to regional bean seed color and market class preferences.

Review Publications
Kelly, J., Vaner, G., Cichy, K.A., Wright, E. 2014. Registration of ‘Zenith' black bean. Journal of Plant Registrations. 9:15-20.
Cichy, K.A., Porch, T.G., Beaver, J.S., Cregan, P.B., Fourie, D., Glahn, R.P., Grusak, M.A., Kamfwa, K., Katuuramu, D., McClean, P., Mndolwa, E., Nchimbi-Msolla, S., Pastor Corrales, M.A., Miklas, P.N. 2015. A Phaseolus vulgaris diversity panel for Andean bean improvement. Crop Science. 55:2149-2160.
Kelly, J., Trapp, J., Miklas, P.N., Cichy, K.A., Wright, E. 2015. Registration of ‘Desert Song’ Flor de Junio and ‘Gypsy Rose’ Flor de Mayo common bean cultivars. Journal of Plant Registrations. 9:133-137.
Kelly, J., Varner, G., Cichy, K.A., Wright, E. 2015. Registration of ‘Alpena' navy bean. Journal of Plant Registrations. 9:10-14.
Kamfwa, K., Cichy, K.A., Kelly, J. 2015. Genome-wide association study of agronomic traits in common bean. The Plant Genome. 8(2):1-12.
Cichy, K.A., Wiesinger, J., Mendoza, F. 2015. Genetic diversity and genome wide association analysis of cooking time in dry bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics. 128(8):1555-1567.
Kamfwa, K., Cichy, K.A., Kelly, J.D. 2015. Genome-wide association analysis of symbiotic nitrogen fixation in common bean. Theoretical and Applied Genetics. 128(10):1999-2017.