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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

2016 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: 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 are being tested for utility as molecular markers for selection. Breeding high iron and zinc bean germplasm: We evaluated F4 black beans lines with high Fe and Zn concentration for agronomic characteristics and canning quality and the best lines were selected and advanced for further evaluation. A total of 32 advanced black bean breeding lines are in preliminary yield trials at the Saginaw Valley Research Farm in Richville, MI. An additional 16 F4 biofortified black beans have been planted for evaluation and selection. Breeding low phytic acid black bean lines: F4 and F5 black bean breeding lines were planted in the field at the Saginaw Valley Research Farm in Richville, MI. Selections have been made for plant architecture and seed type. A molecular marker assay was also used to test for the presence of the low phytic acid trait in the selections. Wide phenotypic variability has been observed in these populations, but thus far it appears that we have been able to produce acceptable plant and seed types in a two way cross without the need for a backcross. We continue to evaluate the backcross lines, but they may not be utilized for the germplasm enhancement goal. Evaluation of bean germplasm for cooking time and canning quality: We evaluated 400 entries of the Andean Diversity Panel for cooking time. These lines were grown in Hawassa, Ethiopia. Cooking times ranged from 15 to 55 min. Genome wide association analysis was conducted and genomic regions associated with cooking time were found on seven chromosomes. We also evaluated canning quality on diverse bean germplasm from Michigan, Colombia, Uganda, and Rwanda. Through the screening, we identified several lines with superior canning quality from the CIAT breeding program that were not previously characterized for this trait. Develop improved cranberry bean germplasm: We currently have 18 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 88 lines in preliminary yield trial and 30 F2 populations. Identify and validate markers for canning quality in black beans: Genomic regions associated with canning quality and color retention were identified. Two regions on chromosome 11 are especially important for color retention and are being tested for utility as molecular markers for breeding.

1. Genotype by environment interaction for cooking time in dry beans. Dry beans are a dietary staple in regions of Africa and Latin America. Dry beans generally require long cooking times which limits their utilization. Pervious germplasm screening by ARS scientists has uncovered wide genetic variability for cooking time and identified several fast cooking bean varieties. To further understand the nature of genetic variability for cooking time, ARS scientists in East Lansing, Michigan conducted a genotype by environment study with 14 select bean varieties across 15 diverse environments; these varieties represented four market classes of beans of economic importance, including kidney, yellow, cranberry and red mottled seed types. Within each seed type, a fast, moderate, and slow cooking variety was included; these varieties were grown in locations in the U.S, Caribbean, and Eastern and Southern Africa and under a range of environmental stresses including drought, heat, and low soil fertility. Variability in cooking time was observed among different locations, however the fastest cooking varieties were consistently faster cooking in the majority of the environments, suggesting that the fast cooking trait is stable across many regions and environmental conditions.

Review Publications
Ai, Y., Cichy, K.A., Harte, J., Kelly, J., Ng, P. 2016. Effects of extrusion cooking on the chemical composition and functional properties of dry bean powders. Food Chemistry. 211:538-545.
Goffnett, A., Sprague, C., Mendoza, F., Cichy, K.A. 2016. Preharvest herbicide treatments affect black bean desiccation, yield, and canned bean color. Crop Science. 56:1-8.
Astudillo, A., Fernandez, A., Cichy, K.A. 2015. Transcriptome characterization of developing bean (Phaseolus vulgaris L.) pods from two genotypes with contrasting seed zinc concentrations. PLoS One. 10(9): e0137157.