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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

2018 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
This five year project resulted in major progress in measuring and understanding the genetic control of dry bean quality attributes and in breeding dry beans with improved end use quality characteristics. There were two major objectives in this research plan, the first pertaining to the genetics of seed nutrient composition and the second pertaining to the genetics of culinary characteristics. Major progress was achieved in understanding the genetic control of seed iron and zinc concentration. A transcriptome analysis of developing bean pods were made from two dry bean varieties, one with high seed zinc concentration, and one with low seed zinc concentration identified differentially expressed genes that function in Zn and/or Fe transport. A meta-analysis compiling seven individual studies on genomic regions important for seed iron and zinc concentration identified eight genomic intervals important to increase both Fe and Zn concentrations which are useful candidates for marker-assisted breeding to simultaneously increase seed Fe and Zn. A diversity panel of Andean beans was compiled, genotyped, and evaluated for the concentration of iron, zinc, and protein and the iron bioavailability in cooked seeds. These efforts identified phenotypic variation for each of the traits, with the highest variation (5.4-fold) found for cooked seed iron bioavailability. The germplasm identified through this screening are being used as parental lines in the breeding program. Research from this project also showed that fast-cooking bean varieties have improved nutritive value as compared to varieties that take a longer time to cook, through greater nutrient retention and improved iron bioavailability. In the breeding program, the single gene low phytic acid mutation was transferred to U.S. adapted black bean germplasm. The low phytic acid lines had 37 to 74% less phytic acid than the wild type siblings. A few lpa lines were identified with favorable yield performance, canning and cooking qualities. Significant progress was also made on the second objective in regards to the genetic and phenotypic evaluation of end use quality traits, namely canning quality and cooking time. The canning quality work largely focused on the black bean market class, where poor color retention after canning is a major industry concern. Through this project genomic regions associated with color retention were identified and found to be linked to anthocyanins concentration. The black bean germplasm of the major public breeding programs was surveyed for canning quality and 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. 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. Genome wide association analysis was conducted to determine genomic regions responsible for color retention and canning quality in black beans. A genomic region associated with color retention and is a candidate for marker assisted breeding. New tools were developed and tested to assess the canning quality of beans. A machine vision system was implemented and tested for automatic inspection of color and appearance and modeled after the results from a trained sensory panel. Using simple color and texture image data, a machine vision system showed potential for the automatic evaluation of canned black beans by COL and/or appearance as a professional visual inspection. In addition tools were developed to predict canning quality on dry intact seeds. Visible/NIRS and HYPERS were effective in predicting texture of canned beans using intact dry seeds. The role of agronomic practices on color retention of canned black beans was studied and it was found that black bean cultivar influenced canned bean color retention (Zenith > Zorro > Eclipse). Preharvest herbicide treatments applied as harvest aids reduced color retention when applied at the early application timing; glyphosate reduced color retention by as much as 24%. Cooking time genetic variability was also explored. Fivefold diversity for cooking time found in a panel of 206 Phaseolus vulgaris accessions. Fastest accession cooks nearly 20 min faster than average. Genotypic regions associated with cooking time on Pv02, 03, and 06.

1. The genetics of fast cooking dry beans. Cooking time is an important consumer trait in dry bean and long cooking times deter greater utilization of beans. To better understand the genetic control of cooking time, USDA-ARS scientists in East Lansing, Michigan developed a population from a slow cooking bean, 70 min cooking time and a fast cooking bean, 30 min cooking time. The cooking times for individual bean lines in the population ranged from 21 min to 135 min. The population was grown in two different climates in Tanzania, under temperate highland tropical climate and hot humid tropical climate for two field seasons. An environmental influence on cooking time was observed with the average cooking time in beans grown in the hot humid zone being 15 min longer those grown in the temperate zone. A strong genetic control for cooking time was also observed and four genomic regions were identified and bean lines with all four of the DNA variants cooked 16 min faster than lines with none of those. This study shows the potential value of integrating cooking time into a breeding program and the utility of molecular markers to aid selection for fast cooking beans.

Review Publications
Kelly, J., Varner, G., Miklas, P.N., Cichy, K.A., Wright, E. 2018. Registration of 'Cayenne' small red bean cultivar. Journal of Plant Registrations. 12:194-198.
Mendoza, F., Cichy, K.A., Sprague, C., Goffnet, A., Lu, R., Kelly, J.D. 2017. Prediction of canned black bean texture (Phaseolus vulgaris L.) from intact dry seeds using visible/near-infrared spectroscopy and hyperspectral imaging data. Journal of the Science of Food and Agriculture. 98(1):283-290.
Kelly, J.D., Varner, G., Chilvers, M., Cichy, K.A., Wright, E. 2018. Registration of ‘Red Cedar’ dark red kidney bean. Journal of Plant Registrations. 12:199-202. doi:10.3198/jpr2017.05.0034crc.
Katuuramu, D.N., Hart, J.P., Porch, T.G., Grusak, M.A., Cichy, K.A. 2018. Genome-wide association study for nutritional composition traits in cooked common bean seeds. Molecular Breeding. 38:44.
Wang, W., Jacobs, J.L., Chilvers, M.I., Mukankusi, C.M., Kelly, J.D., Cichy, K.A. 2018. QTL analysis of Fusarium root rot resistance in an Andean x Middle American common bean RIL population. Crop Science. 58:1166-1180. doi:10.2135/cropsci2017.10.0608.
Izqierdo, P., Astudillo, C., Iqbal, A., Blair, M., Raatz, B., Cichy, K.A. 2018. Meta-QTL analysis of seed iron and zinc concentration in common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics.