Progress 07/23/13 to 05/08/18
Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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. 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. Accomplishments 01 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.
Impacts
(N/A)
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.
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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. QTL analysis for seed iron and zinc concentration: A meta-analysis from seven QTL studies in Andean and Middle American intra and inter genepool populations was conducted to identify the regions in the genome that control the Fe and Zn levels in seeds. In total, 4 Meta QTL specific to Fe and 3 Meta QTL specific to Zn were identified. Additionally, eight Meta QTL that co-localized for Fe and Zn concentration were identified across 8 chromosomes. Individually 10 to 27% of the phenotypic variation was explained by the shared Meta QTL. The physical positions for 15 individual Meta-QTL were identified across six recombinant inbred bi- parental and one advanced backcross population. In the 15 Meta-QTLs we identified 38 candidate genes that belong to six gene families that have been related with transport of iron and zinc in plants. In addition, 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 were tested for utility as molecular markers in black bean breeding lines. These particular markers were not good candidates for marker assisted selection. We will evaluate an alternative approach of using genomic selection methodology for future breeding populations. Breeding high iron and zinc bean germplasm: A total of 33 black bean F2 populations and 45 advanced black bean breeding lines are in advanced yield trials at the Saginaw Valley Research Farm in Richville, Michigan. Breeding low phytic acid black bean lines: Low phytic acid (LPA) black breeding lines were evaluated for phytic acid levels and end use quality. In the F2 generation single plant selections were made for plant architecture, adaptation and seed type. In the F2 through F4 generation, the LPA genotype was classified through high resolution melting curve analysis. F4 selections were field grown and harvested seed was analysed for seed yield, phytic acid concentration, cooking, canning and nutritional quality. The LPA black bean lines had 37 to 74% less phytic acid than the wild type siblings. We found that the LPA lines had exceptionally long cooking times, after three hours in boiling water most were not cooked. The LPA lines had higher levels of Zn in raw seeds as compared to wild type siblings, however when cooked, the LPA lines lost much more Zn than the WT lines and ended up with less actual Zn than wild types. On the basis of yield performance, canning and cooking qualities, two LPA lines (B14-4 and B14-49) were identified as best germplasm for further breeding improvements. We have developed near isogenic LPA lines and they are currently planted at the Saginaw Valley Research Farm. Evaluation of bean germplasm for cooking time and canning quality: A yellow dry bean recombinant inbred line population (ADP0468 x ADP0512) of 227 genotypes were assessed for cooking time, flavor characteristics, and texture. Cooking times ranged from approximately 20 to 40 minutes. A trained sensory panel determined flavor and texture profiles of each genotype using 5-point hedonic scales. A texture analyzer with a 2mm cylindrical probe was used to determine work to bite for each genotype and to support the texture data obtained from the panel. Dry bean genotypes from six market classes were evaluated for their use as a milled flour ingredient. Michigan grown dry beans seeds were treated then milled using a commercial mill. The resulting flours were used to produce single-variety bean pastas. Formulations were optimized using a bench top fresh pasta maker. Consumer sensory panels were conducted for six single variety dry bean pastas with wheat pasta as the point of comparison. The pastas were evaluated for nutritional attributes and compared to boiled whole beans of the same varieties and wheat pasta. Dry bean pastas retained the nutritional profile of boiled whole seeds with respect to protein, starch as well as iron concentrations. They are also nutritionally superior to wheat pasta. Resistant starch (a component of dietary fiber) concentrations in bean pastas were comparable to their boiled whole seed counterparts. Varietal and genotypic differences were observed in the colors and texture of dry bean pastas. No statistically significant differences were observed among the bean pastas for the attributes of appearance, aroma, flavor, texture and overall. However, the wheat control was significantly different from both light and dark colored bean pastas for most attributes. Develop improved cranberry bean germplasm: We currently have 30 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 45 lines in preliminary yield trial and 14 F2 populations. We also have one line that we are considering for a germplasm release and is currently being evaluated in six field locations in Michigan. In addition to cranberry beans, we have early generation yellow, dark and white kidney, and purple speckled bean populations under development. Identify and validate markers for canning quality in black beans: Genetic variability for color retention was evaluated on black bean breeding lines and cultivars from the major U.S. public bean breeding programs. 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. Genome wide association analysis was conducted to determine genomic regions responsible for color retention and canning quality in black beans that were genotyped with 5398 SNP markers. A region on Pv05 at 39Mb was associated with color retention and was polymorphic candidates for MAS. 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. These results are in preparation for a peer reviewed publication. An experimental technique for scanning dry bean seeds using Vis/NIR spectroscopy (over the range of 400�2,498 nm) and hyperspectral imaging (over the range of 400�1,000 nm) was developed and optimized. This involved the spectral and spatial calibration of the optical sensors, selection of the best setting conditions for the spectral fiber sensor or camera and source of light, the sample holder design; as well as, the development of various image processing algorithms for hyperspectral imaging written in MATLAB software including: (i) image reading and preprocessing, (ii) segmentation of seeds from the background, (iii) separation of touching seeds, and (iv) image analysis for computing mean intensity of individual seeds at each spectral wavelength, data transformation using various spectral preprocessing methods, and regression analysis using multivariate methods such as partial least squares, feature selection and multiple regression analysis. All these methods have been intensively tested with a wide range of bean genotypes and different sensorial characteristics in appearance, color retention and firmness. The major noteworthy findings using both Vis/NIR spectroscopy and hyperspectral imaging include: First, the accuracy and robustness of end-use quality models for predicting appearance, color and texture (i.e., firmness/softness) in canned black beans were successfully optimized by applying the appropriate spectral preprocessing method. Second, the accuracy of the models was significantly affected by the genetic variability of the data set. Third, in spite of the sensitivity of the sensing techniques to the genetic variability, the implemented techniques (Vis/NIR or hyperspectral) have confirmed their great potential for predicting from intact dry bean seeds the canned bean texture and color retention. Accomplishments 01 Genetic control of Fusarium root rot resistance. Fusarium root rot (FRR) is the most serious soil borne disease in the U.S. FRR causes major yield losses especially in large seeded Andean beans, such as kidney beans that have little genetic resistance. USDA-ARS scientists, East Lansing, Michigan, in collaboration with Michigan State University and the International Center for Tropical Agriculture in Uganda identified sources of FRR resistance of value to U.S. Andean bean breeding programs. Genomic regions associated with FRR resistance in both greenhouse screening to a specific virulent strain and under natural field FRR disease pressure were identified on three bean chromosome Pv02, Pv07 and Pv11. The identified quantitative trait loci are candidates for marker-assisted selection. It is challenging to select for Fusarium root rot resistance visually because of the strong influence of the environment of this trait, therefore molecular markers are very useful.
Impacts
(N/A)
Publications
- Wiesinger, J.A., Cichy, K.A., Glahn, R.P., Grusak, M.A., Brick, M., Thompson, H., Tako, E.N. 2016. Demonstrating a nutritional advantage to the fast cooking dry bean (Phaseolus vulgaris L.). Journal of Agricultural and Food Chemistry. 64(45):8592-8603.
- Wiesinger, J.A., Cichy, K.A., Hooper, S., Moreno, D.E., Brick, M., Thompson, H. 2016. Carbohydrate profile of a dry bean (Phaseolus vulgaris L.) panel encompassing broad genetic variability for cooking time. Cereal Chemistry. 94(1):135-141.
- Mendoza, F., Kelly, J., Cichy, K.A. 2017. Automated prediction of sensory scores for color and appearance in canned black beans (Phaseolus vulgaris L.) using a color imaging technique. International Journal of Food Properties. 20(1):83-99.
- Kelly, J.D., Varner, G., Hooper, S., Cichy, K.A., Wright, E. 2016. Registration of �Samurai� Otebo Bean. Journal of Plant Registrations. 10(2) :109-114.
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Progress 10/01/15 to 09/30/16
Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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. 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. Accomplishments 01 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.
Impacts
(N/A)
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.
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Progress 10/01/14 to 09/30/15
Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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. 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. Accomplishments 01 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 �g 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.
Impacts
(N/A)
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.
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report Objectives (from AD-416): 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. Approach (from AD-416): 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. A QTL consensus map has been developed by combining QTL data from a black bean recombinant inbred line population and an additional three RIL populations. This analysis identified QTL on chromosomes 6 and 11 that appear to be important for seed Fe and Zn levels across diverse bean germplasm. These consensus QTL are currently being validated. The molecular markers associated with the high seed mineral levels are being screened across bean germplasm for utility in marker assisted selection. Black bean donor lines with high seed Fe and Zn have been crossed into high yielding black bean varieties and one to two backcrosses have been made. These materials have been planted in the field and will be evaluated for agronomic characteristics and advanced to the next generation at which time they will be evaluated for seed mineral levels. Three low phytic acid bean lines were received from the Italian Institute of Biology and Biotechnology. These lines were crossed with high yielding U.S. black bean germplasm and were backcrossed to the adapted parent and/or self-pollinated. The crosses are currently being grown in the field and will be evaluated via SNP melting curve analysis for the presence of the low phytic acid trait. A panel of dry beans from the Andean gene pool have been evaluated for cooking time and canning quality. Lines with superior cooking time and canning quality have been identified. Crosses have been initiated to understand the genetics of these traits as well as for breeding purposes. A cranberry bean breeding program is underway. Crosses were made in the greenhouse over the winter and the F2 generation are currently growing in the field. Also advanced yield trials are being conducted on a group of F4 cranberry lines. Accomplishments 01 Identification of genomic regions association with cooking time in beans. Dry beans (Phaseolus vulgaris L) are a nutrient dense, low cost food and therefore are an excellent value for consumers. In spite of this value, long cooking times limit bean consumption. Understanding the genetic variability for cooking time in beans and genomic control of this trait will help efficiently breed fast cooking bean varieties. A group of 240 Andean bean lines, grown in 2012 and 2013 at the Montcalm Research Farm in Entrican, Michigan were evaluated for cooking time. The lines were characterized for genetic differences. The average cooking time of the 240 lines was 38 min with the fastest line cooking in 19 min and the slowest line cooking in 87 min. Genetic elements associated with cooking time were detected on chromosomes 2 and 10 with evidence suggesting that enzymes coded on chromosome 2 (pectin methyltransferases may influence cooking time. 02 Fast cooking bean varieties retain more nutrients than longer cooking beans. Dry beans (Phaseolus vulgaris L) are a nutrient dense food rich in protein and micronutrients. To make these nutrients available to humans, dry beans must first undergo a thermal transformation. The cooking time required to make beans palatable varies by genotype. Fast, medium, and slow cooking genotypes across four bean market classes-- yellow, cranberry, light red kidney, and red mottled--were selected and evaluated to determine how cooking time influences their nutritional composition in freshly harvested seed and seed stored for one year. Each of the lines was cooked until palatable. In each of the four market classes evaluated, the genotypes that required the shortest cooking time retained a higher percentage of protein and iron in the seed than those that required longer cooking times and therefore would benefit consumers in terms of convenience and added nutrition.
Impacts
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Publications
- Kelly, J.D., Varner, G., Cichy, K.A., Wright, E. 2013. Registration of �Powderhorn� great northern bean. Journal of Plant Registrations. 8(1):1-4.
- Kelly, J.D., Mkwaila, W., Varner, G., Cichy, K.A., Wright, E. 2012. Registration of �Eldorado� pinto bean. Journal of Plant Registrations. 6:223-237.
- Mendoza, F., Cichy, K.A., Lu, R., Kelly, J.D. 2014. Evaluation of canning quality traits in black beans (Phaseolus vulgaris L.) by visible/near- infrared spectroscopy. Food and Bioprocess Technology. DOI: 10.1007/s/ 11947-014-1285-y.
- Cichy, K.A., Fernandez, A., Kilian, A., Kelly, J.D., Galeano, C.H., Shaw, R.S., Brick, M., Hodkinson, D., Troxtell, E. 2014. QTL analysis of canning quality and color retention in black beans (Phaseolus vulgaris L.). Molecular Breeding. 33(1):139-154.
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