Source: MICHIGAN STATE UNIV submitted to NRP
BREEDING COMMON BEAN (PHASEOLUS VULGARIS L.) FOR RESISTANCE TO ABIOTIC AND BIOTIC STRESSES, SUSTAINABLE PRODUCTION, AND ENHANCED NUTRITIONAL VALUE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0223310
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
W-2150
Project Start Date
Oct 1, 2010
Project End Date
Sep 30, 2015
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824
Performing Department
Plant, Soil and Microbial Science
Non Technical Summary
The multistate project will foster collaboration between bean scientists in a number of different disciplines to meet the goals of improving crop productivity, sustainable production and enhanced nutritional quality for consumers. The methods employed will include traditional breeding methods, utilization of marker assisted selection to meet these goals, study of pathogens that attack the crop, identification of sources of resistance, genetics studies to understand the inheritance of resistance and studies to determine nutritional value of beans and their processing quality. Collaborative trials will be conducted to evaluate the potential of new bean varieties in different locations and the processing quality of these varieties will be evaluated at selected locations.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2021410108110%
2031410108150%
2041410108120%
2051410108110%
2121410108010%
Knowledge Area
212 - Pathogens and Nematodes Affecting Plants; 204 - Plant Product Quality and Utility (Preharvest); 205 - Plant Management Systems; 203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants; 202 - Plant Genetic Resources;

Subject Of Investigation
1410 - Beans (dry);

Field Of Science
1081 - Breeding; 1080 - Genetics;
Goals / Objectives
Improving bean yield potential by incorporating resistance/tolerance to major biotic and abiotic stresses, broadening the genetic base, developing genomic resources, and coordinating field trial nurseries. Sub-objectives: 1a) Facilitate the genetic elucidation and breeding for resistance to bacterial, fungal, and viral diseases, facilitated by monitoring and characterizing pathogen variation. 1b) Advance in the genetics and breeding for tolerance to heat and drought in response to global climate change. 1c) Broaden the genetic base of major bean market classes by characterizing and using exotic germplasm. 1d) Develop and utilize genomic resources for marker-assisted breeding. 1e) Coordinate and expand national and regional bean trials. (CA, CO, ID, MI, NE, ND, OR, Puerto Rico) Identify and implement sustainable agricultural systems that improve bean seed yield, conserve natural resources, and protect the environment. (AZ, CA, CO, ID, MI, NY, ND, Puerto Rico) Characterize the genetic control and physiology of nutritional and processing quality traits in bean and elucidate the health benefits of bean consumption. (CA, ID, ND, WA).
Project Methods
The overall strategy is based on collaborative research of constraints shared across different production regions. This collaboration includes germplasm and pathogen exchange, sharing of protocols, regional nurseries and trials, and screening of genotypes for the traits of interest. As a result of this exchange of knowledge and material, breeding projects will be able to introgress and pyramid favorable alleles and QTL for enhanced seed yield potential, nutritional value, and resistance to multiple abiotic and biotic stresses using a multi-disciplinary and multi-institutional team approach. To accomplish these objectives, our research activities are divided into various sub-projects in which researchers from two or more participating states and institutions conduct research on each major problem as a team. A broad genetic base that allows discovery of novel and useful genes and the utilization these genes in breeding programs via germplasm conversion using a three-tiered breeding approach described by Kelly et al. (1998). Concurrently, evolutionary information on pathogen diversity and origins of diversification are also important as Andean and Mesoamerican strains of certain pathogens have been identified (Gepts and Bliss, 1985; Guzman et al., 1995; Geffroy et al., 1999; Mkandawire et al., 2004). Breeding methods and selection techniques employed vary from project to project depending upon the type of population, genetic distance between parents used, inheritance of the traits under improvement, screening or evaluation methods employed, breeding objectives, and resources available. For diseases caused by variable pathogens, plant samples and/or pathogen isolates are collected for characterization using conventional as well as cutting-edge PCR-based fingerprinting and other techniques. Similarly, the W-1150 researchers strive to develop and improve upon the laboratory, greenhouse, and field techniques for efficient and economical screening of germplasm, segregating populations, families, breeding lines, and cultivars. This information is freely shared with the rest of the group so the methods can be used in different programs. Promising germplasm and improved breeding lines and cultivars from all breeding projects are systematically tested yearly in the regional and national project nurseries for agronomic performance, seed yield, nutritional value and cooking qualities, and reaction to major abiotic and biotic stresses. Subsequently, the most promising breeding lines are tested in state and regional trials and in farmers' fields for identification, release, and commercialization of new cultivars. Due to the inter-disciplinary, inter-institutional, multi-state nature of this collaboration, improved cultivars and germplasm is often released jointly among two or more institutions. This collaboration is facilitated by discussions and work plans made during the annual W-1150 meetings.

Progress 10/01/10 to 09/30/15

Outputs
Target Audience:Bean Farmers, Bean Elevator Managers in Michigan; National Food Industry and Food Processors and Consumers; Bean Researchers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Two master's students and two doctoral students graduated from the bean breeding and genetics program in 2015 and their thesis titles are listed below. How have the results been disseminated to communities of interest?Journal articles, bulletins, extension and professional meetings What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Bean Breeding Nurseries The MSU dry bean breeding and genetics program conducted 20 yield trials in ten market classes and participated in the growing and evaluation of the Cooperative Dry Bean, Midwest Regional Performance, and the National Sclerotinia Nurseries in Michigan and winter nursery in Puerto Rico from 2011 to 2015. All yield trials at Frankenmuth were direct harvested. Large-seeded kidney and cranberry trials, at Montcalm were rod-pulled. The white mold trial was direct harvested. Temperatures were moderate for the 2015 season and only exceeding 90F for a few days in July. Overall rainfall for the 3-summer months at SVREC was equivalent to the 30-year average of 8.5". A moderate dry period occurred from June 16-July 13 with only 0.7" of rainfall which reduced the overall plant size and resulted in lower overall yields. A high incidence of common bacterial blight resulted in the nurseries and allowed for selection of resistant lines in a range of seed types. Rainfall patterns at MRF were more extreme with a total rainfall of over 5" within two days of planting. This resulted in major flooding in some areas, soil crusting and compaction in other areas which resulted in low germination. In addition soil temperatures remained low in this critical period and a high incidence of root rots diseases occurred which also reduced germination and stands. The Andean kidney and cranberry beans were the most affected by the stresses whereas the Mesoamerican small and medium seeded black, navy, pinto, GN, and red beans managed to tolerate the conditions and had near normal stands. Overall vigor of the kidney and cranberry beans was poor resulting in small plants that had low overall yields. Plots at MRF had supplemental irrigation did contribute to the development of white mold. Incidence in the National Sclerotinia Initiative nursery was very low in the susceptible checks despite the overall lower temperatures and excess irrigation. The major problem at Montcalm was the presence of severe root rots mainly Fusarium that was accentuated by the cooler soil conditions early in the season. The unfavorable condition allowed for the selection of lines with tolerance to root rot and with resistance to common bacterial blight in the kidney bean nurseries. Black Bean Color Retention Color retention after canning is a major concern for the bean canning industry. Significant genetic variability exits and a molecular marker for color retention would be very useful to breeders. A panel of 71 black bean breeding lines was compiled from the major public U.S. black bean breeding programs, including Colorado State University, Michigan State University, North Dakota State University, University of Nebraska, USDA-ARS in East Lansing, MI, Mayaguez, Puerto Rico, and Prosser, Washington. These lines were grown in replicated field trials at the Saginaw Valley Research Farm, Richville, MI in 2013 and 2014. Each year beans were canned and evaluated for canning quality and color retention. Anthocyanins were also measured on raw and canned samples. The variability for color retention in the panel ranged from a low of 1.75 to a high of 4.75. These values are based on a scale of 1 to 5, where 1 is light brown and 5 is dark black. The ratings were given by a sensory panel of ~20 individuals. Each of the bean lines were genotyped with the BARCBean6K_3 SNP array of 5,398 SNP markers. In total, 2,799 SNP markers were polymorphic. The phenotypic and genotypic information was used for genome wide association analysis. Genomic regions associated with color retention were found on chromosomes Pv02, Pv03, Pv04, Pv05, Pv06, Pv09, and Pv11. Outcomes/Impact Currently the black bean variety Zorro from MSU breeding program is grown on 80% of the acres planted to black beans in Michigan and has provided growers with opportunity to reduce costs by direct harvesting the crop. Certified seed was produced of the new high-yielding, disease resistant, upright full-season black bean variety, Zenith, and the new upright navy bean variety, Alpena that has excellent canning quality and uniform maturity. Zenith possesses superior color retention following canning, a trait the processing industry needs. Alpena exhibits natural dry down at maturity which eliminates the application of desiccants prior to harvest. Foundation and certified seed of both varieties was produced in 2015.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: 1. Astudillo, C., Fernandez A. and Cichy, KA. The transcriptomes of developing bean (Phaseolus vulgaris L.) pods from two genotypes with contrasting seed zinc concentrations. (PLOS One, Accepted Aug 17, 2015) 2. Kamfwa, K., Cichy, K.A., and Kelly, J.D. (2015) Genome-Wide Association Analysis of Symbiotic Nitrogen Fixation in Common Bean. Theoretical and Applied Genetics doi. 10.1007/s00122-015-2562-5 3. Kamfwa, K., Cichy, K.A., and Kelly, J. (2015) Genome-Wide Association Study of Agronomic Traits in Common Bean. The Plant Genome 8: doi:10.3835/plantgenome2014.09.0059. 4. Cichy, K.A., Porch, T., Beaver, J.S., Cregan, P., Fourie, D., Glahn, R., Grusak, M.A., Kamfwa, K., Katuuramu, D., McClean, P., Mndolwa, E., Nchimbi-Msolla, S., Pastor-Corrales, M., Miklas, P. (2015) A Phaseolus vulgaris Diversity Panel for Andean Bean Improvement. Crop Sci. 55:21492160 (2015).doi: 10.2135/cropsci2014.09.0653 5. Cichy, K.A., Wiesinger J.A., and Mendoza F.A. (2015) Genetic Diversity and Genome Wide Association Analysis of Cooking Time in Dry Bean (Phaseolus vulgaris L.) Theoretical and Applied Genetics 128:1555-1567. 6. Hoyos-Villegas, V., W. Mkwaila, P.B. Cregan and J.D. Kelly. 2015. QTL analysis of white mold avoidance in pinto bean (Phaseolus vulgaris). Crop Sci. 55:2116-2129. doi:10.2135/cropsci2015.02.0106 7. Kelly, J.D., Varner, G.V., Cichy, K.A., and Wright, E.M. (2015) Registration of Alpena Navy Bean. J. Plant Registrations 9: 10-14. 8. Kelly, J.D., Varner, G.V., Cichy, K.A., and Wright, E.M. (2015) Registration of Zenith Black Bean. J. Plant Registrations 9: 15-20. 9. Kelly J., Trapp J., Miklas P., Cichy KA., and Wright E.M. (2015). Registration of Desert Song Flor de Junio and Gypsy Rose Flor de Mayo Common Bean Cultivars. J. Plant Registrations 9:133-137. 10. Sousa, L.L., A. O. Gon�alves, M. C. Gon�alves-Vidigal, G. F. Lacanallo, A. C. Fernandez, H. Awale and J. D. Kelly. (2015). Genetic characterization and mapping of anthracnose resistance of Corinthiano common bean landrace cultivar. Crop Sci. 55:1900-1910. doi:10.2135/cropsci2014.09.0604 Book Chapters: None Non-refereed Publications: Berry, M., Cichy, K.A., Ai, Y., and Ng, PKW. 2015. Phytoheamagglutination Activity in Extruded Dry Bean Powder. Bean Improvement Cooperative Annual Report 58:1-2. Zuiderveen, G.H., K. Kamfwa and J. D. Kelly. 2015. Anthracnose resistance in Andean beans. Bean Improvement Cooperative Annual Report 58:9-10. Posters: 1. Zuiderveen, G.H., and J. D. Kelly. 2015. Genome-wide association study of anthracnose resistance in Andean beans. Poster presented at JAHS Annual Meeting in New Orleans Aug. 1-4, 2015. 2. Traub, J., M. Naeem, J. Kelly, G. Austic, D. Kramer, and W. Loescher. 2015. Phenotyping for heat tolerance in bean (Phaseolus spp.) using new and conventional fluorescence and gas exchange parameters. Poster presented at JAHS Annual Meeting in New Orleans. Aug 1-4. 2015. Dissertations: Heilig, J.A. 2015. QTL mapping of symbiotic nitrogen fixation in dry bean; Dry bean performance under organic production systems. Doctoral Dissertation, Michigan State University, East Lansing MI. 153pp. Hoyos-Villegas, V. 2015. Identification of genomic regions and development of breeding resources associated with drought tolerance in common bean (Phaseolus vulgaris L.). Doctoral Dissertation, Michigan State University, East Lansing MI. 132pp. Nakedde, T. 2015. Identification and mapping of QTL associated with Fusarium root rot resistance and root architecture traits in black beans (Phaseolus vulgaris L.). Masters Thesis, Michigan State University, East Lansing. MI. 119pp. Zuiderveen, G.H. 2015.The genetics of anthracnose resistance in common bean. Masters Thesis, Michigan State University, East Lansing MI. 68pp.


Progress 10/01/13 to 09/30/14

Outputs
Target Audience: Bean Farmers, Bean Elevator Managers in Michigan; National Food Industry and Food Processors and Consumers; Bean Researchers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Three Masters level and Six Doctoral level students trained in plant breeding genetics and biotechnology How have the results been disseminated to communities of interest? Extension bulletins and in webinars on PBGWorks E-xternsion site What do you plan to do during the next reporting period to accomplish the goals? conutinue bean breeding research

Impacts
What was accomplished under these goals? Bean Breeding Nurseries The MSU dry bean breeding and genetics program conducted 20 yield trials in ten market classes and participated in the growing and evaluation of the Cooperative Dry Bean, Midwest Regional Performance, and the National Sclerotinia Nurseries in Michigan and winter nursery in Puerto Rico in 2014. All yield trials at Frankenmuth were direct harvested. Large-seeded kidney and cranberry trials, at Montcalm were rod-pulled. The white mold trial was direct harvested. Bean yields at Frankenmuth were exceptional in 2014 averaging 35 cwt/acre with top yields exceeding 50 cwt in some trials. Temperatures were moderate not exceeding 90F and rainfall for 4-summer months was 2.2 inches above the 30-year average. The extra rainfall was well distributed with most falling in July so there was no stress to the crop due to limited moisture or high temperatures at the critical flowering period. White mold was a serious problem in the commercial crop but not in research plots where the extra tile drainage allowed for more rapid drying of the soil surface following rain. Plots at Montcalm had similar rainfall pattern but the supplemental irrigation did contribute to the development of white mold. Incidence in the National Sclerotinia Initiative nursery was very high in the susceptible checks and proved to be an excellent screening nursery. The major problem at Montcalm was the presence of severe root rots mainly Fusarium that was accentuated by the cooler soil conditions early in the season. Despite this, yields in kidney beans approached 40 cwt/acre and many lines with tolerance to root rot and with resistance to common bacterial blight were identified in kidney bean nurseries. A total of 2,742 plots were harvested for yield in 2014 and approximately 2000 single plant selections were made in the early generation nurseries. Other studies included the evaluation of 36-entry certified organic variety trials at two locations. Black Bean Fe and Zn Biofortification: 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. Black Bean Low Phytic Acid Germplasm: 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. Outcomes/Impact The breeding program released a high-yielding, disease resistant, upright full-season black bean variety, Zenith, and a new upright navy bean variety, Alpena that has excellent canning quality and uniform maturity. Zenith possesses superior color retention following canning, a trait the processing industry needs. Foundation seed of both varieties was produced in 2014. Currently the black bean variety Zorro from MSU breeding program is grown on 80% acres planted to black beans in Michigan and has provided growers with opportunity to reduce costs by direct harvesting the crop. Certified seed was also produced of new great northern bean variety Powderhorn released by MSU in 2014.

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2014 Citation: 1. Brisco, E.I., T.G. Porch, P.B. Cregan, and J.D. Kelly. 2014 Quantitative trait loci associated with resistance to Empoasca in common bean. Crop Sci. 54: doi: 10.2135/cropsci2014.02.0159. 2. Cichy, K.A., A. Fernandez, A. Kilian, J.D. Kelly, C.H. Galeano, S. Shaw, M. Brick, D. Hodkinson, and E. Troxtell. 2014. QTL analysis of canning quality and color retention in black beans (Phaseolus vulgaris L.). Mol. Breed. 33:139-154. doi: 10.1007/s11032-013-9940-y. 3. Kelly, J.D., G.V. Varner, K.A. Cichy, and E.M. Wright. 2014. Registration of Powderhorn great northern bean. J. Plant Registrations 8:1-4. doi:10.3198/jpr2013.05.0020crc. 4. Mendoza, F.A., K. Cichy, R. Lu and J.D. Kelly. 2014. Evaluation of canning quality traits in black beans (Phaseolus vulgaris L.) by visible/near-infrared spectroscopy. Food Bioprocess Technol. 7:2666-2678. doi:10.1007/s11947-014-1285-y 5. Miklas, P.N., J. D. Kelly, J. R. Steadman and S. McCoy. 2014. Registration of partial white mold resistant pinto bean germplasm line USPT-WM-12. J. Plant Registrations 8:183186. 6. Mukeshimana, G., L. Butare, P.B. Cregan, M. W. Blair and J. D. Kelly. 2014. Quantitative trait loci associated with drought tolerance in common bean. Crop Sci. 54:923-938. doi: 10.2135/cropsci2013.06.0427. 7. Mukeshimana, G., A.L. Lasley, W.H. Loescher and J.D. Kelly. 2014. Identification of shoot traits related to drought tolerance in common bean seedlings. J. Amer. Soc. Hort. Sci. 139:299309. 8. Sousa, L.L., A. S. Cruz, P. S. Vidigal Filho, V. A. Vallejo, J. D. Kelly and M.C. Gon�alves-Vidigal. 2014. Genetic mapping of the resistance allele Co-52 to Colletotrichum lindemuthianum in the common bean MSU 7-1 line. Aust. J. Crop Sci. 8:317-323. 9. Schmutz, J., P. McClean&J.D. Kelly... S.A. Jackson. 2014. A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics.46:707-713. doi:10.1038/ng.3008. [41 authors: J.D. Kelly no. 26]. 10. Oblessuc, P.R., R. M. Baroni, G. da Silva Pereira, A. F. Chioratto, S.A.M. Carbonell, B. Bri�ez, L. Da Costa E Silva, A. A. F. Garcia, L.E.A. Camargo, J. D. Kelly, and L. L. Benchimol-Reis. 2014. Quantitative analysis of race-specific resistance to Colletotrichum lindemuthianum in common bean. Mol. Breed. 34:1313-1329. doi:10.1007/s11032-014-0118-z
  • Type: Book Chapters Status: Accepted Year Published: 2014 Citation: 1. Musoni, A., J. Kayumba, L. Butare, F. Mukamuhirwa, E. Murwanashyaka, D. Mukankubana, J.D. Kelly, J. Ininda, and D. Gahakwa. 2014. Innovations to overcome staking challenges to growing climbing beans by smallholders in Rwanda. p. 129-136. In: B. Vanlauwe et al. (eds.), Challenges and Opportunities for Agricultural Intensification of the Humid Highland Systems of Sub-Saharan Africa. Springer International Publishing Switzerland doi:10.1007/978-3-319-07662-1_11 2. Vandemark, G.J., M.A. Brick, J.M. Osorno, J.D. Kelly, and C.A. Urrea. 2014. Edible Grain Legumes. p. 87-123. In: S. Smith, B. Diers, J. Specht, & B. Carver (eds.). Yield Gains in Major U.S. Field crops. CSSA Special Pub. 33, Madison, WI.
  • Type: Other Status: Accepted Year Published: 2014 Citation: Non-refereed Publications: 1. Cichy K.A., J. Weisinger, T. Porch, and P.N. Miklas. 2013. Diversity for Cooking Time In Andean Dry Beans. Ann. Rep. Bean Improv. Coop. 57:25-26. 2. dos Santos, H.M., V. Hoyos-Villegas and J.D. Kelly. 2014. Genome-wide association analysis for reaction to white mold in the BeanCAP Mesoamerican panel. Ann. Rep. Bean Improv. Coop. 57:235-236. 3. Heilig, J.A. and J.D. Kelly. 2014. QTL analysis of biological nitrogen fixation and agronomic traits in the Puebla/Zorro RIL population. Ann. Rep. Bean Improv. Coop. 57:101-102. 4. Katuuramu D.N. and K.A. Cichy. 2013. Variability in Seed Mineral and Protein Concentration in an Andean Bean Diversity Panel. Ann. Rep. Bean Improv. Coop. 57:139-140. 5. Kelly, J.D. 2014. The changing face of bean breeding; past and future. Ann. Rep. Bean Improv. Coop. 57: 1-2. 6. Kamfwa, K., K.A. Cichy and J.D. Kelly. 2014. Genetic variability for nitrogen fixation in the Andean diversity panel of Phaseolus vulgaris. Ann. Rep. Bean Improv. Coop. 57:43-44. 7. Ibarra-Perez, F.J., J.G. Waines and B. Ehdaie, J. A. Heilig and J.D. Kelly. 2014. Phenotyping root and shoot traits of Zorro and Puebla 152 common bean (Phaseolus vulgaris L.) cultivars. Ann. Rep. Bean Improv. Coop. 57:107-108. Bulletins: 1. Kelly, J. D., Wright, E. M., Varner, G. V., and Sprague, C. L. 2014. Powderhorn: A new variety of great northern bean for Michigan. Ext. Bulletin E3218.


Progress 01/01/13 to 09/30/13

Outputs
Target Audience: Bean Farmers, Bean Elevator Managers in Michigan; National Food Industry and Food Processors and Consumers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Partial Training for five graduate students in Plant Breeding How have the results been disseminated to communities of interest? yes What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Black bean processing quality: Processing quality was evaluated on 98 black bean genotypes representing cultivars and breeding lines of the major black bean breeding programs in the U.S. The materials were canned and evaluated for color retention, texture, appearance and water uptake. Significant variability was observed for each of these traits. These lines were also tested for high throughput evaluation methods to predict color retention. The methods included measurement of the color of soaked beans and Near Infrared Spectroscopy (NIR) of whole seed. The NIR was better able to predict the color retention than the color of the soaked beans. The most contrasting genotypes for color retention are being genotyped with 6000 SNP markers. This information will be used to identify genomic regions important for color retention. Black bean seed mineral concentration QTL: Seed iron (Fe) and zinc (Zn) concentrations were evaluated on 108 black bean recombinant inbred lines that were grown in a replicated field experiment in 2010 and 2011. A linkage map of 3500 single nucleotide polymorphism markers (SNP) and diversity array markers was developed for the black bean population. The phenotypic data was used to conduct QTL analysis of seed mineral concentration. The analysis identified QTL for seed Fe and Zn concentration on chromosomes 2 and 6. Black bean and cranberry bean breeding: Crossing and evaluating of early generation lines is underway in the black and cranberry market classes. In black bean, crosses were made to combine seed yield and seed mineral concentration. In cranberry beans crosses were made to combine seed yield, resistance to common bacterial blight, and canning quality. Nutrient Density of Dry Bean Seeds: An in-depth study on the nutrient composition of two bean genotypes with similar seed size and color but different cooking times was conducted. The two lines tested are both from the Andean gene pool. One cooks in 24 min (fast cooking) and the other cooks in 42 min (slow cooking). The fast cooking line had 24% more protein and 10% more folate in the cooked seed than the slow cooking line. There are also different levels of minerals in the two seed types. Genetics of seed zinc and iron accumulation in beans: Phaseolus dumosus, a relative of common bean, has higher levels of zinc and iron in the seed as compared to common bean. We are currently conducting field evaluation and gene expression analysis of common bean lines developed at the International Center for Tropical Agriculture (CIAT) with high seed Fe and Zn introgressed from P. dumosus. Characterization and mapping of the ZIP family of metal transporters in dry bean: Zinc (Zn) is an essential mineral for humans and plants. The accumulation of Zn in plants involves many genes such as metal transporters. In total, 23 zinc transporter genes were identified in dry bean. Expression patterns of four of these genes were characterized in two bean genotypes. One of the genes, PvZIP12, showed differential expression between genotypes with contrasting seed zinc levels and also was located to a genomic region important in seed zinc accumulation and is a good candidate gene for increasing seed Zn concentration. This finding may be used to help make beans more nutritious by increasing their mineral content. Application of near-infrared reflectance spectroscopy to assess black bean processing quality: Canned black beans (Phaseolus vulgaris L.) are important bean products in the U.S. Processing presents unique challenges because of discoloration during canning and storage. These quality issues strongly affect consumer acceptance and processor standards for beans. We used visible and near-infrared reflectance (Vis/NIR) spectroscopy to predict how well different bean varieties hold up during the canning process in dry beans. Promising results for Vis/NIR prediction of canning quality were obtained. This is the first report where Vis/NIR on intact dry seed has been used to predict canning quality on canned seed. These findings may help breeders develop black bean varieties with superior canning quality. Outcomes/Impact The breeding program released a high-yielding upright full-season pinto bean variety, Eldorado, early-season white kidney bean, Snowdon; and a new upright pink bean variety, Rosetta that has good seed color. The adoption of new upright black bean variety Zorro from MSU breeding program has provided growers in Michigan with opportunity to direct harvest the crop and thus reduce production costs. In 2012, new high-yielding navy and black bean lines with resistance to anthracnose race 73 and rust race 22:2 and new high-yielding kidney and cranberry bean lines with high levels of resistance to CBB were identified.

Publications

  • Type: Journal Articles Status: Published Year Published: 2012 Citation: 1. Astudillo, C., Fernandez, A., Blair, M., Cichy, K.A. 2013. Phaseolus vulgaris ZIP gene family: identification, characterization, mapping and gene expression. Frontiers in Plant Science. 4:286. 2. Cichy, K.A., A. Fernandez, A. Kilian, J.D. Kelly, C.H. Galeano, S. Shaw, M. Brick, D. Hodkinson and E. Troxtell. 2013. QTL analysis of canning quality and color retention in black beans (Phaseolus vulgaris L.). Molecular Breeding doi: 10.1007/s11032-013-9940-y 3. Kelly, J.D., G.V. Varner, K.A. Cichy, and E.M. Wright. 2013. Registration of Powderhorn great northern bean. J. Plant Registrations 7 (in press). 4. Mukeshimana, G., Y. Ma, A. E. Walworth, G-q. Song, and J. D. Kelly. 2013. Factors influencing regeneration and Agrobacterium tumefaciens-mediated transformation of common bean (Phaseolus vulgaris L.). Plant Biotechnol. Rep. 7:59-70.doi:10.1007/s11816-012-0237-0. 5. Miklas, P.N., L. D. Porter, J. D. Kelly, and J. R. Myers 2013. Characterization of white mold disease avoidance in common bean. European J. Plant Pathology. 135:525543. doi:10.1007/s10658-012-0153-8 6. Porch, T.G., J. S. Beaver, D. G. Debouck, S. Jackson, J.D. Kelly, and H. Dempewolf. 2013. Use of wild relatives and closely related species to adapt common bean to climate change. Agronomy 3:433-461. doi:10.3390/agronomy3020433. Book Chapters: 1. Ferreira, J.J., A. Campa, and J.D. Kelly. 2013. Organization of genes conferring resistance to anthracnose in common bean, pp. 151-181. In: R. K. Varshney and R. Tuberosa (eds). Translational Genomics for Crop Breeding, Volume I: Biotic Stresses, John Wiley & Sons, Inc. 2. Vandemark, G. J., M. A. Brick, J. Osorno, J. D. Kelly, and C. Urrea. 2013. Yield gains in edible grain legumes. In S. Smith, J. Specht, B. Diers, and B. Carver (eds.) Yield Gains in Major U.S. Field Crops. CSSA. Madison, WI. (in press)


Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: The MSU dry bean breeding and genetics program conducted 24 yield trials in ten market classes and participated in the growing and evaluation of the Cooperative Dry Bean, Midwest Regional Performance, and the National Sclerotinia Nurseries in Michigan and winter nursery in Puerto Rico in 2012. All yield trials at Frankenmuth were direct harvested except for 100-entry drought trial that was rod-pulled. The drought trial showed good early moisture stress but late July rains resulted in high yields and later maturity throughout. In addition to yield and agronomic data, roots were sampled and rated and biomass and harvest index were recorded. Large-seeded kidney, cranberry, and white mold trials at Montcalm were rod-pulled. Dry weather early in the season followed by ample rainfall delayed maturity at Frankenmuth. Plots at Montcalm had similar rainfall pattern but the stress was offset with supplemental irrigation and excellent yields were recorded in the kidney and cranberry trials. Screening for resistance to common bacterial blight was very effective in these nurseries. White mold infection developed well in 2012 and genotypic differences were observed. A total of 3,900 plots were harvested for yield in 2012 and 1,977 single plant selections were made in the early generation nurseries. Other studies included the evaluation of 130-entry black bean RIL population for nitrogen-fixation, and certified organic variety trials at two locations. Identification of a low oligosaccharide bean: Mutagenized bean lines have been screened seed oligosaccharide levels. In the first screening of 1000 lines, candidate lines were identified that were potentially low raffinose and/or low stachyose mutants. Based on second and third screening rounds, it appears that none of the lines with low oligosaccharide levels were heritable. Since no mutant was identified, screening continued for natural variation for this trait in 100 diverse Andean bean lines, and one red mottled line from Tanzania, Maulasi, had 64% less stachyose and 26% less raffinose in cooked seeds as compared to average levels of the 100 lines screened. Genetics of seed zinc accumulation in beans: A transcriptome of all the genes expressed and their level of expression has been developed for bean pods of three cultivars that accumulate different levels of zinc in their seeds, Albion, Voyager and T39. This data has been analyzed to identify differentially expressed genes related to zinc and iron transport. In addition all sequence variation in the form of single nucleotide polymorphisms (SNPs) has been identified. PARTICIPANTS: James D. Kelly, Karen A. Cichy TARGET AUDIENCES: Bean Farmers, Bean Elevator Managers in Michigan; National Food Industry and Food Processors and Consumers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The breeding program released a high-yielding upright full-season pinto bean variety, Eldorado, early-season white kidney bean, Snowdon; and a new upright pink bean variety, Rosetta that has good seed color. The adoption of new upright black bean variety Zorro from MSU breeding program has provided growers in Michigan with opportunity to direct harvest the crop and thus reduce production costs. In 2012, new high-yielding navy and black bean lines with resistance to anthracnose race 73 and rust race 22:2 and new high-yielding kidney and cranberry bean lines with high levels of resistance to CBB were identified. Sensory quality of historically important dry beans: Dry bean breeding efforts in the U.S. begun in the early 1900's and has focused on improving yields and agronomic characteristics while meeting strict consumer requirements for seed color, shape, and size expectations. Except for canning quality, other sensory characteristics of beans have not received as much attention by breeders. ARS scientists in East Lansing, MI evaluated the sensory quality, including, flavor, appearance, and canning quality of historically important bean varieties from different eras of three market classes. Canning quality has been consistently good in the five most important Navy bean varieties in the US since the 1900's. Flavor is better in a new navy bean variety as compared to a foundational Navy landrace that precludes breeding. Canning quality, consumer visual appeal and color retention is superior in recent black bean releases as compared to older varieties. A new pinto cultivar exhibits inferior canning quality and acceptance of appearance by consumers. These findings are valuable to breeders interested in improving sensory attributes of their next generation of bean varieties.

Publications

  • Kelly, J.D., G.V. Varner, K.A. Cichy, and E.M. Wright. 2012. Registration of Rosetta pink bean. J. Plant Registrations 6: 229-232. doi: 10.3198/jpr2012.03.0142crc.
  • Kelly, J.D., G.V. Varner, W. Mkwaila, K.A. Cichy, and E.M. Wright. 2012. Registration of Eldorado pinto bean. J. Plant Registrations 6: 233-237. doi: 10.3198/jpr2012.02.0140crc.
  • Kelly, J.D., G.V. Varner, K.A. Cichy, and E.M. Wright. 2012. Registration of Snowdon white kidney bean. J. Plant Registrations 6: 239-242. doi: 10.3198/jpr2012.03.0146crc.
  • Heilig, J.A., and J.D. Kelly. 2012. Performance of dry bean genotypes grown under organic and conventional production systems in Michigan. Agron. J.104:1485-1492. doi:10.2134/agronj2012.0082.
  • Mukeshimana, G., Y. Ma, A. E. Walworth, G-q. Song, and J. D. Kelly. 2012. Factors influencing regeneration and Agrobacterium tumefaciens-mediated transformation of common bean (Phaseolus vulgaris L.). Plant Biotechnol. Rep. doi:10.1007/s11816-012-0237-0.
  • Kelly, J.D. and K.A. Cichy. 2012. Dry Bean Breeding and Production Technologies, pp. 23-54. In: Common Beans and Pulses: Production, Processing, and Nutrition. Editors: M.A. Uebersax, M. Siddiq, K.D. Dolan John-Wiley Publishing Co.
  • Roman-Aviles, B., J.M. Lewis and J.D. Kelly. 2012. Fusarium Genetic Control: A Long Term Strategy, pp. 65-108. In: Control of Fusarium Diseases, Editors: Fernando M. Alves-Santos, Julio J. Diez, Research Signpost 37/661, Kerala, India. ISBN: 978-81-308-0470-5.
  • Brisco, E.I. 2012. Empoasca leafhopper species resistance in common bean, Phaseolus vulgaris: field screening and QTL identification. Doctoral Dissertation, Michigan State University, East Lansing MI.
  • Lasley, A.L. 2012. Evaluation of root traits associated with drought tolerance in common bean (Phaseolus vulgaris L.). Masters Thesis, Michigan State University, East Lansing MI.
  • Mukeshimana, G. 2012. Dissecting the genetic complexity of drought tolerance mechanisms in common bean (Phaseolus vulgaris L.). Doctoral Dissertation, Michigan State University, East Lansing MI. 203pp.


Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: The MSU dry bean breeding and genetics program conducted 32 yield trials in ten market classes and participated in the growing and evaluation of the Cooperative Dry Bean, Midwest Regional Performance, BeanCAP and the National Sclerotinia Nurseries in Michigan and winter nursery in Puerto Rico in 2011. All yield trials at Frankenmuth were direct harvested, whereas the large-seeded kidney, cranberry, white mold and beancap drought trials at Montcalm were rod-pulled and biomass was calculated on the drought trial. As a result many of the early-season materials double-set, whereas the longer-season blacks and navies matured normally ahead of pinto, and great northern trials. Some entries in the 300-entry beancap nursery remained green and never matured. Plots at Montcalm had similar rainfall pattern but the stress was offset with supplemental irrigation and excellent yields were recorded in the kidney and cranberry trials. The beancap drought trial showed good early moisture stress but following late July rains, the entire trial re-grew, resulting in high yields and later maturity throughout. In addition to yield and agronomic data, roots were sampled and rated and biomass and harvest index were recorded. White mold infection was slow to develop in 2011 and never reached high levels of severity. A total of 5600 plots were harvested for yield in 2011 and over 2600 single plant selections were made in the early generation nurseries. Other studies included the evaluation of two RIL populations for reaction to potato leafhopper (Empoasca fabae), 130-entry black bean RIL population for nitrogen-fixation, certified organic variety trial, a cooperative canning trial with a private company, three beancap nurseries, and the first flor-de-mayo and mayacoba trials. The USDA-ARS East Lansing Dry Bean Genetics Program has conducted germplasm screening to identify beans with low levels of oligosaccharides. A population of 1200 chemically mutagenized beans of the cultivar BAT 93 was analyzed for seed raffinose, stachyose, and sucrose levels via high performance liquid chromatography. Average levels of these three sugars were 0.45%, 1.4% and 2.1% of the dry weight of uncooked seed. The initial screen identified 28 lines that were outliers for one or more of the compounds measured. To determine if the seed sugar level differences were heritable, the 28 lines were planted in the greenhouse. This seed was measured for sugar concentration resulting in 4 potential mutant lines which have again been planted in greenhouse to confirm the mutant phenotype. Characterization of the raffinose synthase and stachyose synthase genes in common bean seed is underway and genome screening has revealed this family to contain 13 genes. An additional chemically mutagenized population of the kidney bean Red Hawk is being developed and 640 unique M2 lines have been harvested. PARTICIPANTS: James D. Kelly, Maurice Bennink, Karen A. Cichy TARGET AUDIENCES: Bean Farmers, Bean Elevator Managers in Michigan; National Food Industry and Food Processors and Consumers PROJECT MODIFICATIONS: None

Impacts
In 2011, the breeding identified new high-yielding navy and black bean lines with resistance to anthracnose race 73 and rust race 22:3; program observed continued high performance of upright full-season pinto line P07863, early-season white kidney K08961; and a new upright pink line S08418 with good seed color. These three breeding lines are under consideration for release as new varieties. The breeding program was also able to identify sources of bacterial blight resistance in adapted cranberry and kidney bean lines. In Michigan, the adoption of new upright black bean varieties from MSU breeding program has provided growers with opportunity to direct harvest the crop and thus reduce production costs. Seed phytic acid levels were measured colorimetrically on 249 bean lines of the BeanCAP grown at two locations (East Lansing, MI and Prosser, WA). The average seed concentration of phytic acid phosphorus was 4.2 mg g-1 in both MI and WA and the range in WA was 2.6 -6.5 mg g-1 and in MI it was 2.7 -6.0 mg g-1. The correlation coefficient between the phytic acid phosphorus levels in the lines grown in the two locations was only 0.26. Pink beans had the lowest average phytic acid phosphorus levels in both MI and WA at 3.76 mg g-1, which is 10.5% less than the average of all 249 lines.

Publications

  • Mkwaila, W., K.A. Terpstra, M. Ender, and J.D. Kelly. 2011. Identification of QTL for resistance to white mold in wild and landrace germplasm of common bean. Plant Breeding 130:665-672.
  • Miklas, P.N., S. P. Singh, H. Teran, J. D. Kelly, and J. R. Smith. 2011. Registration of common bacterial blight resistant cranberry dry bean germplasm line USCR-CBB-20. J. Plant Reg. 5:98-102.
  • Roman-Aviles, B., J.M. Lewis and J.D. Kelly. 2011. Fusarium Genetic Control: A Long Term Strategy. In: Control of Fusarium Diseases, Editors: Fernando M. Alves-Santos and Julio J. Diez. 2011:000-000 ISBN: 978-81-308-0470-5.
  • Wright, E.M., and J.D. Kelly. 2011. Mapping QTL for seed yield and canning quality following processing of black bean (Phaseolus vulgaris L.). Euphytica 179:471-484.
  • Abawi, G.S., T.G. Porch, and J. D. Kelly. 2011. Field and greenhouse evaluation of bean germplasm for root rot and other diseases in New York, 2010. Annu. Rep. Bean Improv. Coop. 54:142-143.
  • Astudillo, C., Cichy, K.A. 2011. Characterization and expression analysis of a dehydrin gene in Phaseolus vulgaris. Bean Improvement Cooperative Annual Report. 54:16-17.
  • Brisco, E.I., T. G. Porch, and J.D. Kelly. 2011. Comparison of choice versus no-choice tests of a dry bean IBL population for resistance to potato leafhopper. Annu. Rep. Bean Improv. Coop. 54:88-89.
  • Butler, N., Cichy, K.A. 2011. Protein Content and Canning Quality of Historically Important Navy Bean Varieties in Michigan. Bean Improvement Cooperative Annual Report. 54:8-9.
  • Mkwaila, W., and J. D. Kelly. 2011. Heritability estimates and phenotypic correlations for white mold resistance and agronomic traits in pinto bean. Annu. Rep. Bean Improv. Coop. 54:134-135.