Common Bean Coordinated Agricultural Project

COMMON BEAN COORDINATED AGRICULTURAL PROJECT

Sponsoring Institution

National Institute of Food and Agriculture

Project Status

TERMINATED

Funding Source

AFRI COMPETITIVE GRANT

Reporting Frequency

Annual

Accession No.

0219849

Grant No.

2009-85606-05964

Project No.

ND05058

Proposal No.

2010-03615

Multistate No.

(N/A)

Program Code

91710

Project Start Date

Sep 1, 2009

Project End Date

Aug 31, 2014

Grant Year

2011

Project Director
McClean, P.

Recipient Organization
NORTH DAKOTA STATE UNIV
(N/A)
FARGO,ND 58105

Performing Department
Plant Sciences

Non Technical Summary
SITUATION. Plants are a rich source of basic sugars, proteins, and lipids essential for our normal growth and development, and supply vitamins and minerals required for many of the basic cellular processes necessary for life. Legumes are considered to be some of the healthiest foods in our diet. Although some provide the full complement of 15 minerals required for human metabolism), levels of the minerals vary among crops within the family. Among legumes, common bean are consumed by humans more than any other crop. Health benefits from eating beans are numerous and include reducing the blood cholesterol and sugar levels which in turn prevents or alleviates certain types of cancer, Type 2 diabetes, and cardiovascular diseases. Diets rich in zinc and iron, two micronutrients abundant in bean, can delay the onset of AIDS. Recent research has shown that beans significantly reduce the onset of breast cancer, colon cancer, and biomarkers for heart disease risk. PURPOSE. The Common Bean Coordinated Agricultural Project (BeanCAP) will strengthen the bean research, education, and extension communities by focusing on the genetics and genomics aspects of nutrition in this important food crop. The research component will translate current and newly developed genomic information into markers with broad utility to improve any trait of interest among the various bean market classes grown in the United States. The markers will be used in the first ever nation-wide project to define loci controlling a large collection of nutritionally important traits at both the species and market-class-specific levels. Each breeding program can then design the best strategy for the nutritional improvement of the market classes they work with. A genotyping service will support all public US breeding programs improving traits of local importance. Low cost markers that leverage the information from the high throughput marker screening will be developed for the long-term improvement of common bean. The marker and phenotypic data generated by this project will be organized along with all available genetic map, marker, and loci data into a database that is fully operable with other legume databases. The extension component will develop WWW-deliverable learning communities and learning sites that focus on the theme "Nutritional Genetics and Genomics: Healthy Foods from the Field to the Table." These sites will inform educators and the public about the biology, genetics, and genomics of nutrition. High quality, narrated animations will be the primary learning tool. The educational component of the BeanCAP will also initiate a modern plant breeding training program focusing on early career recruitment and practical breeding/genomics training that illustrates, as an example, how the integration of genomic and phenotypic data can be used to improve nutritional traits in plants. This will provide a stream of students interested in filling the plant breeding human resource pool.

Animal Health Component

(N/A)

Research Effort Categories

Basic

35%

Applied

55%

Developmental

10%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1410	1081	45%
202	1410	1081	10%
701	1410	1010	10%
703	1410	1010	10%
903	1410	1010	25%

Knowledge Area
202 - Plant Genetic Resources; 703 - Nutrition Education and Behavior; 903 - Communication, Education, and Information Delivery; 701 - Nutrient Composition of Food; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1410 - Beans (dry);

Field Of Science
1010 - Nutrition and metabolism; 1081 - Breeding;

Goals / Objectives
OBJECTIVE 1: Develop high throughput, market-class-specific markers for the predominant common bean market classes produced in the US, convert those markers into breeder-friendly markers, and genotype breeder-defined populations with these markers. OUTPUTS: Year 1: SNP analysis of 196 genotypes; sequence data for additional genotypes; race specific SNPs defined, 66 CAP loci developed. Year 2: SNP analysis of ~2000 genotypes; 66 CAP loci developed. Years 3-4: SNP analysis of ~2000 genotypes; ~20 CAP markers for specific agronomic traits. OBJECTIVE 2: Discover genetic loci associated with nutritional traits that define "healthy beans" by combining genotype and nutritional profile data of association mapping and bi-parental populations. OUTPUTS: Year 1: Collect nutritional/agronomic performance data for ~300 dry bean and ~150 snap bean grown under controlled greenhouse conditions. Year 2: Collect nutritional/agronomic performance data for ~300 dry bean and ~150 snap bean grown under field conditions. Year 3: Discover marker loci associated with nutritional and agronomic traits. Year 4: Confirm loci associated with nutritional and agronomic traits. OBJECTIVE 3: Integrate common bean phenotypic, genotypic, and molecular marker data with other emerging legume genomic resources into breeder-friendly bioinformatic tools. OUTPUTS: Years 1-2: Establish the Phaseolus Genes database and integrate historical mapping and QTL data into the database; establish working relationships with other legume databases. Years 2-4: Incorporate emerging sequence data into the database; establish principles and FAQs that engage plant breeders in the use of the database OBJECTIVE 4: Launch the "Nutritional Genetics and Genomics: Healthy Foods from the Field to the Table" WWW presence that uses high-quality animations and other multimedia to highlight the biology and technology associated with the genomic-based improvement of nutritional traits. OUTPUTS: Year 1: Launch the BeanCAP WWW site, the Ning learning community, the Moodle learning site. Years 1-4: Develop animations that focus on nutrition, genomics, and plant breeding topics; develop associated images and quizzes for the animations. Years 2-4: Populate the Ning and Moodle sites with nutrition, genomics, and plant breeding learning materials; create FAQs questions for the project topics. OBJECTIVE 5: Initiate a modern plant breeding training program that focuses on early career recruitment and provides practical training that illustrates how the integration of genomic and phenotypic data can be used to improve nutritional traits in plants. OUTPUTS: Year 1: Develop promotional materials for the high school audience describing plant breeding will be developed, collate and deliver advanced learning materials from other CAP projects into the BeanCAP WWW site; develop curriculum for summer and year-round internships; Years 1-4: offer summer and year-round internships at participating university (8 total); perform high school visits with a target of 300 students; Years 1-2: leaders attend national agricultural conferences to announce the BeanCAP education program.

Project Methods
OBJECTIVE 1: SNPs will be developed for each common bean race and used to characterize a large set of common and breeding-program specific unique genotypes using the Illumina Golden Gate assay system. The sequence data will be developed from massively parallel sequencing of several genotypes within the Durango, Mesoamerican, and Nuevo Granada genotypes. CAP markers will be developed from the SNP diversity analysis by focusing on inexpensive enzymes for the analysis. OBJECTIVE 2: ~300 dry bean and ~150 snap bean genotypes will be grown in the greenhouse and then at four field locations. ~100 dry bean genotypes will be grown under controlled water stress conditions. The seed will then be used to analysis for 16 minerals, nutritional availability, antioxidants, phenolics, anthocyanins, soluble and insoluble carbohydrates, protein, oil, fiber, phytate, carotenoids, and vitamin C. Data for a suite of dry bean and snap bean specific traits will also be collected. The nutritional and agronomic data will be coupled with SNP genotype data and analyzed using association mapping techniques to discover genetic associations between specific markers and each of the nutritional and agronomic traits. Association mapping will include defining population structure using several procedures, the determination of the best structure characterization for each trait, and mixed linear model analysis that incorporates population structure parameter(s) and marker allele data to discover association. The false discovery rate will be used to determine those marker loci associated with the trait. OBJECTIVE 3: The project genotypic and phenotypic data will be incorporated the Phaseolus Genes Database. The sequence data will be stored in GBrowse while the linkage data will be accessible via GMap. The marker/trait data will be stored in a WWW-accessible hierarchial classification scheme. A trait ontology will be established along with other legume databases. FAQs and How-Tos will be developed based on breeder input to provide easy access to marker data. OBJECTIVE 4: A WWW accessible Ning learning community, a Moodle learning site, and FAQs will be created and populated with nutrition, genomics, and plant breeding learning materials using HTML mark-up language. Animations will be developed using the Maya 3D modeling software. Stills and quizzes based on the animations will be developed. OBJECTIVE 5: Paper-based promotional materials for the high school audience describing plant breeding will be developed. Learning materials from other CAP projects will be incorporated into the BeanCAP WWW site using HTML mark-up language. Learning exercises will be created that engage interns into the aspects of plant breeding associated with it as a career. Change in action of the target audience will be fostered by educating breeders, educators, and students about the BeanCAP deliverables. Change in action will be monitored by assessing: 1) the degree of incorporation of the marker data into plant breeding programs; 2) the usefulness of the Ning learning community, Moodle site, and animations as learning tools to educations; and 3) the interests of students in plant breeding as a career.

Progress 09/01/09 to 08/31/14

Outputs
Target Audience: Plant molecular geneticists, plant breeders, nutrition specialist, agricultural education media developers Changes/Problems: None, final report What opportunities for training and professional development has the project provided? Undergraduate students, graduate students, postdoctoral scientists, plant breeders How have the results been disseminated to communities of interest? Refereed publications, informal presentations to commodity groups, formal conference presentations, meeting abstracts, BIC reports, What do you plan to do during the next reporting period to accomplish the goals? Final report.

Impacts
What was accomplished under these goals? OBJECTIVE 1, Marker development: During the project, SNP and indel molecular markers were developed. Based on in-depth the (~4x) sequencing of 16 genotypes, a total of 1,859,249 SNPs was discovered. From this data, three Illumina chip sets were developed (n=10,280 SNPs). Collectively these three chips were used to screen 517 genotypes including 379 dry beans and 138 snap beans. These chip sets were used to genotype the Stampede x Redhawk population (n=267) and develop a molecular map with 7015 SNPs. The map was used to anchor assembled scaffolds into pseudochromosomes as part of the USDA funded common bean genome sequencing project. This large set of genotypes were filtered further to develop the BeanCAP BARC 6k Illumina-Infinium SNP chip which collectively contains at least 3000 SNPs for the pinto, great northern, pink, navy, black, and kidney market classes. The SNP chip set was used to screen >5000 genotypes that represented multiple diversity panels and mapping populations that were provided by project participants. The populations SNP data was then to map QTL. (See results below). At project’s end, reagents for ~3000 genotypes are available for additional analysis by project scientists. The vendor also has residual reagents which have been and will continue to be made available to private companies at the project cost point. For a subset of these genotypes which comprise the Mesoamerican Diversity Panel (MDP; n=300), genotype-by-sequencing data was also collected (n=~35,000 SNPs). New technologies associated with next generation sequencing allowed us to dramatically increase the number of breeder friendly-markers from the 66 CAPs markers initially propose to ~3000 indel markers. These markers have the same reaction conditions thus facilitates multiplexing genotyping. All of the data needed for the application of the markers is available from the project WWW site at: http://www.beancap.org/Research.cfm. OBJECTIVE 2, Genetic mapping: The populations for which SNP data was collected were mapped for a number of traits, and one study at Michigan State (co-PD Kelly) used a RIL population and 2122 SNPs to discover 14 QTL for multiple traits associated with yield components and phenology. Multiple genome-wide association studies (GWAS) were performed using standard mixed model approaches that controlled for population structure, genotype relatedness, or both. GWAS of the MDP grown in the same year in ND, CO, NE, and MI discovered GWAS peaks and candidates for the following traits: days to flower (5 peaks, 8 candidates), days to maturity (7,9), growth habit without determinate genotypes (4,2), growth habit with determinate genotypes (5,7), lodging (5,7), canopy height (5,6), seed weight (7,8), seed yield (7,13). A representative candidate gene is Phvul.001G189200 for growth habit which is an ortholog of the determinacy gene Dt1 in soybean. GWAS studies of the MDP (n=4 locations) for nutritional traits discovered GWAS peaks and candidates for the following traits: iron (5, 5) and zinc (5, 4). A representative candidate is Phvul.010G021600 for seed iron content which encodes an ortholog of the Arabidopsis vaculor transport gene VTI1. GWAS analyses are underway for the seed concentration of the following minerals: B, Ca, Co, Cu, K, Mg, Mn, Mo, Ni, P, and S. GWAS studies of the MDP (n=1 location, CO) for fiber traits discovered GWAS peaks and candidates for the following fiber traits: insoluble dietary fiber ( 10,2), soluble dietary fiber ( 1,2 ), insoluble and soluble dietary fiber combined (2,3), total dietary fiber (3,4), raffinose (7,2), stachyose (2,1), verbascoes (5,2), and oligosaccharides (4,6). Phvul.001G214300, which encodes stachyose synthase, is a candidate gene for raffinose, stachyose, verbascose and oligosachharide content. A four location (WA,CO,NE,PR) drought GWAS study discovered the following number of GWAS peaks: days to flower (2 peaks), days to maturity (3), growth habit with determinate genotypes (2), lodging (2), canopy height (2), seed weight (3), seed yield (3). The snap bean diversity panel was analyzed at one location (OR), and GWAS discovered 3 GWAS peaks and 3 candidates for the stringless phenotype and 3 peaks for white mold data. OBJECTIVE 3, PhaseolusGenes database: The PhaseolusGenes database was developed as part of this project (http://phaseolusgenes.bioinformatics.ucdavis.edu/). The database integrates common bean phenotypic, genotypic, and molecular marker data. The data was collated from publications and data shared by project personnel and others throughout the world. The database also contains a genome browser that places all of the markers in the context of the assembled common bean and soybean genomes. The browser features allows users to quickly locate other markers near a candidate marker in case the candidate marker is monomorphic in a particular mapping population. A total of 129,959 markers are presently (January 8, 2015) found in the database, and 95.6% of the markers contained sequence data for quick mapping of traits to the 11 bean chromosomes. Primer and amplification conditions, where available, can also be found in the database. Tutorials for using the database are available, as well as the methods and data sources used to develop the database. OBJECTIVE 4, Nutrition education: A suite of learning materials collectively entitled “Now Serving: Beans” was developed. The suite consists of a bingo game, a MS Powerpoint presentation (with script), and handouts. The suite was developed to introduce young (<12yrs) individuals to beans as a food source. A preschool curriculum entitled “Spillin’ the Beans” was developed and widely promoted at national and state conferences. 2,000 educational CDs on the topic were distributed. A large collection (n=17) of mini-documentaries that feature bean preparation and recipes were developed featuring 17 NDSU under graduate students. These are deposited on the BeanCAP YouTube channel at: https://www.youtube.com/user/ndsubeancap/videos. Total running time for these is 66:53 minutes. OBJECTIVE 5, Developing interest in plant breeding: Six mini-documentaries (total time: 36:43 min) and one feature length documentary (total time: 27:05 min) were developed to introduce students to plant breeding. These are available from the BeanCAP YouTube channel. The mini-documentaries are: BeanCAP: Introduction to Plant Breeding, Norman Borlaug & The Green Revolution, Genetic Variation & the Story of Stem Rust, BeanCAP: Bean Plant Architecture, BeanCAP: What’s Plant Breeding, A Journey Through the Bean Breeding Process, and the feature length documentary is entitled Plant Breeding: Science + Creative Problem Solving. In addition, we developed three mini-documentaries (total time: 25:27 min) that focus on root and root phenotyping to provide students a view of the biology of mineral uptake (Plant Nutrition: Mineral Absorption), the structure of roots (Root Biology), the complexity of root phenotyping (Shovelomics). Multiple visits to high schools reached ~600 students collectively in ND, CO, NE, MI. 51 students were exposed to plant breeding during summer internships at NDSU, CSU, UNL, and MSU. Of these seven entered graduate plant breeding programs for training at four universities, NDSU, UNL, Kansas State Univ., and Washington State Univ.

Publications

Type: Journal Articles Status: Published Year Published: 2014 Citation: Schmutz J, McClean P, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam S M, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudma,D , Lee R, Richard MMS, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Want M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics 46:707-713
Type: Journal Articles Status: Published Year Published: 2014 Citation: Bello MH, Moghaddam SM, Massoudi M, McClean PE, Cregan PB, Miklas PN (2014) Application of in silico bulked segregant analysis for rapid development of markers linked to Bean common mosaic virus resistance in common bean. BMC Genomics 15:903
Type: Journal Articles Status: Published Year Published: 2014 Citation: Mafi Moghaddam S, Song Q, Mamidi S, Schmutz J, Lee R, Cregan P, Osorno JM, McClean PE (2013) Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L. Frontiers in Plant Science 5:185
Type: Journal Articles Status: Published Year Published: 2014 Citation: O'Rourke JA, Iniguez LP, Fu F, Bucciarelli B, Miller SS, Jackson SA, McClean PE, Li J, Dai X, Zhao PX, Hernandez G, Vance CP (2014) An RNA-seq based gene expression atlas of the common bean. BMC Genomics 15:886
Type: Journal Articles Status: Published Year Published: 2014 Citation: Goretti D, Bitocchi E, Bellucci E, Rodriguez M, Rau D, Gioia T, Attene G, McClean P, Nanni L, Papa R (2014) Development of single nucleotide polymorphisms in Phaseolus vulgaris and related Phaseolus spp. Molecular Breeding 33:531-544
Type: Journal Articles Status: Published Year Published: 2014 Citation: Gon�alves-Vidigal M C, Cruz AS, Lacanallo,GF, Vidigal Filho PS, Sousa LL, Pacheco CMNA, McClean PE, Gepts P, Pastor-Corrales MA (2013) Co-segregation analysis and mapping of the anthracnose Co-10 and angular leaf spot Phg-ON disease-resistance genes in the common bean cultivar Ouro Negro. Theoretical and Applied Genetics 126:2245-2255
Type: Journal Articles Status: Published Year Published: 2014 Citation: O'Rourke J A, Iniguez L P, Bucciarellli B, Roessler J, Schmutz J, McClean PE, Jackson,SA, Hernandez G, Graham MA, Stupar RM, Vance CP (2013) A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar. Frontiers in Plant Science, 4:210
Type: Journal Articles Status: Published Year Published: 2014 Citation: Aranda, L., Porch, T. G., Bassett, M. J., Lara, L., & Cregan, P. B. (2014). Genetics and Mapping of the Cl Gene for Circumlineated Pattern in Common Bean Using AFLP-based Bulk Segregant Analysis and SNP-based Bidirectional Selective Genotyping. Journal of the American Society for Horticultural Science, 139(2), 213-218.
Type: Journal Articles Status: Published Year Published: 2014 Citation: Mukeshimana, G., Butare, L., Cregan, P. B., Blair, M. W., & Kelly, J. D. (2014). Quantitative trait loci associated with drought tolerance in common bean. Crop Science, 54, 923-938.
Type: Journal Articles Status: Published Year Published: 2014 Citation: Brisco, E. I., Porch, T. G., Cregan, P. B., & Kelly, J. D. (2014). Quantitative Trait Loci Associated with Resistance to Empoasca in Common Bean. Crop Science, 54(6), 2509-2519.
Type: Book Chapters Status: Published Year Published: 2014 Citation: Osorno, J. M., & McClean, P. E. (2014). Common Bean Genomics and Its Applications in Breeding Programs. In Legumes in the Omic Era (pp. 185-206). Springer New York.
Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: McClean P, Schmutz J, Mamidi S, Wu GA, Moghaddam SM, Cregan P, Song Q, Rokshar DS, Jackson SA. (2014). Domestication of Common Bean. In Plant and Animal Genome XXII Conference Abstracts, San Diego, January 2014; https://pag.confex.com/pag/xxii/webprogram/Paper11622.html.
Type: Journal Articles Status: Published Year Published: 2014 Citation: Miklas, P. N., Fourie, D., Trapp, J., Davis, J., & Myers, J. R. (2014). New Loci Including Conferring Resistance to Halo Bacterial Blight on Chromosome Pv04 in Common Bean. Crop Science, 54(5), 2099-2108.
Type: Journal Articles Status: Published Year Published: 2014 Citation: Cichy, K. A., Fernandez, A., Kilian, A., Kelly, J. D., Galeano, C. H., Shaw, 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.
Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Mamidi S, Lee R, Myers R, Miklas P, McClean P (2014) Identification of genes responsible for white mold in common bean (Phaseolus vulgaris L). In Plant and Animal Genome XXII Conference Abstracts, San Diego, January 2014; https://pag.confex.com/pag/xxii/webprogram/Paper11138.html.
Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Modgaddam SM, Stonehouse R, Lee R, Mamidi S, Bello M, Miklas P, McClean P, Bett K (2014) Molecular genetic analysis of the Phaseolus vulgaris P locus. In Plant and Animal Genome XXII Conference Abstracts, San Diego, January 2014; https://pag.confex.com/pag/xxii/webprogram/Paper10921.html
Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Moghaddam SM, Mamidi S, Brick MA, Cregan P, Kelly JD, Miklas P, Osorno JM, Porch T, Song Q, Urrea C, McClean P (2013) Genome-wide association study of agronomic traits in common bean (Phaseolus vulgaris L.) In Plant and Animal Genome XXI Conference Abstracts, San Diego, January 2013; https://pag.confex.com/pag/xxi/webprogram/Paper6619.html
Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Jackson S, Campbell TJ, Rokhsar DS, Schmutz J, McClean P, Wu GA (2013) Genomic analysis of introgressions in crop legumes: soybean and common bean. In Plant and Animal Genome XXI Conference Abstracts, San Diego, January 2013; https://pag.confex.com/pag/xxi/webprogram/Paper7460.html
Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2012 Citation: McClean P (2012) Applications of the Phaseolus vulgaris genome sequence: genomics in the age of plant breeding. Annual Report of the Bean Improvement Cooperative 55:xix-xxi.
Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Chavarro MC, Kim KD, El-baidouri M, Gao, D, Abernathy B, Gonzales M, Jackson SA (2014) Small RNA and methylation patterns comparison in common bean (Phaseolus vulgaris L). In Plant and Animal Genome XXII Conference Abstracts, San Diego, January 2014; https://pag.confex.com/pag/xxii/webprogram/Paper12351.html
Type: Journal Articles Status: Published Year Published: 2012 Citation: Felicetti, E., Song, Q., Jia, G., Cregan, P., Bett, K., & Miklas, P. N. (2012). Simple sequence repeats linked with slow darkening trait in pinto bean discovered by single nucleotide polymorphism assay and whole genome sequencing. Crop Science, 52(4), 1600-1608.
Type: Journal Articles Status: Published Year Published: 2013 Citation: Simple sequence repeats linked with slow darkening trait in pinto bean discovered by single nucleotide polymorphism assay and whole genome sequencing
Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Soltani A, Moghaddam SM, Osorno J, McClean P (2015) Identifyiing genomic regions controlling plant architecture characteristics in dry bean (Phaseolus vulgaris L). In Plant and Animal Genome XXIII Conference Abstracts, San Diego, January 2015; https://pag.confex.com/pag/xxiii/webprogram/Paper16431.html
Type: Journal Articles Status: Published Year Published: 2012 Citation: Garden-Robinson, J. (2012). Spilling the Beans: A Survey of Educators' Knowledge, Use, and Preferred Communication Methods Related to Dry Edible Beans. Journal of Nutrition Education and Behavior, 44(4), S71-S72.
Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Mamidi S, Moghaddam SM, Lee R, Myers R, Miklas P, McClean P (2015) Next generation sequencing identifies regions of introgression and differentially expressed genes for Sclerotinia resistance in common bean. In Plant and Animal Genome XXIII Conference Abstracts, San Diego, January 2015; https://pag.confex.com/pag/xxiii/webprogram/Paper16088.html
Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Moghaddam SM, Echeverria D, Thompson HJ, Brick MA, Brick LA, Mamidi S, Lee R, McClean P (2015) Discovering the genetic architecture of dietary fiber and oligosaccharide content in common beans (Phaseolus vulgaris). In Plant and Animal Genome XXIII Conference Abstracts, San Diego, January 2015; https://pag.confex.com/pag/xxiii/webprogram/Paper16059.html

Progress 09/01/12 to 08/31/13

Outputs
Target Audience: Plant molecular geneticists, plant breeders, nutrition specialist, agricultural education media developers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Graduate students, postdoctoral scientists, plant breeders. How have the results been disseminated to communities of interest? Refereed publications, meeting abstracts, public presentations. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? SNP screening with the BeanCAP BARCBean6K3 Illumina Infinium chip was performed by the Cregan Lab for the following Co-PDs (with number of lines in parentheses): Miklas (384), Singh (96), Porch (288), Gepts (288), McClean (120), Cichy (480), Nienhuis (288), Pastor-Corrales (384), Myers (192), and Osorno (576). In addition, the service was extended to bean researchers in Colombia( Raatz, CIAT, n=96), and Brazil (Souza, EMBRAPA, n=408). This marker system provided useful based on the following highlighted projects. An international collaboration between Michigan State University (MSU), USDA/ARS/Belstville, CIAT, and Rwanda Agricultural Board scored a RIL population and discovered 2,122 polymorphic SNPs, and QTL mapping discovered 14 QTL for seed yield under drought and days to flower, maturity and seed fill; harvest and pod index; and number of pods per plant, seeds per pod, 100-seed weight and seed yield per day. 440 genotypes of Andean origin were evaluated at MSU for biological nitrogen fixation, cooking time, and seed protein, mineral, and phytic acid levels. Cooking time was associated with SNP markers on chromosomes Pv02 and Pv05. At USDA/ARS/Prosser, a major QTL for common bacterial blight was discovered on Pv11, and fine-mapping three halo blight resistance genes on Pv04. Collectively, these QTL loci for many major agronomic and nutrition traits create a framework for targeted plant improvement. ~35,000 SNPs were discovered from genotype-by-sequences (GBS) methodology for 284 genotypes of the Mesoamerican Diversity Panel (MDP). This collection of ~35,000 SNPs will increase the accuracy of genome-wide association studies (GWAS) in common bean. Genome-wide association studies (GWAS) were performed with phenotypic data from four sites throughout the US. These allowed us to discover association peaks for days to flower (Pv01), days to maturity (Pv11), growth habit (Pv01,Pv11), lodging (Pv07), plant height (Pv07), seed weight (Pv06, Pv10), and seed yield (Pv01, Pv03, Pv05). The days to flower association peaks were near two genes (KNU, SEU) that act as general development regulators, while the lodging and plant height peaks are identical and are located in a LRR receptor kinas gene. The MDP and the large set of SNP (chip and GBS based) identified major white mold association peaks. GWAS studies enable candidate gene discovery for these traits. The PhaseolusGenes database has grown to include 129,960 markers by the addition of additional indel and SSR markers. A total of 198 QTL are now found in the database. The “Now Serving: Beans” materials (Bingo game, PowerPoint with script, handout) and “Spillin’ the Beans” preschool curriculum were promoted at three national conferences and three state conferences, and added to an educational CD and other materials distributed to more than 2,000 participants. 12 new bean nutrition and food videos were added to the BeanCAP YouTube channel. Videos featuring the principals of plant breeding (What Is Plant Breeding?) and breeding and plant architecture (Bean Plant Architecture) were added to the channel. These videos can be used as recruitment tools for the plant breeding profession.

Publications

Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Mafi Moghaddam, S., Q. Song, S. Mamidi, J. Schmutz, R. Lee, P. Cregan,J.M. Osorno, and P.E. McClean 2013. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L. Frontiers in Plant Science, 4 (in press).
Type: Journal Articles Status: Published Year Published: 2013 Citation: Blair MW, Izquierdo P, Astudillo C, Grusak MA (2013) A legume biofortification quandary: variability and genetic control of seed coat micronutrient accumulation in common beans. Front Plant Sci 4:275. Kleintop, A.E., D. Echeverria, L.A. Brick, H.J. Thompson, and M.A.Brick. (2013) Adaptation of the AOAC 2011.25 Integrated Total Dietary Fiber Assay to Determine the Dietary Fiber and Oligosaccharide Content of Dry Edible Bean. J. Food Ag.Chemistry. DOI: 10.1021/jf403018k Reinprecht, Y. Z. Yadegari, G.E. Perry, M. Siddiqua, L.C. Wright, P.E. McClean, and K.P. Pauls. 2013. In silico comparison of genomic regions containing genes coding for enzymes and transcription factors for the phenylpropanoid pathway in Phaseolus vulgaris L. and Glycine max L. Merr. Frontiers in Plant Science, 4:317. Shin, S.H., Q. Song, P.B. Cregan and M.A. Pastor-Corrales. 2013. Simple sequence repeat DNA markers linked with broad-spectrum rust resistance in common bean PI 310762. Phytopathology 103(Suppl. 2):S2.132
Type: Other Status: Published Year Published: 2013 Citation: Brick, M.A., D. Echeverria, A. Kleintop, H. Thompson, and J. Osorno. 2013. Dietary fiber content in dry edible bean cultivars. Abstracts Biennial Meeting of Bean Improvement Cooperative, Oct 2013, Portland, OR, p. 6. Davis, J.W., J. Myers, D. Kean, N. Al Bader, B. Yorgey, P. Cregan, Q. Song and C. Quigley. 2013. A SNP-based linkage map of snap bean (Phaseolus vulgaris). Abstracts Biennial Meeting of Bean Improvement Cooperative, Oct 2013, Portland, OR, p. 23. Garden-Robinson, J., L. Whigham, and S. Wang. 2013. S. Spilling the beans: a preschool gardening and nutrition education curriculum to increase the use of dry edible beans. [Abstract]. Journal of Nutrition Education and Behavior 45(4S):S14. Grusak, M.A., P.E. McClean, M.A. Brick, J.D. Kelly, J.M. Osorno, T.G. Porch, and C.A. Urrea. 2013. Seed mineral concentrations in diverse BeanCAP bean lines. Abstracts Biennial Meeting of Bean Improvement Cooperative, Oct 2013, Portland, OR, p. 26. Linares, A.M., C.A. Urrea, T.G. Porch, S. Mamidi, P.E. McClean, and J.M. Osorno. 2013. Drought tolerance QTL identified in the Buster x SER 22 RIL population. Abstracts Biennial Meeting of Bean Improvement Cooperative, Oct 2013, Portland, OR, p. 8. McClean, P.E., P.B. Cregan, S.A. Jackson, R. Lee, S. Mafi Moghaddam, S. Mamidi, D.S. Rokshar, J. Schmutz and Q. Song. 2013. Behind the scenes of the common bean genome. Abstracts Biennial Meeting of Bean Improvement Cooperative, Oct 2013, Portland, OR, p. 3. Oraguzie O.B., M.H. Bello, P.E. McClean, P.B. Cregan and P. Miklas. 2013. Association mapping of white mold resistance in a panel of North American breeding lines and cultivars representing the Middle American gene pool. Abstracts Biennial Meeting of Bean Improvement Cooperative, Oct 2013, Portland, OR, p. page 32. Shin, S-H., Q. Song, P.B. Cregan, M.A. Pastor-Corrales. 2013. SSR DNA markers linked with broad-spectrum rust resistance in common bean PI 310762 discovered by bulk segregant analysis using a large set of SNP DNA markers. Abstracts Biennial Meeting of Bean Improvement Cooperative, Oct 2013, Portland, OR, p. 34. Trapp, J., P. Miklas, C. Urrea, and P. Creagan. 2013. Identification of QTL for drought tolerance and characterization of extreme phenotypes in the Buster x Roza mapping population. Abstracts Biennial Meeting of Bean Improvement Cooperative, Oct 2013, Portland, OR, p. 18. Trapp, J., P. Miklas, C. Urrea, P. Cregan. 2013. Identification of QTL for drought tolerance and characterization of extreme phenotypes in the Buster X Roza mapping population. Abstracts Biennial Meeting of Bean Improvement Cooperative, Oct 2013, Portland, OR, p. 18. Urrea, C.A. 2013. Evaluation of the Andean BeanCAP lines to terminal drought in western Nebraska. Abstracts Biennial Meeting of Bean Improvement Cooperative, Oct 2013, Portland, OR, p. 9. Viteri, D.M., J. Trapp, P.B. Cregan, P.N. Miklas and S.P. Singh. 2013. Host QTL by strain interaction and discovery of new QTL for common bacterial blight resistance in the VAX dry bean breeding lines. Abstracts Biennial Meeting of Bean Improvement Cooperative, Oct 2013, Portland, OR, p. 14.
Type: Other Status: Published Year Published: 2013 Citation: Garden-Robinson, J. and K. McNeal. 2013. All About Beans: Nutrition, Health Benefits, Preparation and Use in Menus. North Dakota State University Extension Service, Fargo, ND. Available at www.ag.ndsu.edu/pubs/yf/foods/fn1643.pdf Garden-Robinson, J.,K. McNeal, S. Wang, C. Langfus, and C. Kjera, C. 2013. Spillin the Beans: Dry Edible Bean and Snap Bean Recipes, Nutrition Information and Tips (Online cookbook). . North Dakota State University Extension Service, Fargo, ND. Available at www.ag.ndsu.edu/pubs/yf/foods/fn1646_full.pdf Urrea, C.A. 2013. 2012 University of Nebraska dry bean breeding program activities in western Nebraska. The BeanBag. 31(3): 9, 10, 12, and 17. Urrea, C.A. 2013. Breeding dry beans for multiple disease resistance with high performance. The StarHerald. May 26, 2013. p. 4.

Progress 09/01/11 to 08/31/12

Outputs
OUTPUTS: Objective 1: Marker development. We completed the development of the 6K Illumina Infinium chip, and the genotyping service is now available to all public common bean breeders and geneticists. A new SNP map, with ~7800 SNP marker loci, from the cross Stampede x Redhawk was developed. Using the map and the version 1.0 assembly of the common bean genome, linkage disequilibrium was measured in multiple population samples. Combining the mapping data and the genome assembly, low recombination regions were discovered. The development of a set of >2800 indel markers was completedd and released to bean breeding and genetics community. Objective 2: Analysis of national association mapping trials. Results from the large national association mapping (AM) trial (n=300; locations =4), analyzed using multiple statistical models that account for population structure collectively discovered a total of 30 significant peaks for the following agronomic traits: days to flower, days to maturity, growth habit, lodging, plant height, seed weight, and seed yield. One region on chromosome Pv01 appeared to affect multiple traits. The gene nitrate reducatase mapped near (1.1 Mb) the seed weight locus on Pv08. In a separate trial, a total of 37 significant peaks were discovered for eleven root known to affect performance. For both of these analyses, significant factors were noted on all chromosomes. A subset of the national trial was grown under normal and terminal drought conditions. For some traits, the same loci were significant under both conditions. Additionally, many of the same loci were significant under normal conditions in this trial (n=96) and in the national trial with three times the number of genotypes. Objective 3: Database. The PhaseolusGenes. PhaseolusGenes (http://phaseolusgenes.bioinformatics.ucdavis.edu/search/) is now offering the recently released common bean genome as a reference, along with soybean. This extends its functionality by allowing for locating markers directly to it common bean location. Additional markers and traits are being added to the database. A total of 2144 markers are now in the database, and a total of 125,000 SSRs have been defined. The database currently contains QTL data for 196 traits, each with multiple markers for each traits. Objective 4: Outreach. Mini-documentaries that feature various released via the BeanCAP@NDSU YouTube channel (http://www.youtube.com/user/ndsubeancap) that feature the following plant breeding topics: Plant Breeding and Food Security (http://www.youtube.com/watchv=7zPK_GI03N0&feature=plcp); Norman Borlaug and the Green Revolution (http://www.youtube.com/watchv=Lg9-HTtgFOk&feature=plcp); Genetic Variation and the Story of Stem Rust (http://www.youtube.com/watchv=kd6B706ByZg&feature=plcp); and Bean Plant Architecture (http://www.youtube.com/watchv=wf_nOs7DP-o&feature=plcp). Objective 5: Plant breeding education. Project personnel made six high school visits and described the plant breeding career. Ten undergraduate and six high school students participated in the project intern program. Two graduates of the intern program began graduate programs in plant breeding. PARTICIPANTS: North Dakota State University: Phil McClean, PD; Juan Osorno, Co-PD; Julie Garden-Robinson, Co-PD; Christina Johnson, Animation Lead; Shane Reetz, Documentary lead; Bree Reetz, Education video development; Samira Mafi Moghaddam, Marker development, Association mapping, Sujan Mamidi, Statistical analysis, Association mapping, Emily Driessen, Undergraduate, Marker analysis, Erin Sullivan, Undergraduate, Marker analysis, Ryan Lenz, Undergraduate, Marker analysis, Lucia Smith, undergraduate plant breeding intern, Alex Kallmeyer, undergraduate plant breeding intern, Casey Kjera, Undergraduate nutrition intern, Abby Plucker, Undergraduate nutrition intern, Stephanie Anderson, Undergraduate nutrition intern, Johanna Christenson, Undergraduate nutrition intern, Brooke Nell, Undergraduate nutrition intern, Nicole Seaburg, Undergraduate nutrition intern, Kimberly Beauchamp, Graduate student nutrition education. USDA/Houston: Michael Grusak, Co-PD; William Carter, Micronutrient analysis, Jenna Emerick, Micronutrient analysis, Rida Khan, Micronutrient analysis. University of California/Davis: Paul Gepts, Co-PD; Sarah Kuzay, Database development , Paige Hamilton-Conaty, Database development. Eastern Wyoming College: Skye Martin, undergraduate breeding intern. University of Nebraska, Lincoln: Carlos Urrea, bean breeding. Western Nebraska Community College: Nathan Marquez, undergraduate breeding intern, Scout Wilson, undergraduate breeding intern. Colorado State University: Mark Brick, Nutrition analysis, Intern lead; Henry Thompson, nutrition; Adrienne Kleintop, Nutrition; Dimas Echeverria, Research Assistant; Donny Hodgkinson, Undergraduate intern, Emily Troxell, Undergraduate intern, Nathan Pohl, High school intern. Michigan State University: Jim Kelly, Co-PD; Karen Cichy, Phytate analysis; Cynthia Amstutz, Undergraduate intern; Lucas Costanza, Undergraduate intern; Mary Harris, Undergraduate intern; Yusong Mu, Undergraduate intern. Oregon State University: Jim Myers, Co-PD. Penn State University: Jonathan Lynch Root analysis; Jimmy Burridge, Root analysis. TARGET AUDIENCES: Common bean breeders: phenotypic and diversity increases their productivity. Common bean geneticists: new marker tools improve their ability to understand genetic factors controlling nutrition and agronomic traits. Common bean nutritionist: nutritional data affects decisions regarding approach to improving the nutrition value of common bean. Plant breeding industry: students are filling a human resource pipeline devoid of new individuals interested in the field. Canning industry: supports cultivar decision choices on those best suited as nutritional products. Bean producers: provides new cultivars of interest to the public interested in nutritional foods. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Objective 1: Marker development. The 6K Illumina Infinium chip to date has been used to genotype 950 samples. The genotyping service will increase the marker density for many public mapping projects in common bean. The new Stampede x Redhawk SNP map was used in the common bean sequencing project to create the chromosome level assembly. Linkage disequilibrium (LD) decayed to r2<0.5 within 100kb in a collection of 520 common bean genotypes representing both the Mesoamerican and Andean gene pools. Within a Mesoamerican sample of genotypes, LD decayed was at 9Mb, while it was at 12Mb in an Andean sample. The LD estimates informs bean geneticists and breeders as to the marker density required for mapping experiments. The location of low-recombination regions defines boundaries where greater number of recombinants will be required for map-based cloning. The indel marker set provides a new low cost marker set that utilizes a single reaction condition, has gel-based screening capability and has market class specificity. Objective 2: Analysis of national association mapping trials. The background association mapping statistical framework is now completed on the Mesoamerican association mapping panel, and that data can now be combined with phenotypic data by other researchers to discover significant associations. New associations define new markers that will be useful for the selection of the seven agronomic traits. The discovery of the gene for nitrate reductase near the seed weight locus on Pv08 will support efforts to describe the biology that underlies this important common bean agronomic trait. Objective 3: Database. The PhaseolusGenes. The addition of the common bean genome as a reference sequence in the databse extends its functionality by allowing for locating markers directly to its common bean location. The linkage of additional QTL data to a genomic location supports research to uncover shared genes that control common phenotypes among multiple legume species. Objective 4: Outreach. The plant breeding mini-documentaries support efforts to recruit students into plant breeding. Objective 5: Plant breeding education. Two plant breeding mini-documentaries were used in an on-line survey with two sections of a Genetics course (junior level) to determine students' knowledge of plant breeding and their career aspirations in plant breeding before and after viewing the documentaries. Analysis showed that students exhibited a significantly increased knowledge of the key concepts presented in the short videos. 10% of students "somewhat agreed", "agreed" or "strongly agreed" that at some point in the future they plan to enroll in a plant-breeding program. Visits to high school enhanced knowledge of the plant breeding career. Two new graduate students in plant breeding expanded the human resource pool for the profession.

Publications

Mafi Modhaddam, S., Mamidi, S., Osorno, J.M., Lee, R., Cregan, P., McClean, P.E. January, 2012. Developing marker-class specific indel markers from next generation sequence data in Phaseolus vulgaris. Poster, Plant and Animal Genome Conference, San Diego, CA.
Mamidi, S, Felicertti, E., Moghaddam, S., Lee, R., Miklas P., McClean. P.E. January, 2012. Introgression and gene expression difference in common bean (Phaseolus vulgaris L. responsible for white mold. Poster, Plant and Animal Genome Conference, San Diego, CA.
Hernandez, G., Iniguez, L.P., McClean, P.E., Shoemaker, R.C., Jackson, S., Vance, C.P. January, 2012. Transcriptome of common bean (Phaseolus vulgaris) through RNA-seq: nodulation, symbiotic nitrogen fixation, transcription factors. Poster, Plant and Animal Genome Conference, San Diego, CA.
McClean, P.E. April, 2012. Genomics in the Era of Plant Breeding. Dermot Coyne Lectureship, Oral presentation, University of Nebraska, Lincoln, NE.
McClean, P.E. June, 2012. Genome-wide Association Studies and the Phaseolus Genome. Oral presentation, Phaseomics, 2012. Guanajuato Mexico.
Garden-Robinson, J. June 2012. Spilling the Beans: A Survey of Educators' Knowledge, Use and Preferred Communication Methods related to Dry Edible Beans. Poster, Society for Nutrition Education and Behavior, Washington, D.C.
Garden-Robinson, J., Whigham, L. and Wang, S. September, 2012. Spilling the Beans: A Preschool Gardening and Nutrition Education Curriculum to Increase the Use of Dry Edible Beans. Poster, National Extension Association of Family and Consumer Sciences (NEAFCS), Columbus, OH.
Kleintop, A.E., D. Echeverria, L.A. Brick, M.A. Brick, and H.J. Thompson. 2012. Variation in total dietary fiber content in dry edible bean cultivar/lines. Annu. Rep. Bean Improv. Coop. 55: 57-58.
Brick, M.A., A. Kleintop, D. Echeverria, and H.J.Thompson. 2012. Variation in Total Dietary Fiber Content among Dry Edible Bean Cultivars. Abstract Western Society of Crop Science Annual Meeting, July 11‐13, Pullman, WA.
Kleintop, A.E., D. Echeverria, M.A. Brick, and H.J. Thompson. 2012. Dietary Fiber and Oligosaccharide Content in a Diverse Collection of Dry Edible Beans. Abstract Crop Science Society of America Annual Meeting, October 20-25, Cincinatti, OH.
Grusak, M., Etcheverry, P., Center, L., McClean, P.E., Mafi Moghaddam, S., Mamidi, S., Miklas, P. 2012. Potential of common bean to enhance dietary iron availability in humans: germplasm diversity and QTL analysis. Oral presentation, ASA.CSSA Symposium. Cincinnati, OH.
Kleintop, A.E., Echeverria, D., Brick, M.A., Thompson, H.J. October, 2012. Dietrary fiber and oligosaccharide content in a diverse collection of dry edible beans. Oral presentation, ASA.CSSA Symposium. Cincinnati, OH.
McClean, P.E. October, 2012. Translational Genomic Resources for Common Bean: The BeanCAP Support System. Oral presentation, ASA.CSSA Symposium. Cincinnati, OH.
Jackson, S., Wing, R., Ware, D., McClean, P., Schmutz, J., Grimwood, J., Shoemaker, R., Cregan, P.B., Doyle, J. October, 2012. Utilization of crop wild diversity: application of genomics. Oral presentation, ASA.CSSA Symposium. Cincinnati, OH.

Progress 09/01/10 to 08/31/11

Outputs
OUTPUTS: Objective 1: Marker development. Within and between market class SNPs were discovered using Illumina GAII generated sequence data for eighteen genotypes representing the pinto, navy, black, Great Northern, and kidney market classes. 1,859,249 SNPs were discovered. The most diverse market class was the pintos with 213,087 SNPs. The SNP data was used to develop a 6000 SNP Illumina Infinium SNP detection chip that was used to develop a ~2600 SNP map and evaluate sequence variation with the major market classes. The pinto sequence data was evaluated, and ~8800 insertion/deletions of >7 bp were detected. 218 gel-based markers were used to evaluate core breeding parents from the CSU, MSU, NDSU, and UNL breeding programs. Objective 2: Nutritional analysis and field trial. Greenhouse grown seed for 247 dry bean cultivars was evaluated for 16 minerals for which five were below detection level. The cultivars exhibited at least a 2X difference for 11 minerals. Within market class differences were detected for most minerals. Association mapping using the SNP and nutritional data discovered 8 loci significantly associated with iron content in the seed, one of which maps within 110kb (less than the LD distance) of a gene known to be involved in Fe metabolism. Field trials of 300 Mesoamerican cultivars were established in CO, MI, ND, and NE. Objective 3: Database. The PhaseolusGenes (http://phaseolusgenes.bioinformatics.ucdavis.edu/search/) database was populated with 795 SSR, 633 STS, 76 SCAR, and 38 gene-based markers. 21,825 new SSRs were discovered using 1x methyl-filtrated sequence data and mapped relative to the soybean genome. 888 QTL were identified from literature searches and entered into the database. A GBrowse version of the database was developed to display the marker data. Objective 4: Outreach. The "Now Serving: Beans!" teaching kit for teens and adults that provides nutritional facts about beans and ideas for adding them to menus was beta tested with 150 Family and Consumer Science teachers and Extension agents and released. Two bean recipe videos were released on the BeanCAP YouTube channel (http://www.youtube.com/user/ndsubeancap). A 4:22 minute video describing the role of plant breeding in food security was developed and released on the channel. The animation team completed the first pair of modules that focus on 1) root biology and the role soil chemistry plays on nutrient uptake; and 2) the flow of soil minerals from the root to various parts of plants. Objective 5: Plant breeding education. The ongoing hands-on internships occurring at four institutions (CSU, MSU, NDSU, and UNL) have proven to be the most successful way to spark interest in the students exposed. A total of 18 students (high school and undergraduates) across all institutions on the everyday activities of a breeding program with the goal of letting the students learn by practical experiences and not just in a passive manner. High school visits emphasized the role of plant breeding in the food system and plant breeding as a career. Presentations at national meetings focused on the unique aspect of the project and served as a recruitment vehicle. PARTICIPANTS: North Dakota State Univ: Phillip McClean, PD; Juan Osorno, Co-PD, education lead, breeding; Julie Garden-Robinson, Co-PD, extension; Michelle Grant, Administrative assistant; Bradley Bisek, intern; Nicole Dallman, intern; Kataryna Cookman, intern; Mitchell Bauske, intern; Lyndsie Park, intern; Peter Totten, intern; Christina Johnson, Artistic lead; Shane Reetz, Documentary lead; Bree Malingnen, Infrographics artist; Samira Mafi Moghaddam, Marker development; Rian Lee, Marker development; Sujan Mamidi, Statistical analysis; Stacy Halvorson, extension associate; Leah Whigham, nutrition researcher; Deb Habedank, childcare director; Todd Weinmann, extension agent; Steve Sagaser, extension agent; Chelsea Langus, intern; Alexandra Idso, intern; Aimee Henning, intern, Kendra Otto, intern; Emily Westrom, intern; Amy Hutchinson, intern; Kayla Bahtiraj, intern. Univ Nebraska, Lincoln: Carlos Urrea, , Co-PD; Nicole Schnitger, intern; Misty Griffitts, intern; Scout Wilson, intern; Charity Berkey, intern; Danielle Becker, intern; USDA/Houston: Michael Grusak, Co-PD, nutritional analysis; Paz Etcheverry, cooperator; David Dworak, technician; Lori Center, technician; William Carter, intern; Oregon State Univ: Jim Myers,; Co-PD, Nutritional analysis, breeding; Annie Chozinski, faculty research assistant; Kara Young, intern; Katrina Maguelli, intern. Univ California, Davis: Paul Gepts, Co-PD, data base development; Shelby Repinski, Graduate student, QTL entry to database; Adriana Navarro Gomez, Graduate student, QTL entry to database; Sun Lei, Graduate student; Tania Gioia, Graduate Student; Dawei Lin, Bioinformatics and database lead; Jose Boveda, Database/web programmer; Joe Fass, Lead programmer; Nikhil Joshi, Bioinformatics programmer; Monica Britton, Bioinformatics analyst; Zhi-Wei Lu, Bioinformatics analyst. Michigan State Univ: Jim Kelly, Co-PD, Breeding, education; Evan Wright, technician; Amy Lasley, MSU, graduate student; Valerio Hoyos Villegas, graduate student; Rosa Castanon, intern; Brittany Lane, intern. USDA/Prosser: Phil Miklas, Co-PD, Field increase of core population; Susan Swanson, technician; Jennifer Trapp, technician; Jeff Coulson, technician. USDA/Beltsville: Perry Cregan, Co-PD, Marker development and screening; David Hyten, Marker development and screening; Edward Fickus, Marker development technician; Qijiain Song, Bioinformatics analysis; Gaofeng Jia, marker and bioinformatics analysis; Josaine Rodriques, Federal University of Vicosa, Brazil, SSR analysis, graduate; Charles Quigley, research DNA sequencing. Seminis: Ken Kmecik, Greenhouse/field increase of core population. Colorado State Univ: Mark Brick, Breeding, education, nutrition analysis; Henry Thompson, Nutrition analysis; Soni Hueftle, intern; Griffin Carpenter, intern; Keera Brown, intern; Alyssa Bollig, intern; Dimas Echeveria Moreno, Research associate, nutrition analysis. USDA/East Lansing: Karen Cichy, Co-PD, Nutritional analysis; Nicole Butler, graduate student; USDA/Mayquez, PR: Tim Porch, Co-PD, Field stress analysis; Abraham Montes, technician; Franquie Colon, research assistant; Gregory Howard, research; Edlin Gonzalez, research. TARGET AUDIENCES: Common bean breeders: phenotypic and diversity increases their productivity. Common bean geneticists: new marker tools improve their ability to understand genetic factors controlling nutrition and agronomic traits. Common bean nutritionist: nutritional data affects decisions regarding approach to improving the nutrition value of common bean. Plant breeding industry: students are filling a human resource pipeline devoid of new individuals interested in the field. Canning industry: supports cultivar decision choices on those best suited as nutritional products. Bean producers: provides new cultivars of interest to the public interested in nutritional foods. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
Objectives 1 and 2: Marker development and nutritional analysis. The discovery of 1,859,249 SNPs among 18 genotypes suggests a single SNP chip is possible for genotyping all of the major market classes in common bean. The discovery of 213,087 SNPs within the pinto market class demonstrated the clear possibility that market class specific markers are possible. This is of great value to bean breeders, who primarily improve the crop by making within market-class crosses, because it opens the possibility of tracking beneficial alleles in crosses of closely related individuals. The abundance of indels within the pinto market class also provided evidence that mapping with low-cost markers that can pinpoint a trait to an interval of interest and that the interval can be further mined with other low-cost markers. The discovery that the approach can identify markers associated with well-defined intervals for two previously mapped loci (Str; P) confirmed the utility of association mapping common bean. Identifying a marker associated with seed iron content to a region found in soybean to be associated with iron metabolism demonstrated that the suggested phenotypic synteny between common bean and soybean indeed exists and that leveraging the genotypic synteny can positively affect improvement in both crops. The most extensive assay of mineral content in common bean shows that the BeanCAP association mapping panel contains significant variation to detect loci associated with seed mineral content. The first large scale genetic study of mineral content is common bean is now possible. Objective 3: Database. The availability of common bean SSR markers mapped relative to soybean provides the community with a new abundant set of markers. Coupling this data with an overview of QTL location enables finer mapping of the agronomic QTL loci mapper previously. This points further to the value of integrating common bean and soybean genotypic, phenotypic, and mapping data. A comparison of soybean and grasses major gene and QTL traits with those in common bean points to the need of developing a common bean specific trait ontology. Objective 4: Outreach. Education tools are available to teach young (4-6 years old) the importance of legumes in their diet. Recruiting tools that speak to the young demographic from which the next generation of plant breeding will come are developed. Objective 5: Plant breeding education. Two graduates of the BeanCAP year-long undergraduate intern program have entered graduate school in plant breeding.

Publications

McClean, P.E., Burridge, J., Beebe, S., Rao, I.M., Porch, T.G. (2011) Crop improvement in the era of climate change: an integrated, multi-disciplinary approach for common bean (Phaseolus vulgaris L.). Functional Plant Biology. (in press).

Progress 09/01/09 to 08/31/10

Outputs
OUTPUTS: Objective 1: Marker development. A 1536 Illumina Golden Gate SNP set was developed. The SNP information was distributed to other researchers interested in common bean SNP technology. A broad collection of 400+ dry bean and 150+ snap bean genotypes was developed. A sub-collection of 192 common bean genotypes, representing all of the US market classes, was developed. These collections were distributed to BeanCAP, and other, researchers. SNP data set was collected for the 192 core seta and for various mapping populations by USDA/Beltsville. Race specific SNPs distributed throughout the bean genome were identified. Core genotypes from the CSU, MSU, NDSU, and UNL breeding programs were collected and scored with is SNP subset. Objective 2: Seed increase and nutritional analysis. Seed of the large collection was distributed to Seminis and MSU and grown in the greenhouse. Greenhouse seed was grown in the field at MSU, USDA/Prosser, and Seminis seed farm (Idaho). Remnant seed was delivered to CSU and USDA/Houston for nutrient analysis. Snap beans were grown in OSU greenhouse and later in a OSU field trial. Pods were collected for nutrient analysis. Objective 3: Database. The PhaseolusGenes (http://phaseolusgenes.bioinformatics.ucdavis.edu/search/) database was launched. It contains fragment size, Tm, primer sequence, reference, URLs data for 1396 markers or sequence-tagged sites was entered into the database. White mold QTL data was integrated into the database. The soybean pseudochromosomes were entered into a database linked to PhaseolusGenes, and BLAST functionality was included for similarity searches. Objective 4: Outreach. The BeanCAP WWW site (http://www.beancap.org) was launched and populated with project related information and activities. Animations that focused on the themes of 1) root biology and the role soil chemistry plays on nutrient uptake; and 2) the flow of soil minerals from the root to various parts of plants are nearing completion. Live action plant breeding and field evaluation activities were filmed. Film was edited along with still photos and narration to develop short (3-5 minutes) documentaries that highlight 1) the importance of the plant breeding to world food security, and 2) the role of plant breeding in the development of the semi-dwarf cereals that alleviated hunger. The BeanCAP was promoted to the Bean Improvement Cooperative, US Dry Bean Council, Bush Brothers and ConAgra. Objective 5: Plant breeding education. The plant breeding internship program was presented via posters to the Minorities in Agriculture, Natural Resources, and Related Sciences and the North American Plant Breeders conferences. Contacts were established with multiple local high schools, and the program introduced to over >300 high school students. Educational pamphlets describing the program and student-generated presentations focusing on the interns were developed. Eight students participated in summer internships, and eight students worked with the NDSU, UNL, CSU, and MSU breeding programs during the school year. Educational materials were describing the program were developed (http://www.beancap.org/Education.cfm). PARTICIPANTS: Phillip McClean, North Dakota State University (NDSU), PD; Juan Osorno, NDSU, Co-PD, education lead, plant breeding; Julie Garden-Robinson, NDSU, Co-PD, extension; Michelle Grant, NDSU, Administrative assistant; Christina Johnson, NDSU, Artistic lead; Shane Reetz, NDSU, Documentary lead; Lindsey Duppong, NDSU, Infrographics artist; Samira Mafi Moghaddam, NDSU, Marker development; Rian Lee, NDSU, Marker development; Sujan Mamidi, NDSU, Statistical analysis; Alexander Johnson, NDSU, Undergraduate plant breeding intern; Mariah Smith, NDSU, High school plant breeding intern; Austen Lund, NDSU, High school plant breeding intern; Angela Linares, NDSU, Graduate student, intern training/seed dispersal; Albert J. Vander Wal, NDSU, Research technician, seed dispersal; Carlos Urrea, University of Nebraska, Lincoln (UNL), Co-PD; Doug Valade, UNL, High school summer intern student; Misty Griffitts, UNL, Undergraduate summer intern student; Nicole Schnittger, UNL, Undergraduate summer intern student; Tania Torres, UNL, Undergraduate school term intern student; Emily Hoehn, UNL, Undergraduate school term intern student; Michael Grusak, USDA/Houston, Co-PD; David Dworak, USDA/Houston, Research technician; Stephanie Mercado, USDA/Houston, Research technician; Jim Myers, Oregon State University; Co-PD, Nutritional analysis, plant breeding; Deborah Kean, OSU, Faculty research assistant, field (retired); Annie Chozinski, OSU, Faculty research assistant, field; Joel Davis, OSU, Faculty research assistant, lab nutrition analysis; Michelle Bullock, OSU, Student field worker; Paul Gepts, University of California, Davis (UCD), Co-PD, data base development; Shelby Repinski, UCD,Graduate student, QTL entry to database; Adriana Gomez, UCD, Graduate student, QTL entry to database; Dawei Lin, UCD, Bioinformatics and database lead; Jose Boveda, UCE, Database/web programmer; Joe Fass, UCD, Lead programmer; Nikhil Joshi, UCD, Bioinformatics programmer; Monica Britton, UCD, Bioinformatics analyst; Jim Kelly, Michigan State University (MSU), Plant breeding, education; Jacob Emmendorfer, MSU, High school plant breeding intern student; Damien Johnson, MSU, High school plant breeding intern student; Philip Munoz, MSU, Undergraduate plant breeding intern student; Mary Harris, MSU, Undergraduate plant breeding intern student; Phil Miklas, USDA/Prosser, Co-PD; Field increase of core population; Perry Cregan, USDA/Beltsville,Marker development and screening; David Hyten, USDA/Beltsville, Marker development and screening; Edward Fickus, USDA/Beltsville, Marker development technician; Ken Kmecik, Seminis, Greenhouse/field increase of core population; Mark Brick, Colorado State University (CSU), Plant breeding, education, nutrition analysis; Henry Thompson, CSU, Nutrition analysis; Sarah Dominick, CSU, Undergraduate plant breeding intern; Hannah Walters, CSU, Undergraduate plant breeding intern; Bryan Fisher, CSU,High school plant breeding intern; Colton Heeney, CSU, High school plant breeding intern; Jordon Leone, CSU, High school plant breeding intern; Leslie Brick, CSU, Research associate, nutrition analysis; Dimas Echeveria Moreno, CSU, Research associate, nutrition analysis. TARGET AUDIENCES: Providing new genetic stocks to public and private common bean breeders Providing new markers systems to public and private common bean molecular geneticists Providing nutrition survey data to common bean nutrition researchers Hands-on plant breeding training to freshman college students Hands-on plant breeding training to junior and senior high school students Providing nutrition survey data to common bean canning industry Providing nutrition survey data to common bean seed industry PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Objective 1: Marker development. The SNP genotyping data from the 192 sub-core set demonstrated the utility of the technology to plant breeders. The data revealed that although this first SNP set had broad utility for cross gene pool comparisons, the set was of limited value for within market class analysis. This was demonstrated by the observation that only 7% (black) to 25% (pinto) of the SNP from this set were polymorphic within a market class. Therefore, the "locus-by-locus resequencing approach" to SNP discovery was abandoned. Instead, the most polymorphic individuals within each market class were selected for next-generation sequencing, and the data will be analyzed to discover market class specific SNPs that will be used to develop market class specific SNP sets. Sequence comparison showed >35,000 indels (>6bp in length) between the two gene pools. 100s of SNPs were discovered within a single market class. This abundance of sequence data from multiple projects suggested the CAP-based marker system should be abandoned and SNP or.indel-based markers should be substituted. SNP and indel-based markers were developed for several disease QTL. Objective 2: Seed increase and nutritional analysis. Rather than relying only on public programs, the value of public-private partnerships was emphasized by interactions with private industry for the nutritional analysis. We accepted an offer by Seminis to use their large dry bean greenhouse block for the initial seed increase. That seed was grown in their disease-free seed nursery in ID to increase seed for the 2011 trial. This increase augmented others in MI and WA. Genetic diversity for insoluble, soluble, and total fiber content was observed within all market classes. ConAgra agreed to provide processed samples from the upcoming field trial for the project to assess the impact of processing on nutritional value. Objective 3: Database. Significant synteny was discovered between common bean and soybean. This provides another source of data for marker discovery. Therefore, soybean BLAST functionality was added to the database. Objective 4: Outreach. Extensive discussions with young staff impressed upon us the need to appeal to their desire to improve society. Short documentaries that highlight how plant breeding improves society by increasing food security were added as an outreach objective. Beans are not widely appreciated among younger students for their nutritional value. An education game targeted to K-12 educators was developed and delivered. Assessment data will be collected as the game is used in classrooms. Surveys of modern learning methods pointed to infographics as a new method that emphasizes facts in learning modules. These were included as components of animations. Objective 5: Plant breeding education. During classroom visits, it was discovered that plant breeding was a relatively unknown profession. Educational materials will now include short documentaries that feature the profession as a valuable career. Urban students showed little interest in the program internships. New strategies need to be designed.

Publications

Hyten, D.L., Song, Q., Fickus, E.W., Quigley, C.V., Lim, J.-S., Choi, I.-Y., Hwang, E.-Y., Pastor-Corrales, M.P., Cregan, P.B. ( 2010) High-throughput SNP discovery and assay development in common bean. BMC Genomics 11:475.
McClean, P.E., Mamidi, S., Chikara, S., Lee, R., Gepts P. (2010) Leveraging common bean/soybean synteny to saturate the Pv7 common bacterial blight QTL in common bean (Phaseolus vulgaris L.) Crop Science (under review).
Lin, D., Gepts, P., Schaal, A., Boveda, J., dos Santos, J.V.G., Fass, J., Kami, J., Joshi, N., Britton, M., Lu, Z. (2010) PhaseolusGenes: a genomics information management and marker discovery toolkit for a non-model organism. Plant and Animal Genome Conference http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_917.html
Osorno, J.M., J.D. Kelly, M. Brick, C.A. Urrea, J. Garden-Robinson, and P. McClean. 2010. Early recruitment of the next generation of plant breeders: The BeanCAP effort. Abstr. 1st Annu. Meet. of the Nat. Assoc. of Plant Breeders. Aug. 15-17, Johnston, IA.
Osorno, J.M., J.D. Kelly, M. Brick, C.A. Urrea, J. Garden-Robinson, and P. McClean. 2010. Strategies and challenges finding the next generation of plant breeders: The BeanCAP effort. Abstr. ASA-CSSA-SSA Ann. Meet. Oct. 31st to Nov. 4th. Long Beach, CA. Goncalves-Vidigal, M.C., Cruz, A.S., Garcia, A., Kami, J., Vidigal Filho, P.S., Sousa, L.L., McClean, P., Gepts, P., Pastor-Corrales, M.A.. 2010. Linkage mapping of the Phg-1 and Co-1^4 genes for resistance to angular leaf spot and anthracnose in the common bean cultivar AND 277. Theoretical and Applied Genetics (under review).
Harveson, R.M., and C.A. Urrea. 2010. Evaluating germplasm and breeding disease resistance for chickpeas and dry beans in western Nebraska. Scottsbluff Star-Herald. April 4, page2.
Hansen, Sandra. 2010. New program aimed at recruiting young scientists. Scottsbluff Star-Herald. March 13, page 1.
Hansen, Sandra. 2010. Hands-on experiences fill lives of WNCC students. Scottsbluff Star-Herald. March 13, page 2.
Hansen, Sandra. 2010. Summer is the best time to learn. Scottsbluff Star-Herald. August 22, page 2-3.
Dominick, Sarah. 2010. Dry bean research involves undergraduate and high school students. Colorado State University College of Agriculture Newsletter. http://www.agsci.colostate.edu/news/e-connection_summer10/DryBeans.ht ml