EFFECT OF ROOT AND SHOOT ARCHITECTURE ON SEED NUTRITION IN DRY BEAN

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: AFRI COMPETITIVE GRANT
• Reporting Frequency: Annual
• Accession No.: 1019377
• Grant No.: 2019-67012-29732
• Cumulative Award Amt.: $156,910.00
• Proposal No.: 2018-07687
• Project Start Date: Jun 1, 2019
• Project End Date: May 31, 2022
• Grant Year: 2019
• Program Code: [A7201]- AFRI Post Doctoral Fellowships

Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824

Performing Department
PLANT SOIL MICROBIAL

Non Technical Summary
Dry beans are an important source of plant-based protein and micronutrients. Historically, they have been bred for an upright architecture which allows for high-throughput harvesting. We now know that in many species, the components of shoot development overlap with root development. With the predicted rise in abiotic stressors such as drought and temperature from pending climate change, root architecture and seed nutrition content will be reduced. Although recent studies show that increasing shoot biomass reduces seed nutrition, we do not yet have equivalent knowledge for roots. To better understand root architecture, this postdoctoral research project aims to characterize the relationship between dry bean root architecture, shoot architecture, and seed mineral nutrition using a multifaceted approach. This proposal reflects AFRI priorities related to sustainability. Root systems with better nutrient acquisition require less fertilizer, are more resilient, and have more nutritious seeds and results from this project will facilitate breeding for root architecture in dry beans with the potential to promote resilience and seed nutritional content.

Animal Health Component

(N/A)

Research Effort Categories

Basic

100%

Applied

(N/A)

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
102	1410	1050	100%

Knowledge Area
102 - Soil, Plant, Water, Nutrient Relationships;

Subject Of Investigation
1410 - Beans (dry);

Field Of Science
1050 - Developmental biology;

Keywords

phaseolus vulgaris

diversity panel

growth habit

root architecture

seed mineral nutrition

Goals / Objectives
Consumed as a staple food in many regions of the world, dry beans (Phaseolus vulgaris) contribute key dietary nutrients, such as protein, iron, and fiber, and are sometimes the main source of these nutrients. In 2012, nearly 1.7 million acres of dry bean were harvested in the United States, leading to annual consumer sales in excess of $2 billion. Michigan is the second largest producer of dry bean, behind North Dakota. The primary factors limiting production of dry bean are abiotic stresses associated with the changing climate and increased disease pressures. The severity and duration of spring flooding and late summer droughts are continuality increasing in major production areas including US Midwest. By 2050, the greatest limitation to bean production will likely be related to heat stress.The majority of agriculturally based climate change research emphasizes the role of shoot, leaf, and flower development in mitigating loss due to abiotic stress. Most studies do not include root- based measurements or characteristics as relevant phenotypes or breeding targets. Despite this, root architecture has incredible potential to improve resilience to climate change. The primary role of root physiology is acquisition of water and mineral nutrients, and root development is altered under abiotic stress. Drought increases root depth in many species. Elevated temperature can have various effects on root architecture, generally increasing root biomass until a "threshold temperature" is met, in which root biomass is reduced. Drought and elevated temperature reduce nodule numbers in some legumes. Because roots are central to mitigating yield loss due to abiotic stress, we must have a firm understanding of the architecture, development, and natural variation of root systems.Historically, dry bean shoot architecture traits have been targeted to optimize seed productivity, harvestability, and disease avoidance for pathogens such as white mold and anthracnose. Although root architecture is the primary source for optimal mineral nutrient acquisition and a resource for climate-resilient breeding strategies, little is known on how root architecture affects seed mineral nutrition. Root and shoot development share overlapping mechanisms and it is likely that root architecture has inadvertently been selected upon due to heavy selection on shoot architecture. This project has three aims: (1) Construct the bean architecture association panel (BAAP) using a meta-analysis approach; (2) Explore the link between plant architecture traits and nutrient content in bean; (3) Identify loci controlling root architecture phenotypes linked to agronomically important traits. This proposal reflects AFRI priorities related to sustainability as root systems with better nutrient acquisition require less fertilizer, are more resilient, and have more nutritious seeds. This proposal incorporates both domestic and international research as the outcomes (i.e. parental candidates and markers for selection) will apply to dry beans cultivars grown worldwide.

Project Methods
Aim 1. Construct a diversity panel. Using meta-analysis approach and available genomic resources, I will create a diversity panel for further testing of dry bean root architecture, shoot architecture, and seed nutrition. Phenotypic data for seed mineral nutrition, shoot architecture, and root architecture will be collected from publically available data. Weighted means will be determined using meta-analytic procedures. The panel will include commonly used cultivars and genotypes with phenotypic and genotypic diversity.Aim 2. Screen the diversity panel. Using the information generated in Aim 1, I will screen the diversity panel in Aim 1 for relevant root architecture traits and seed mineral nutrition. To ensure each pot is receiving the same amount of nutrients, all applications will be weighed or measured as needed. Seed minerals will be analyzed using inductively coupled plasma spectroscopy. Seed total starch will be measured using the Megazyme Total Starch assay. Root traits will be phenotyped both under greenhouse and field conditions and scans will be analyzed with the appropriate root image analysis software.Aim 3. Identify genetic loci using genome wide association study. Using the phenotypic information from Aim 2 and available genotypic data, a genome-wide association study will be employed to identify loci governing root architecture phenotypes linked to agronomically important traits. Best linear unbiased predictors will be calculated using a mixed linear model (SAS 9.4) and used to identify regions of SNP association. An efficient mixed-model association approach will correct population structure and reduce false positives. This will also identify potential markers and parental lines for future breeding strategies. Candidate parents will be confirmed across several field settings

Progress 06/01/19 to 05/31/22

Outputs
Target Audience:The target audience for this reporting period include dry bean (Phaseolus vulgaris) breeders and plant science researchers who are interested in shoot and root architecture or indirect effects of selection. Outreach activities also target the general public to increase awareness of the importance of breeding to everyday life. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has provided many opportunities for training and professional development by working one-on-one with mentors Robin Buell and Karen Cichy who are experts in their respective fields of genomics and dry bean breeding. Frequent meetings and close collaborations between these two mentors promoted skill development in both scientific writing and dissemination. In addition to the publications reported, there are three publications in preparation of which PI Haus is corresponding author. These interactions and pursuits have resulted in PI Haus to be offered a tenure-track associate professor position in the Department of Horticulture at Michigan State University. The ability to pursue independent research provided the opportunity to train threeundergraduates. The first, Logan Pierz, who has since graduated and is first author of a manuscript recently accepted to Applications in Plant Science(of which PI Haus is corresponding author). The second undergraduate, Rylee Hyrnyak, whopresented the findings of this proposal for the Pinto bean marketclass at MSU's Mid-SURE conference. Finally, Paige Smith, is pursuing related research that builds on this project by asking about evolutionary relationships in wild beans that predate the indirect selection of dry bean breeding programs. Finally, PI Haus has also acted as a leader in her community by training peers. PI Haus led a workshop on developing novel equipment for testing hypotheses by embracing principles in the Maker Movement. She also hosts the MSU biweekly root journal club meeting in which graduate students and postdoctoral researchers discuss the latest research related to root biology. How have the results been disseminated to communities of interest?PI Haus has presented research at the 2019 Bean Improvement Cooperative and presented a poster at MSU's Beet and Bean Symposium, an extension event in which she was able to discuss priorities and challenges of shareholders and growers. PI Haus has written a blog pot in conjunction with the Crop Science Society of America highlighting the importance of breeding programs for developing cultivars for everyday use and how wild beans may be able to provide insight into novel sources of genetic material. PI Haus has also informally updated dry bean researchers during the Phaseolus Crop Germplasm Committees annual meeting via a 10-15 minute presentation and through conversation during the attendance of the 2021Bean Improvement Cooperative meeting. Manuscripts are in preparation for dissemination through peer reviewed journals (target journal: Crop Science). What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? To understand how 100 years of breeding efforts for shoot architecture could indirectly affect root architecture, we created a panel of dry bean lines the encompasses four Middle American market-classes. This panel include two wild bean species and 20 cultivars that represent historical breeding target milestones such as reaching a type 4, type 3, and type 2 growth habit. This panel was screened for shoot and root architecture traits at two different developmental timepoints in a greenhouse and a field setting. We collected root architecture phenotypes from dry beans at the flowering stage for two field seasons at MSU's Montcalm Research Farm. For these two growing seasons, wecollected root phenotypes, growth habit,maturation data, and flowring data. We sent leaves and seeds to A & L Great Lakes fornutrient analysis. Preliminary analyses have been performed showing marketclass-specific alteration in root architecture, but consistent alteartions in nutritional changes across breeding programs. Advanced statistical analyses are ongoingin preparation for publication(s).

Publications

• Type: Journal Articles Status: Accepted Year Published: 2022 Citation: Pierz, Logan D., Heslinga, Dilyn R., C. Robin Buell, and Miranda J. Haus. An Image-Based Technique for Automated Root Disease Severity Assessment using PlantCV. Accepted: Applications in Plant Sciences.
• Type: Journal Articles Status: Other Year Published: 2022 Citation: Awale, H. E., Wiersma, A. T., Buell, C. R., Kelly, J. D., Cichy, K. A., and Haus, M. J. Anthracnose and Bean common mosaic necrosis virus Resistance in Wild and Landrace Phaseolus vulgaris (L.) Genetic Stocks. In preparation, target submission: Crop Science.
• Type: Conference Papers and Presentations Status: Other Year Published: 2022 Citation: Hyrnyak, R., Buell, C. R., Cichy, K. A., and Haus, M. J. Characterization of Dry Pinto Beans Nutritional Trends Over Time in MSU Breeding Programs. Michigan State University Mid-SURE Poster Presentation.

Progress 06/01/20 to 05/31/21

Outputs
Target Audience:The target audience for this reporting period include dry bean (Phaseolus vulgaris) breeders and plant science researchers who are interested in shoot and root archicture or indirect effects of selection. Outreach activities also target the general public to increase awareness of the importance of breeding to everyday life. Changes/Problems:Due to COVID-related research restrictions, I have asked for (and received) a no-costextension on this project. What opportunities for training and professional development has the project provided?This project has provided many opportunities for training and professional development by working one-on-one with mentors Robin Buell and Karen Cichy who are experts in their respective fields ofgenomics and dry bean breeding. Frequent meetings and close collaborations between these two mentors promoted skill development in both scientific writing and dissemination. In addition to the publications reported, there are two publications in preparation of which PI Haus is corresponding author of one.These interactions and pursuits have resulted in PI Haus to be offered a tenure-track associate professor position in the Department of Horticulture at Michigan State University. The ability to pursue independent research provided the opportunity to train two undergraduates. The first, Logan Pierz, who has since graduated and is first author of a manuscript in preparation (of which PI Haus iscorresponding author). The second undergraduate, Paige Smith, is pursuing related research that builds on this project by asking about evolutionary relationships in wild beans that predate the indirect selection of dry bean breeding programs. Finally, PI Haus has also acted as a leader in her community by training peers. PI Haus led a workshop on developing novel equipment for testing hypotheses by embracing principles in the Maker Movement. She also hosts the MSU biweekly root journal club meeting in which graduate students and postdoctoral researchers discuss the latest research related to root biology. How have the results been disseminated to communities of interest?PI Haus has written a blog pot in conjunction with the Crop Science Society of America highlighting the importance of breeding programs fordeveloping cultivars for everyday use and how wild beans may be able to provide insight into novel sources of genetic material. PI Haus has also informally updated dry bean researchers during the Phaseolus Crop Germplasm Committees annual meeting via a 10-15 minute presentation. What do you plan to do during the next reporting period to accomplish the goals?With the completion of the second field season, the goals of this next reporting period are to 1) characterize leaf and seed mineral nutrition of the historic bean panel, 2) analyze the data sets to identify possible effects of indirect selection, and 3) disseminate the results to the broader plant science and agriculture communities via publication and conference presentations.

Impacts
What was accomplished under these goals? To understand how 100 years of breeding efforts for shoot architecture could indirectly affect root architecture, we created a panel of dry bean lines the encompasses four Middle American market-classes. This panel include two wild bean species and 20 cultivars that represent historical breeding target milestones such as reaching a type 4, type 3, and type 2 growth habit. The primary activity of the first year of this project was to evaluate root and shoot architecture phenotypes. This panel was screened for shoot and root architecture traits at two different developmental timepoints in a greenhouse and a field setting. Wecollectedroot architecture phenotypes from dry beans at the flowering stage and grown in MSU's Montcalm Research Farm. The primary activity of the second year of this project focused on evaluating leaf and seedmacro- and micronutrient concentrationstoaddress the second aim of determining whether changes in root architecture have affected nutrient content. Wehave also repeated the fieldexperimentfor a second growth season. Wehave collected root phenotypes, maturation data, leaf nutrient analysis,and arecurrently preparingseed for nutrient analysis. We are currently analyzing the root phenotype data in preparation for publication.

Publications

• Type: Journal Articles Status: Published Year Published: 2021 Citation: Miranda J. Haus, Logan D. Pierz, Janette L. Jacobs, Andrew T. Wiersma, Halima E. Awale, Martin I. Chilvers, C. Robin Buell, Karen E. Cichy. (2021). Preliminary evaluation of wild bean (Phaseolus spp.) germplasm for resistance to Fusarium cuneirostrum and Fusarium oxysporum. Crop Science. https://doi.org/10.1002/csc2.20495
• Type: Journal Articles Status: Other Year Published: 2022 Citation: Pierz, Logan D., C. Robin Buell, and Miranda J. Haus. An Image-Based Technique for Automated Root Disease Severity Assessment using PlantCV. In preparation, Target Submission: Applications in Plant Sciences.
• Type: Websites Status: Published Year Published: 2021 Citation: Haus, M. J. and Susan V. Fisk. Old beans may have new uses. Sustainable, Secure Food Blog. Crop Science Society of America. September 22, 2021. https://sustainable-secure-food-blog.com/2021/09/22/old-beans-may-have-new-uses/#respond

Progress 06/01/19 to 05/31/20

Outputs
Target Audience:The target audience for this reporting period include dry bean (Phaseolus vulgaris)breedersand plant scienceresearchers who are interested in shoot and root archicture or indirect effects of selection. Extension and outreach events also targetMichigan dry bean farmers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?PI Haus has presented research at the 2019 Bean Improvement Cooperative and presented a poster at MSU's Beet and Bean Symposium, an extension event in which she was able to discuss priorities and challenges of shareholders and growers. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?The historic dry bean panel will be evaluated for the final replication in the greenhouse this fall. To explore the link between plant architecture traits and nutrient content in bean, seeds will be collected at the end of the 2020 field season. Leaf and seed samples will be sent for macro- and micronutrient analysis. We will identify if root architecture has been affected by breeding for a type 2 growth habit, and if so, does this reflect nutrient acquisition. Results will be disseminated through a research article and conference presentations.

Impacts
What was accomplished under these goals? Tounderstand how 100 years ofbreeding efforts for shoot architecture could indirectly affect root architecture, we created a panel of dry bean lines the encompasses four Middle American market-classes. This panel include two wild bean species and20 cultivars that represent historical breeding target milestones such as reaching a type 4, type 3, and type 2 growth habit. The primary activity of the first year of this project is to evaluate root and shoot architecture phenotypes. This panel has been screened for shoot and root architecture traits at two different developmental timepoints in a greenhouse and a field setting. We are currently collecting root architecture phenotypes from dry beans at the flowering stage and grown in MSU's Montcalm Research Farm. To address the second aim of determining whether changes in root architecture have affected nutrient content, we have collected soil and leaf samples for macro- and micronutrient analysis.

Publications

• Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Haus, M.J, Wang, W., and Cichy, K., Exploring Common Bean Root Response to Fusarium brasiliense in a Middle American x Andean population. Oral presentation at: Bean Improvement Cooperative Meeting. November, 2019.
• Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Haus, M. J., Wang, W., Peplinski, H., Jacobs, J. L., Chilvers, M. I., Buell, C. R., and Cichy, K. (2020) Root Crown Response to Fungal Root Rot in Phaseolus vulgaris Middle American x Andean lines. Plant Disease. https://doi.org/10.1094/PDIS-05-20-0956-RE
• Type: Journal Articles Status: Under Review Year Published: 2020 Citation: Haus, M. J., Pierz, L. D., Jacobs, J. L., Wiersma, A., Awale, H., Chilvers, M. I., Buell, C. R., and Cichy, K. Characterizing Wild Bean (Phaseolus spp.) Germplasm for Resistance to Fusarium Root Rot and Fusarium Wilt. In Revision at Crop Science.