Development of New Selection Tools and Crop Varieties for Sustainable Agriculture

Final report for GW18-062

Project Type: Graduate Student
Funds awarded in 2018: $24,443.00
Projected End Date: 03/31/2019
Grant Recipient: University of California - Davis
Region: Western
State: California
Graduate Student:
Principal Investigator:
Paul Gepts
University of California - Davis
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Project Information


Sustainably managed agroecosystems are profoundly different than those that are managed conventionally. Unfortunately, most crop varieties are bred to perform well under conventional systems, and sustainable farmers most often grow varieties that are not optimally suited to their conditions. Evidence suggests that most of the difference in yield between conventional and organic farms, for example, is simply due to the fact that the varieties have been selected based on performance in a conventional, rather than sustainable environment.

Beginning in 2013, we surveyed organic farmers in California to identify their most pressing needs. One major concern for these growers is weed control. With limited use of herbicides, sustainable farmers need access to crop varieties with alternative canopy structures that allow for mechanical weed control and reduce hand-weeding costs. It is also vital for crop canopies to grow rapidly early in the season to outcompete weeds. Finally, sustainable growers need crops that are sensitive to abiotic pressure, such as heat stress, in a rapidly changing climate. To date, selection for these characteristics has been slow, expensive, and imprecise, but improvement of these traits is crucial for sustainable agriculture.

In the last three years, we have developed inexpensive, cutting-edge imagery acquisition and processing methods that facilitate the selection of varieties with an optimal canopy structure and vigorous growth rate. These have been disseminated to the next generation of agricultural innovators through on-farm field day demonstrations, personalized trainings with academic and industry partners, a new course offered at UC Davis, and workshops and presentations at scientific conferences. These methods have now been employed to study rice, alfalfa, spinach, wheat/triticale, grapes, tree crops, and several species of bean. Next, we identified genetic patterns associated with vigorous growth rate across multiple populations of common bean, which will be useful for efficient marker-assisted selection of improved varieties. We then screened breeding populations using these tools, and identified patterns of improvement in our breeding populations relative to their heirloom parents. Finally, we have conducted multi-location trials of advanced-generation breeding lines that excel in terms of yield, product value, and disease resistance. These selection tools and new varieties will be tremendously valuable for sustainable farmers in the western United States.

Project Objectives:

1) Develop high-throughput phenotyping methods for stress resilience and yield that can be used by growers or breeders. Physiological characteristics such as canopy temperature and NDVI are correlated with plant health, and may be associated with faster growth rate. They are also correlated with yield and abiotic stress resistance, but methods for analyzing the data have lagged behind the ability to collect it.

2) Identify the genetic basis of vigorous early season growth. We have developed a population descended from a slow growing, bushy dry bean parent (Orca) and a fast-growing, viney parent (Black Nightfall). With genotype data, we will be able to determine the genetic cause of variation in these traits.

3) Release new varieties of dry bean that excel in early season growth rate, canopy structure, and yield under variable environmental conditions. We will use high-throughput phenotyping and marker-assisted selection to improve early season growth rate, canopy structure, and other characteristics in dry bean. These releases will primarily fall into high-value heirloom market classes, which fetch a higher price than commodity market classes.

4) Disseminate breeding tools and new crop varieties to a wider audience We will disseminate our precise and inexpensive phenotyping methods through publications targeting growers and researchers. Genetics results will be published in peer-reviewed scientific literature accessed by plant breeders. Our new varieties will be showcased at our annual on-farm field days, and will be trialed by collaborating growers that produce common bean commercially. Publications on their release will be found in a variety of formats read by scientists and sustainable growers.


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  • Mike Reeske (Researcher)


Materials and methods:

Three main populations have been evaluated in this project. One population, the BeanCAP Middle American Diversity Panel (MDP), includes 280 highly diverse common bean varieties that are all descended from one of the domestication events in common bean. These were genotyped by Illumina BARCBean6K_3 Beadchip and Genotyping by Sequencing (GBS). These were grown to identify the genetic basis of canopy height, growth rate, and other canopy characteristics. A second population was developed specifically to study early season growth rate. It consists of 240 recombinant inbred lines descended from crosses between Black Nightfall and Orca. Black Nightfall is a fast growing variety that competes effectively against weeds. Orca is very slow growing, and is not competitive against weeds. This population segregates for early season growth rate. DNA from each RIL was extracted through a modified CTAB procedure, and genotyped with the BARCBean6K_3 BeadChip. A genetic map was constructed based on this data using the ASMap package in R, and QTL mapping was conducted using R/qtl. The third population is a diverse assemblage of breeding materials and the heirloom varieties and university-developed types they are descended from. Hundreds of heirloom varieties were grown between 2013 and 2016 to identify promising candidates. No heirloom lines combined rapid early season growth rate, bean common mosaic virus (BCMV) resistance, and consistently high yields. Donors for these characteristics were carefully chosen, and cross-pollinations were conducted between heirloom types and breeding lines developed by universities. The breeding program has progressed by a) the pedigree method, selecting for the above-mentioned characteristics and ideal seed coat color, and b) recurrent backcrossing for BCMV resistance. In the latter case, naturally occurring resistance alleles are "diluted" into the genetic background of the heirloom by a series of selections and cross-pollinations with the heirloom parent (recurrent backcrossing).

During the growing season, flights were conducted weekly from 3 weeks after planting (WAP) to 6 WAP for all populations. Until 3 WAP, the plants are small and the aerial imagery is not sufficiently detailed to generate meaningful data. Starting around 6 WAP, the plants transition into reproductive growth and begin to lodge, so increased canopy area after this point is not necessarily beneficial. Later flights were conducted throughout the season to continue the evaluation of canopy health throughout the growing season. This series of flights was conducted using a Phantom 3 Pro over the MDP and breeding population in 2016. In 2017, Phantom 3s were used to collect true color red/green/blue (RGB) and multispectral data over the MDP and Black Nightfall/Orca populations. The RGB and multispectral data were collected using a stock camera and Parrot Sequoia, respectively. Flights were typically planned in DJI Ground Station Pro. Imagery was processed into orthomosaics and digital surface models using Pix4Dmapper Pro. QGIS was used to extract data from each plot in the field, and advanced data extraction and statistical analyses and were done in R.

RGB, multispectral, and thermal data were collected for all populations in 2018. The 2018 breeding populations had been narrowed down to 10 breeding lines, five heirloom varieties, and three varieties released by universities as controls. These breeding lines were grown in three replicates in each of three organic field locations, along with a single replicate in one conventional field. In 2017 and 2018, the MDP was grown as two independent augmented designs, while the Black Nightfall/Orca population was grown in a single augmented design. The 2018 breeding trials were located on certified organic farms in San Diego, Monterey, and Yolo counties in California. In 2016, the MDP was grown in a single augmented design. In 2019, the Black Nightfall/Orca population is being grown in two augmented designs for a third and final season. The 2019 breeding trials include three replicates of eight breeding lines, five heirloom parents, and three university-developed controls. This trial is being conducted in Yolo, San Mateo, San Luis Obispo, and San Diego counties in California, and at Fedco seeds (two replicates) in Maine. Tests of some of these lines is also occurring in Shasta county and a second location in Yolo county. Row 7 seeds is conducting a taste test of the varieties. 

Raw imagery from drones was compiled into orthomosaics and digital surface models using Pix4Dmapper. Using QGIS, a grid of shapefiles was laid over each field using the vector grid function. Normalized Difference Vegetation Index (NDVI) orthomosaics were then used to separate canopy from soil based on an NDVI threshold of 0.5. This layer was used to calculate canopy area and eliminate soil values as needed. Digital surface models were used to extract the heights of plants and soil in each plot. The median elevation of the soil was subtracted from the mean canopy elevation to determine the average height of plants in a plot. Maximum plant heights were determined based on the median soil elevation subtracted from the maximum canopy elevation. This process requires only a few minutes to accomplish per field once the models are loaded into QGIS, regardless of the number of plots, making it scale efficiently for large trials. UAV-determined canopy heights were then compared to hand-measured heights. Genome wide association studies (GWAS) were carried out for changes in canopy area, height, and other characteristics in the MDP. This was done by GLM in TASSEL through the SNiPlay web interface. A minor allele frequency threshold of 0.1 was used for all tests, with a correction for population structure using the first five principal components of the genetic data. Significance was determined based on a Bonferroni correction based on an alpha of 0.05. 

We employed several strategies to help disseminate the products of this project. Our new phenotyping methods were taught to students in a new course on Unmanned Aerial Vehicles (UAVs) in Agriculture, taught twice at UC Davis. The class was highly experiential and hands-on, teaching students all aspects of planning successful and achievable drone-based projects. This includes programming flights, collecting imagery from a variety of sensors and UAVs, processing these into 3D high-resolution composite field models, and systematically extracting the desired information from all plots in a field simultaneously. Additional trainings included a two-week instruction for PhD candidate Felicien Zida, two one-day trainings for Lundberg Family Farms, a 3-hour intensive computer workshop at the Pacific GIS and RS conference, and numerous one-on-one trainings and consultations for other laboratories at UC Davis. We have reached out to farmers through four field days specifically targeting farmers since the summer 2017, an article in Organic Farmer magazine, reports on TV and radio, and announcements sent directly to farmers growing high-value heirloom bean varieties. We have addressed the general public by hosting a booth on UAVs in Agriculture at Picnic Day (the UC Davis open house) for the last two years and at the 2019 UC Davis drone fair. I gave a talk in January 2019 at the Leonardo Art and Science Evening Rendezvous (LASER) talks at UC Davis to discuss how drones are used to improve agriculture today.
Research results and discussion:
Growth rate in the Black Nightfall/Orca population
Black Nightfall and Orca have widely different growth rates. In 2016, Black Nightfall had approximately double the canopy area growth rate as Orca. In 2017, there was a fivefold difference in canopy growth rate between Black Nightfall (522 sq cm/plot/day) and Orca (93 sq cm/plot/day). Black Nightfall had a higher germination rate, but it still maintained a per-plant growth rate more than double that of Orca (44.5 sq. cm/plant/day vs. 19.5 sq. cm/plant/day). The progeny showed transgressive segregation, with individuals more extreme than either parent.
Black Nightfall and Orca were also grown as controls in the MDP. Here the plants show many of the same patterns.
QTL mapping
QTL mapping produced the most significant results for canopy cover growth rate in the Black Nightfall/Orca population on chromosome 7, indicating that this region is the most closely associated with growth rate. The region around this QTL includes PvTFL1z, a gene believed to play a role in determinacy (Kolkman and Kelly, 2003, Kwak et al. 2009), but which may have other, more subtle effects on growth habit. This has also been mapped as a lodging-related locus in common bean (Tar'an et al. 2002, Moghaddam et al. 2016).
Canopy volume at 28 days after planting is most affected by genes on chromosome 6. The exact gene models responsible for this variation is still unclear, and will warrant continued investigation.
QTL mapping for hand-measured height at 42 days after planting also identified a major peak on chromosome 7. This is likely related to lodging and canopy architecture, and is of considerable economic value. 
Trait mean (BN) mean (Orca) SD (BN) SD (Orca) p-value (two-tailed t-test) Significance
2016 emergence 44.83 41.33 14.13 12.69 0.66 ns
2017 emergence 26.38 12.75 6.39 7.07 0 **
2018 emergence 159.63 109.88 6.36 19.19 0 ***
2016 canopy growth rate per PLOT (cm2/(plot*day)) 400.29 207.11 124.08 50.12 0.01 **
2017 canopy growth rate per PLOT (cm2/(plot*day)) 895.68 193.46 168.61 82.76 0 ***
2018 canopy growth rate per PLOT (cm2/(plot*day)) 2807.86 1628.28 142.27 167.67 0 ***
2016 canopy growth rate per PLANT (cm2/(plant*day)) 9.2 5.63 1.82 2.7 0.02 *
2017 canopy growth rate per PLANT (cm2/(plant*day)) 34.62 17.22 5.65 5.58 0 ***
2018 canopy growth rate per PLANT (cm2/(plant*day)) 17.60 15.26 0.78 2.96 0.06 ns
2016 canopy height 42 DAP (cm) 38.31 28.15 2.46 2.94 0 ***
2017  canopy height 42 DAP (cm) 49.37 39.29 1.35 1.65 0 ***
2018  canopy height 42 DAP (cm) 51.59 43.66 2.00 2.61 0 ***


2017 GWAS of early season growth rate (3-6 WAP) in the MDP. SNPs on chromosomes 7 and 10 are significantly associated with early season growth rate. SNPs on chromosome 3 are nearly significant and may also play a role in growth rate.

2018 GWAS of early season growth rate in the MDP. The region on chromosome 7 is highly significantly associated with growth rate, even more so than in 2017. This greater significance may be the result of replication and improved emergence in the 2018 growing season.
The loci with the greatest effect on height in the MDP at 28 days after planting are on chromosome 7 rather than chromosome 6. This may be the result of large-effect alleles found in Black Nightfall or Orca being found at low frequency in Middle American beans generally. These results further demonstrate the important role of chromosome 7 on growth rate.
The equipment used in this project has also been used to study drought stress tolerance in garbanzo bean, a major California crop. A series of flights near the end of the field season showed strong correlations between several major vegetation indices and canopy temperature.
Thermal orthomosaic of field in West Side, CA.
Strong correlations exist between canopy temperature and vegetation indices that indicate canopy health. In this study, all three camera types were able to distinguish between well-watered and drought-stressed plants. The correlation between NDVI determined by separate cameras on separate aircraft at different altitudes, indicates the high degree of reproducibility of UAS-based results. These results are promising, as UAVs carrying high-quality RGB cameras are well within the price range of many farmers (~$1000). These data indicate that even these affordable cameras can provide very useful information about canopy health, which could help inform farmers of management decisions.
Our drone-based results indicate that university-developed varieties, including our breeding lines, are more capable of taking advantage of soil nutrients to turn biomass into high yields. For example, the breeding nursery at the UC Davis student farm suffered from non-uniform water availability in 2018, due to poor field leveling and a soil compaction gradient. In this strong gradient, plants on the poor-performing side of the field were strongly stunted in terms of canopy cover. In better performing parts of the field, the university-developed varieties (above, in blue) used the nutrients at their disposal to improve yields, while yields of heirloom types (above, in orange) were relatively flat, as these were inefficient in turning the additional biomass into yield that can be harvested. Among university-developed varieties, UAVs were able to predict yield based on early-season canopy cover alone (R^2=0.62), despite the considerable genetic variation between the varieties. Among heirloom varieties, the amount of canopy biomass is not predictive of final yield (R^2 = 0.01).
The breeding project has advanced 8 lines of high-value, high-yielding dry bean. All of these are resistant to bean common mosaic virus (BCMV), based on testing with genetic markers and greenhouse inoculations. In 2017, the selected breeding lines averaged 364% higher yields than the heirloom varieties they closely resembled. In the replicated multi-location 2018 trials, all ten breeding lines had higher yields than the heirloom parents they resembled. The smallest gains were in Tiger's Eye types. The BCMV-resistant breeding lines of this type displayed yield gains of 39% relative to the heirlooms, despite 15/16 of the breeding line's ancestry coming from the heirloom. Larger gains were found in the other seed classes, including 424% higher yields in a breeding line with an Anasazi-type seed pattern relative to the heirloom with a similar seed coat type.
The skills developed during this project have been applied to several other crops. For example, our drone imagery data analysis pipeline has been applied to accurately predict yield in alfalfa (R^2=0.904, above left) and spinach (R^2 =0.433). In the example of alfalfa, the few hours required to fly, process imagery, and extract data from the field is minimal compared to the amount of labor required to cut, dry, bag, and weigh hundreds of plots individually. Students in PLS 198 have used these methods to characterize phenology in grapes (above, right), to identify a correlation between leaf greenness and increased lodging in wheat and triticale, and identify patterns of plant health among perennial and annual wheats, among other projects. The methods, genetic tools, and new varieties developed in this project will be an asset to sustainable growers for many years to come.
Kolkman, J. M., & Kelly, J. D. (2003). QTL conferring resistance and avoidance to white mold in common bean. Crop Science43(2), 539-548.
Kwak, M., Velasco, D., & Gepts, P. (2008). Mapping homologous sequences for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris). Journal of Heredity99(3), 283-291.
Moghaddam, S. M., Mamidi, S., Osorno, J. M., Lee, R., Brick, M., Kelly, J., ... & Grimwood, J. (2016). Genome-wide association study identifies candidate loci underlying agronomic traits in a Middle American diversity panel of common bean. The plant genome9(3).
Tar'an, B., Michaels, T. E., & Pauls, K. P. (2002). Genetic mapping of agronomic traits in common bean. Crop Science42(2), 544-556.
Participation Summary
10 Producers participating in research

Research Outcomes

3 Grants received that built upon this project
10 New working collaborations

Education and Outreach

3 Consultations
3 Curricula, factsheets or educational tools
3 On-farm demonstrations
2 Published press articles, newsletters
5 Webinars / talks / presentations
2 Workshop field days

Participation Summary:

40 Farmers participated
10 Ag professionals participated
Education and outreach methods and analyses:

Knowledge gained through this project has been disseminated in several ways. The Gepts lab field day, which attracts dry bean growers from across California, included an in-field discussion of the project and a UAV demonstration flight. Another field day for organic growers and undergraduates lent exposure to the organic breeding fields. This project was also discussed as a poster presentation and UAV demonstration flight at the National Association of Plant Breeders annual meeting in August 2017, and a poster was presented on it at the Student Organic Seed Symposium, which attracts graduate students and industry representatives. Another poster was presented at the International Plant and Animal Genomics meeting and the UC Davis Plant Science symposium. 

Knowledge gained using this equipment prepared the graduate student to develop a course on the use of UAVs in Agriculture. The course was the first of its kind at UC Davis, and was offered in Spring 2018. Students ranged from first year undergraduates to graduate students and a post-doctoral researcher. The class combined theoretical knowledge about aircraft, sensors, and legal regulations with practical knowledge on planning autopilot missions, generating orthomosaics and 3D digital surface models, and data extraction. Students ultimately completed a final project in which they posed original research questions and answered them using UAV imagery they collected themselves. Subsequently, a graduate student from Burkina Faso and industry representatives from a major organic company have been trained on the use of UAVs. Knowledge gained from this project has been passed on to a new generation of agricultural scientists, greatly increasing its total impact.

Outreach has also targeted the general public. The project was featured in a UC Davis press release that was circulated widely on social media (see An article for Organic Farmer magazine is planned for publication in autumn 2018. The project will also be featured on a PBS special. Filming for this program began in July 2018 with on-farm field visits, interviews, and demonstration flights. Filming will continue for the chef-led flavor evaluations at Rio del Rey Farm in autumn 2018. These opportunities will help generate public awareness for the crop varieties, and will serve as a form of marketing for them as emerging products. Ultimately, this will increase demand and improve sustainable farm profitability.

5 Farmers intend/plan to change their practice(s)
5 Farmers changed or adopted a practice

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Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.