Updated February 2, 2025:
Short summary
Two new varieties were disclosed to ISURF: IAS27C1 and IAS27HPHO1. Foundation seed increase was completed.
Seven journal research or review papers, one book chapter, one magazine article, and ten conference or pre-prints were published. Project objectives were successfully completed, including planting, data collection, plant selections, harvest, variety selection and data analysis.
Research advances were made in biotic and abiotic stress tolerance traits, with applications in variety development.
Full report:
NEW VARIETIES
IAS27C1 has high yield in multiple states, and resistance to sudden death syndrome, white mold and soybean cyst nematode, and good tolerance to iron deficiency chlorosis. It has improved tolerance to flooding. It is 2.7 RM soybean with black hilum. In MI-Central it ranked 3rd out of 73 entries in the test. In WI-South, it ranked 9th out of 32 entries in the test. In IA-North and IA-Central it ranked 17th out of 36 and 39 entries, respectively, in the tests. In Illinois (regions 1, MG2.7-3.4), it ranked 6th out of 29 entries. In Illinois (region 2, MG2.4-3.2), it ranked 21 out of 26 entries.
IAS27HPHO1 is a high protein line (42-43% dw) with oleic acid >75%. It has yellow hilum and 2.7 RM. It’s seed yield was comparable to yellow hilum check, IA2102.
RESEARCH REALTED PAPERS
Several papers were published that relate to the Iowa Soybean Association supported projects.
Journal Articles
1. Chiozza, M. V., Parmley, K. A., Schapaugh, W. T., Asebedo, A. R., Singh, A. K., & Miguez, F. E. (2024). Changes in the leaf area-seed yield relationship in soybean driven by genetic, management, and environments: Implications for high-throughput phenotyping. in silico Plants, 6(2), diae012. https://doi.org/10.1093/insilicoplants/diae012
2. Chiranjeevi, S., Saadati, M., Deng, Z. K., Koushik, J., Jubery, T. Z., Mueller, D. S., O’Neal, M. E., Merchant, N., Singh, A., Singh, A. K., Sarkar, S., Singh, A., & Ganapathysubramanian, B. (2024). InsectNet: Real-time identification of insects using an end-to-end machine learning pipeline. PNAS Nexus. https://doi.org/10.1093/pnasnexus/pgae575
3. Feuer, B., Joshi, A., Cho, M., Chiranjeevi, S., Deng, Z. K., Balu, A., Singh, A. K., Sarkar, S., Merchant, N., Singh, A., Ganapathysubramanian, B., & Hegde, C. (2024). Zero-shot insect detection via weak language supervision. Plant Phenome Journal, 7(1), e20107. https://doi.org/10.1002/ppj2.20107
4. Fotouhi Ardakani, F., Menke, K., Prestholt, A., Gupta, A., Carroll, M. E., Yang, H. J., Skidmore, E. J., O’Neal, M. E., Merchant, N., Das, S. K., Kyveryga, P., Ganapathysubramanian, B., Singh, A. K., Singh, A., & Sarkar, S. (2024). Persistent monitoring of insect pests on sticky traps through hierarchical transfer learning and slicing-aided hyper inference. Frontiers in Plant Science, 15, 1484587. https://doi.org/10.3389/fpls.2024.1484587
5. Saadati, M., Balu, A., Chiranjeevi, S., Jubery, T. Z., Singh, A. K., Sarkar, S., Singh, A., & Ganapathysubramanian, B. (2024). Out-of-distribution detection algorithms for robust insect classification. Plant Phenomics, 6, 0170. https://doi.org/10.34133/plantphenomics.0170
6. Singh, A. K., Balabaygloo, B. J., Bekee, B., Blair, S. W., Fey, S., Fotouhi Ardakani, F., Gupta, A., Jha, A., Martinez-Palomares, J. M., Menke, K., Prestholt, A., Tanwar, V. K., Tao, X., Vangala, A., Carroll, M. E., Das, S. K., Depaula, G., Kyveryga, P., Sarkar, S., … Valdivia, C. (2024). Smart connected farms and networked farmers to improve crop production, sustainability, and profitability. Frontiers in Agronomy, 6, 1410829. https://doi.org/10.3389/fagro.2024.1410829
7. Young, T. J., Chiranjeevi, S., Elango, D., Sarkar, S., Singh, A. K., Singh, A., Ganapathysubramanian, B., & Jubery, T. Z. (2024). Soybean canopy stress classification using 3D point cloud data. Agronomy, 14(6), 1181. https://doi.org/10.3390/agronomy14061181
Book Chapters
1. Ayanlade, T., Jones, S. E., Van der Laan, L., Chattopadhyay, S., Elango, D., Raigne, J., Saxena, A., Singh, A., Ganapathysubramanian, B., Singh, A. K., & Sarkar, S. (2024). Multi-modal AI for ultra-precision agriculture. In Harnessing Data Science for Sustainable Agriculture and Natural Resource Management, Studies in Big Data (Vol. 161, pp. 299–334). https://doi.org/10.1007/978-981-97-7762-4_13
Pre-Prints & Conference Papers
1. Arshad, M. A., Jubery, T. Z., Roy, T., Nassiri, R., Singh, A. K., Singh, A., Hegde, C., Ganapathysubramanian, B., Balu, A., Krishnamurthy, A., & Sarkar, S. (2024). AgEval: A benchmark for zero-shot and few-shot plant stress phenotyping with multimodal LLMs. arXiv. https://arxiv.org/abs/2407.19617
2. Feng, J., Blair, S. W., Ayanlade, T., Balu, A., Ganapathysubramanian, B., Singh, A., Sarkar, S., & Singh, A. K. (2024). Robust soybean seed yield estimation using high-throughput ground robot videos. arXiv. https://arxiv.org/abs/2412.02642
3. Jones, S. E., Ayanlade, T., Fallen, B., Jubery, T. Z., Singh, A., Ganapathysubramanian, B., Sarkar, S., & Singh, A. K. (2024). Multi-sensor and multi-temporal high-throughput phenotyping for monitoring and early detection of water-limiting stress in soybean. arXiv. https://arxiv.org/abs/2402.18751
4. Khosravi, M., Carroll, M. E., Tan, K. L., Van der Laan, L., Raigne, J., Mueller, D. S., Singh, A., Balu, A., Ganapathysubramanian, B., Singh, A. K., & Sarkar, S. (2024). AgGym: An agricultural biotic stress simulation environment for ultra-precision management planning. arXiv. https://arxiv.org/abs/2409.00735
5. Kim, B., Blair, S. W., Jubery, T. Z., Sarkar, S., Singh, A., Singh, A. K., & Ganapathysubramanian, B. (2024). Soybean maturity prediction using 2D contour plots from drone-based time series imagery. arXiv. https://arxiv.org/abs/2412.09696
6. Saleem, N., Balu, A., Jubery, T. Z., Singh, A., Singh, A. K., Sarkar, S., & Ganapathysubramanian, B. (2024). Class-specific data augmentation for plant stress classification. arXiv. https://arxiv.org/abs/2406.13081
7. Van der Laan, L., Elango, D., Ferela, A., O'Rourke, J. A., & Singh, A. K. (2024). High temperature and microbiome conditions affect gene expression in soybean. bioRxiv. https://doi.org/10.1101/2024.11.04.620947
8. Van der Laan, L., Parmley, K. A., Saadati, M., Torres Pacin, H., Panthulugiri, S., Sarkar, S., Ganapathysubramanian, B., Lorenz, A. J., & Singh, A. K. (2024). Genomic and phenomic prediction for soybean seed yield, protein, and oil. bioRxiv. https://doi.org/10.1101/2024.11.01.621550
9. Van der Laan, L., Peixoto, L. D. A., & Singh, A. K. (2024). Genetic dissection of heat stress tolerance in soybean through genome-wide association studies and the use of genomic prediction to enhance breeding applications. bioRxiv. https://doi.org/10.1101/2024.04.27.591454
10. Yang, C. H., Feuer, B., Jubery, T. Z., Deng, Z. K., Nakkab, A., Hasan, M. Z., Chiranjeevi, S., Marshall, K. O., Baishnab, N., Singh, A. K., Singh, A., Sarkar, S., Merchant, N., Hegde, C., & Ganapathysubramanian, B. (2024). Arboretum: A large multimodal dataset enabling AI for biodiversity. arXiv. https://arxiv.org/abs/2406.17720
Magazine Article
1. Ganapathysubramanian, B., Bell, J. M. P., Kantor, G. A., Merchant, N., Sarkar, S., Schnable, P. S., Segovia, M. S., Singh, A., & Singh, A. K. (2024). AIIRA: AI Institute for Resilient Agriculture. AI Magazine, 45(1), 94–98. https://doi.org/10.1002/aaai.12151
RESEARCH PROJECT REPORT
Soybean [Glycine max L. (Merr.)] is grown globally and is an important source of food, fuel, and commercial products. Efforts in soybean improvement have long focused on developing highly productive cultivars with high yield potentials. Less focus has been placed on developing soybean cultivars with improved seed composition, or improved stress tolerance. As omics methods have evolved, many new approaches are being developed which allow breeders to apply new tools as part of the breeding process and to better understand the genetic architecture for established and novel traits of interest.
Research on Seed oil and Protein (Liza Van der Laan; Ph.D. project; partially supported by Iowa Soybean Association and Plant Sciences Institute): Soybean seed protein and oil are important traits due to the use of soybean as a primary source of food and fuel around the world. Because of the importance of seed yield and composition traits in soybean, in-season prediction of experimental accessions has potential uses in breeding programs by allowing for earlier selections and more rapid cycling of breeding material. We explored the use of genomic and phenomic prediction models for soybean seed yield, protein, and oil, and compared the predictive abilities between the two models on 292 soybean accessions. We show that phenomic prediction can outperform genomic prediction for seed yield, but not for the seed composition traits. These different models give breeders flexibility for what types of data should be collected and used in prediction models. It gives options for soybean breeders to select which tool is most feasible for their unique budgets and constraints, allowing for maximization of their prediction resources.
Research on Heat stress (Liza Van der Laan; Ph.D. project; partially supported by Iowa Soybean Association and Iowa Soybean Research Center, and Plant Sciences Institute): Heat stress is increasingly becoming a limiting stress factor in plant species as global temperatures continue to rise. Soybean response to heat stress has been minimally studied, and an understanding of how soybean responds to heat stress is necessary for breeding heat stress tolerance. The genetic control of heat stress tolerance in soybean is particularly understudied, and an understanding of these genetic mechanisms underpinning heat stress responses can aid in accelerating the development of accessions with heat stress tolerance. By taking advantage of a soybean diversity panel with 450 accessions and GWAS methodologies, we characterized how different soybean traits were affected by heat stress, as well as the genetic control of these responses. Different markers were detected between optimal and heat stress growing conditions, which indicates a genetic divergence in soybean response to temperature. One marker was significant for an index of soybean response to heat, with putative candidate genes include laccase proteins and a NAC transcription factor. Genomic prediction was found to perform moderately for prediction of soybean biomass traits in heat stress, and this should be further expanded for testing yield predictions in stress conditions. Additionally, heat tolerant accessions were identified to be used as parents in the breeding program, allowing for development of more heat tolerant cultivars to be available to farmers.
Along with studying the genomics of soybean heat stress, we also used transcriptomics to further investigate the genetic response of soybean to heat stress. This was additionally paired with studying the effect that the soil microbiome has on the response to heat stress. Recent studies indicate that the soil microbiome may play a role in how plants respond to stress, and the microbiome may help mitigate the effects of the stress. Using transcriptomic tools to study the effect of heat stress and a soil microbiome, we provided insights into how genes are regulated by these different factors. Different genes were expressed under heat stress due to changes in the soil microbiome, indicating that the microbiome does play a role in how soybean responds to stress. Of the differentially expressed genes, photosynthetic and heat shock protein (HSP) genes were especially affected by heat stress. We identified a gene encoding for a heat shock factor (HSF) that seems to play a role in regulating the response to heat stress, regardless of soil microbiome and indicate this as a gene for further study. This gene should be further investigated and validated and could serve as a promising marker for developing heat tolerant soybeans via traditional tools or genome editing.
Research on soybean drought tolerance (Sarah Jones; Ph.D. project; partially supported by Iowa Soybean Association and United Soybean Board, and Plant Sciences Institute):
Drought stress can be a significant yield-limiting factor in soybean production, necessitating improved drought-tolerant genetics in soybean to protect yield and promote resiliency under stress and underscoring the need for advancements in stress monitoring for crop breeding and production. A diverse panel of 450 maturity group 0 - III soybean PI accessions and checks were screened in a non-irrigated drought nursery for three years in 2020 - 2022 in Muscatine, Iowa. Select lines were also screened in a near-field abiotic stress tolerance system for more controlled drought testing in 2023 in Ames, Iowa. And two recombinant inbred lines populations were developed for joint flood and drought tolerance and were also screened in multi-state trials in Kansas and North Carolina. Visual and sensor-based measurements were collected via RGB, hyperspectral, and multispectral sensors via ground and UAV based platforms. This project combines multi-modal information to identify the most effective and efficient automated methods to study drought response and developed a machine learning based pipeline for rapid classification of soybean drought stress symptoms and pre-visual early detection of drought stress. During germplasm screening, a wide range of phenotypic diversity was observed and slow canopy wilting accessions were identified for introduction into upper Midwest breeding programs. Using more controlled field-based screening, differential patterns of recovery were observed using hyperspectral reflectance. Finally, five genomic regions were identified by at least two methods of GWAS. Three quantitative trait loci (QTL) identified in QTL mapping of the two recombinant inbred line populations were also identified in GWAS. These regions identified across analyses, backgrounds, and environments could hold potential candidate genes for further exploration.
The use of drones and ground robots with sensors in a breeding program (Sam Blair; M.S. project; partially supported by Iowa Soybean Association and Plant Sciences Institute):
In a soybean breeding program, seed yield and days to maturity are very important traits. The need to test thousands and potentially tens of thousands of plots makes the data collection process for both of these tasks time-consuming and labor-intensive. The goal for each of these projects was to make an automated relative maturity rating and seed yield estimate system using an unpiloted aerial system (UAS) or ground robot system, respectively, along with machine learning (ML).
Soybean breeding programs, in the early stages of the breeding pipeline, assign relative maturity ratings to experimental varieties that indicate their suitable maturity zones. The goal for our relative maturity rating system was to introduce a tool that can be utilized by soybean breeders to save time normally dedicated to maturity note-taking. Current methods for taking maturity notes require human raters to go out to the fields and take notes on every plot in the fields multiple times a week for several weeks. For a field with 10,000 plots, this can take up to 228 labor hours. Our research introduces a method for using UAS to capture time series imagery, which is then used to train an ML model to make relative maturity classifications automatically, drastically reducing the time and labor needed for note-taking. Data collected for this project consists of 22,043 plots imaged from 2021-2023 from six fields. We utilize 2-dimensional contour plots extracted from the imagery to train our ML model. This model then classifies plots into either four, five, or seven distinct maturity groups with up to 85% accuracy. The use of this system has shown a 95% decrease in time needed for note taking allowing for the reallocation of labor resources to other tasks.
Yield data is likely the most critical data to collect for a soybean breeder to make decisions on which soybean lines to continue for further testing and cultivar release. In order to get an accurate assessment of a new soybean line’s yield, it must be tested in multiple locations. Current methods of collecting this data require plot harvesters to be deployed to these outside locations requiring specialized transportation equipment and licensing. In this project, we introduce a method for estimating yield data based on side-view ground robot videos of mature soybean plants. Operating small ground robots requires less training and is safer than traditional harvesting equipment. Break down costs are also far cheaper on small robots and they are much easier to transport. In this project, we deployed the Terrasentia robot equipped with fisheye lens cameras mounted to either side of the robot to capture comprehensive video of the entire plant from bottom to top. We then used imagery extracted from the video to train our P2PNet-Yield model. This model utilizes the Feature Extraction Module from P2PNet-Soy to detect individual soybean seeds and make yield estimates in tons/hectare. Our data consists of video taken at all times of day from a wide variety of genotypes representing different pubescence and seed coat colors. We report a genotype yield ranking accuracy of up to 83%. This project introduces a new tool for breeders to use to make yield data collection easier and more efficient.
We continued our partnership with the Iowa Soybean Association with funded projects, AIIRA, COALESCE, and SIRAC, that USDA and NSF supported. These unique linkages provide farmer-motivated solutions that enhance breeding and crop production using machine learning and robotics. These also leverage ISA support with other agency support enabling research.
Two new varieties were disclosed to ISURF: IAS27C1 and IAS27HPHO1. Foundation seed increase was completed.
Seven journal research or review papers, one book chapter, one magazine article, and ten conference or pre-prints were published. Project objectives were successfully completed, including planting, data collection, plant selections, harvest, variety selection and data analysis.
Research advances were made in biotic and abiotic stress tolerance traits, with applications in variety development.