A research hub at South Dakota State University
Closing the gap between sensing and decision.
ARISE-Institute combines AI, sensing, and genetics to better understand G2P relationship and help breeders and growers to make better crop decisions — anchored in the Northern Great Plains.
Mission & Vision
Data-driven crop improvement and ag sustainability.
ARISE-Institute is a South Dakota State University research hub that turns field, sensor, and genetic data into understanding the G2P relationship, leading to better crop decisions — from the breeding program to the commercial farm.
Holds up under stress
Built for real growing conditions: Biotic and Abiotic stress and broader adaptability.
Grounded in the full data
Decisions built on comprehensive genomic and phenomics data — not a shortcut summary of them.
Built for the long run
Sustainable Ag (plant, soil, and environment) and sustainable research cluster.
Vision
An AI-powered crop genomics and phenomics research center that helps connect G2P and improve selection and management decisions — open to researchers, seed companies, and producers worldwide.
Two equations behind the mission
Crop improvement runs on genetics; better management runs on limits.
Genetics · Aim 2
R response to selection · h² heritability · S selection differential
The breeder's equation: each generation's genetic gain depends on how heritable a trait is and how hard breeders select for it. ARISE's phenomics work raises h² by measuring traits more precisely — directly increasing genetic gain, generation over generation.
Management · Aim 3
Growth = f( min of N, P, K, water, light… )
Liebig's Law of the Minimum: a crop's growth is capped by whichever resource is scarcest, not the sum of all of them. ARISE's precision-management tools are built to find that one limiting factor, field by field, and fix it.
Three research aims
From measuring plants to breeding and managing them better.
Aim 1 — Scalable phenomics
AI that measures plant traits automatically — from whole-field patterns down to individual leaves and grains — far faster than scoring them by hand.
Aim 2 — AI-enabled breeding & functional genomics
Combining smartphone, drone, and microscope images with genetic data to help breeders pick better parent lines, faster.
Aim 3 — Precision crop management & digital twins
Satellite-to-soil sensing that helps producers fine-tune water, nutrients, and soil health across the season.
Seven stages, field to impact
The research pipeline behind every ARISE project, from an open question to a usable product.
Biological questions & challenges
Addresses the core measurement bottleneck in crop improvement.
- How do crops adapt to heat and drought?
- Which root, leaf, and canopy traits best predict resilience and grain quality?
- Can better models predict performance in genotypes and environments never tested?
Engineering tools & platforms
Modular, low-cost tools built to extend across crops.
- Field instrumentation: cameras, thermal and hyperspectral sensors, drones
- Controlled-environment and root phenotyping (rhizotrons, imaging)
- Leaf and grain analysis: microscopy, spectroscopy, composition
Multiscale phenotyping
Root to canopy to grain, across time and environments.
- Canopy — drone and field imagery
- Leaf — physiology
- Root — architecture
- Grain — quality
AI pipelines & data integration
Scalable, reproducible, and transparent AI methods.
- Multimodal data processing and trait extraction
- Machine-learning models for trait estimation and cross-environment transfer
- Integration with genomic and environmental data
G2P analysis & discovery
From data to biological insight and better prediction.
- Genotype × environment × phenotype analysis
- Identifying the traits and mechanisms that matter
- Better prediction for genotypes, sites, and seasons never tested
Secure data management & sharing
Durable, shared infrastructure for the research community.
- A governed data-and-model commons across partner states
- Secure, FAIR data with access control and provenance
- Shared tools, workflows, and models for reuse
Products & impact
Resilient cereals. Stronger communities. A more secure food future.
- Improved wheat germplasm for heat and drought resilience
- Open-source instruments and AI tools, trained workforce, cross-state collaboration
Every output feeds a commercialization cycle run with SDSU's Technology Transfer Office — one that loops back into new Discovery work rather than ending at publication.
Why now
The tools haven't kept pace with the problem.
Agriculture needs to produce more with fewer resources, but the tools that could help — computer vision, sensors, genetics — are scattered across different fields and disciplines. ARISE exists to bring them together.
Most traits are controlled by many genes working together, which makes it hard to connect genetics to real field performance.
Measuring traits by hand is slow, subjective, and doesn't scale to the size of modern breeding programs.
AI models trained on one field or season often don't hold up in the next.
Public breeding programs have access to far fewer AI tools than industrial-scale operations that can build their own.
Work with us
Bring your field, your data, or your question.
ARISE partners with breeding programs, students, and producers across the Northern Great Plains and beyond.
Students & researchers
Join the work
Graduate students and postdocs across quantitative genetics, remote sensing, and machine learning — tell us what problem you want to work on.
Breeding programs
Pilot a tool
Public breeding and extension programs looking to pilot trial-design, spatial-analysis, or decision-support methods on a real nursery.
Funders & partners
Back public-good AI
Foundations, agencies, and companies aligned with open methods for food security rather than closed, proprietary ones.
Team
Core leadership, an SDSU bench, and a national network.
ARISE is led by three SDSU faculty spanning plant breeding, geospatial science, and agricultural engineering — backed by collaborators across campus and a growing list of partner institutions.
Crop Biology & Genetics
Dr. Sunish K. Sehgal
Principal Investigator — Professor & Winter Wheat Breeder, Dept. of Agronomy, Horticulture & Plant Science, CAFES, SDSU.
AI & Modeling
Dr. Maitiniyazi Maimaitijiang
Co-Principal Investigator — Assistant Professor, Dept. of Geography & Geospatial Sciences, College of Natural Sciences, SDSU.
Engineering
Dr. Mazhar Sher
Co-Principal Investigator — Assistant Professor, Agricultural & Biosystems Engineering, CAFES, SDSU.
Melanie Caffe
Oat breeding · Agronomy Horticulture and Plant ScienceGengjun Chen
Food quality · Dairy & Food ScienceSachin Dhanda
Weed science · Agronomy Horticulture and Plant ScienceDavid Karki
Extension · Agronomy Horticulture and Plant ScienceChulwoo Pack
Computer vision · EE&CSGovinda Shrestha
Entomology · Agronomy Horticulture and Plant SciencePappu Yadav
Precision ag sensing · Agricultural & Biosystems EngineeringIdentified during the institute's planning phase — formal roles and commitment will be finalized as we progress.
Eduard Akhunov
KSU · rootsKatherine Frels
UNL · stem sawfly, FHBUpinder Gill
NDSU · rustsMary Guttieri
USDA-ARS · stem sawflyMory Rugg
Arthur Companies · small grainsJagdeep Sidhu
Mizzou · rootsWant to join the bench or the network?
Get in touch →Grants & Funding
A funded portfolio, with a center-scale proposal ahead.
ARISE is already backed by six active grants, with an SDSU Research Cluster planning award building toward a bigger federal proposal.
Support: South Dakota Board of Regents (SDBOR)
Center-scale planning grant
SDSU Research Cluster supported with seed money of $30,000 to assemble a center-scale proposal.
Funded portfolio
Six active grants, $1,064,551 total, spanning USDA-NIFA, USDA-ARS, USDA-USWBSI, KSU-WGRC/IUCRC, the BGRI Global Wheat Health Alliance, and General Mills.
Dual-Purpose Beardless Winter Wheat: Enhancing Profitability, Sustainability, and Resilience in the Northern Great Plains
USDA-NIFA2026–2030 · $497,677 · Award No. 2026-67014-47153
AI-assisted phenotyping platform for wheat stem sawfly (WSS) resistance traits
USDA-ARS2026–2028 · $98,205
Harnessing Wild Wheat Root and Coleoptile Traits for Drought-Resilient Wheat
KSU-WGRC-IUCRC2026–2028 · $55,001
AI-Powered Smart Tool for Rapid Assessment of Wheat FHB and FDK for Breeders and Producers
USDA-USWBSI2026–2027 · $199,708 · Award No. 0500-00053-005-218-G
OatAI: AI-driven high-throughput phenotyping of oat traits for breeding applications
General Mills2026–2028 · $193,560
Field-calibrated smartphone phenotyping of Fusarium head blight: a transferable workflow for CIMMYT's international screening
BGRI Global Wheat Health Alliance2026–2028 · $20,400 · Seed Grant in Translational Wheat Health ↗
Innovative Infrastructure for Biological Research (Innovation)
NSF 23-578Data Science for Food and Agricultural Systems (DSFAS)
USDA-NIFA AFRI · A1541Phase 1 — Alignment & data kickoff
Phase 2 — Pilot curation & consultation
Phase 3 — Proposal, review & submission
Research organizations
USDA-ARS, NDSU, UMN, CSU, UMD, KSU, Mizzou, UNL, TAMU, and CIMMYT — benchmarking AI models against global datasets.
Industry & technology partners
Letters of support secured from Arthur Companies (ND) and Albert Lea Seeds (MN), aligning data pipelines with commercial deployment.
Producer & commodity stakeholders
Feedback and support from the South Dakota Wheat Commission and the Kansas Wheat Commission, grounding priorities in NGP realities.
Breeding & genetics collaborators
A network of public and private breeders and geneticists validating the framework across diverse germplasm and conditions.
Beyond the planning phase, ARISE is building toward multiple funding sources (NSF, USDA-NIFA, USDA-ARS, USDA-USWBSI), a commercialization path through SDSU's Technology Transfer Office, and a "co-design" approach that keeps producer and industry priorities central.
Have a program this fits?
Get in touch →Publications
Already in print, with more underway.
ARISE's work is already producing peer-reviewed results, built on WheatAI — the lab's image-to-trait platform.
Figure 1 · Smart Agricultural Technology · CC BY-NC-ND
Kaushal, S., Maimaitijiang, M., Subedi, S., Thapa, S., Koupal, D.J., Singh, M., Kaur, K., Kumar, P., Sitaula, P.R., Billah, M.M., Sehgal, S.K. — Smart Agricultural Technology, art. 1025214.
Counting wheat tillers by hand across breeding plots is slow, yet tiller counts strongly shape eventual grain yield. The team flew multispectral drones over SDSU wheat trials and combined dozens of color and texture measurements from the imagery. An attention-based neural network predicted tiller counts with about 82% accuracy (R²=0.82, ~15% average error), beating simpler models. That turns a days-long field survey into a few-minute drone flight, helping breeders screen more lines faster.
Figure 5 · Frontiers in Plant Science · CC BY
Billah, M.M., Maimaitijiang, M., Kaushal, S., Millett, B., Khan, S.N., Halder, J., Kleinjan, J., Sehgal, S.K. — Frontiers in Plant Science, 17, art. 1812052.
Breeders need early estimates of wheat's grain yield, protein content, and test weight well before harvest. Researchers flew multispectral drones repeatedly over seven South Dakota fields in 2022 and compared several machine-learning and deep-learning models. A 3D convolutional neural network using multiple flight dates performed best, explaining up to 69% of the variation in test weight and roughly 65% in yield. Imagery from the booting stage was especially informative, showing drones can forecast both yield and quality traits in-season.
Figure 5 · Scientific Reports · CC BY-NC-ND
Ghimire, H., Maimaitijiang, M., Thapa, S., Kaushal, S., Koupal, D.J., Billah, M.M., Poudel, K., Sehgal, S., Singh, M., Subedi, S., Sehgal, S.K. — Scientific Reports, 16, art. 27355.
Counting wheat spikes and the spikelets inside them by hand is tedious, even though these counts predict a field's eventual grain yield. The team built a huge labeled image library — over 48,000 spikes and 60,000 spikelets — and trained two recent YOLO detection models to find them using tightly rotated boxes. The best spike detector matched manual counts almost perfectly (95.8% precision, 0.99 correlation), and the spikelet detector reached 99% accuracy. This gives breeders a fast, camera-based way to track yield-building traits at a scale manual counting can't match.
Figure 1 · The Plant Phenome Journal · CC BY
Kaushal, S., Billah, M.M., Halder, J., Maimaitijiang, M., Sehgal, S.K. — The Plant Phenome Journal, 9(1), e70085.
A yield-prediction model trained in one year or field often fails badly when applied somewhere new, limiting its real-world use. Researchers paired drone-based spectral and texture data with deep transfer learning, which lets a model retrain itself using just a slice of new data. Fine-tuning with only 20% of a new year's data lifted accuracy from a failing score to R²=0.83, and 40% of new-field data lifted cross-location accuracy to 0.29–0.69. This makes drone-based yield prediction far more reliable across years, fields, and growth stages.
Flagship platform
WheatAI — turning field images into genetic insight
Turns raw field, greenhouse, and microscope images into standardized trait measurements using automated computer vision — built with NSF PGRP support.
Using a wheat exome panel of 365 accessions (3 million SNPs) to link genotype to specific cellular and architectural features. Stay tuned.
Annotated multiscale phenotyping database
In progressMulti-seasonal UAS canopy imagery, smartphone close-range shots, and high-resolution microscopy, with ground-truth labels for leaf architecture, spike morphology, stomata morphometrics, and disease symptoms.
Want to collaborate on one of these?
Get in touch →Tools
One flagship platform, several tools in motion.
ARISE's technology stack runs from image capture to breeding decision — anchored by WheatAI and extending across all three research aims.
WheatAI
LiveTurns raw field, greenhouse, and microscope images into standardized trait measurements — the foundation the rest of ARISE's tools build on.
wheatai.net ↗Wheat Tiller Density Mapper (Wheat-TDM)
Live prototypeSatellite-data and AI-based subfield, fine-scale mapping of wheat tiller density.
Launch prototype ↗AI-Assisted Crop Damage Mapper (AI-CDM)
Live prototypeSatellite- and AI-based fine-scale, subfield mapping of crop damage from extreme weather events, particularly hail and high winds.
Launch prototype ↗Multiscale Phenotyping Database
In developmentA structured, annotated repository spanning population, plant, organ, and tissue-level traits across field, greenhouse, and microscopy imagery.
Aim 1 · Scalable phenomicsAI-Enabled Breeding Platform
PlannedCombines genetic mapping with image-based traits to help breeders pick better lines, faster.
Aim 2 · Breeding & functional genomicsPrecision Management & Digital Twins
PlannedCombines satellite and soil data so producers can fine-tune water and nutrients across the field, in real time.
Aim 3 · Precision managementSouth Dakota Winter Wheat Dashboard
UpcomingHosts the SD State Variety Trial data, winter wheat variety selection, and head-to-head variety comparisons.
Variety selectionWheatAI is designed for seamless integration with the tools breeding programs already use.
Want early access, or want to pilot one of these on your own trials?
Get in touch →Training
Growing the next generation of AI-assisted plant scientists.
The ARISE team provides interdisciplinary training to graduate and undergraduate students, preparing early-career researchers for AI-assisted genomics and phenomics.
Subash Thapa
Agronomy Horticulture and Plant Science · PhDMandeep Singh
Agronomy Horticulture and Plant Science · PhDHorender Sharma
Agronomy Horticulture and Plant Science · PhDGable Kaura
Agronomy Horticulture and Plant Science · PhDMohammad Maruf Billah
Geospatial Science · PhDKushal Poudel
Geospatial Science · MSSaneth Kalhara
Agricultural & Biosystems Engineering · MSHillson Ghimire
Geospatial Science · MS · now at Rice UniversitySwas Kaushal
Agronomy Horticulture and Plant Science · PhD · now at SyngentaML for seedling traits
Dr. Mohammad Ashik Alahe
Trained on machine-learning methods for detecting and classifying early-stage seedling traits.
Imaging for machine learning
Dr. Sikander Ameer
Trained on image-based data pipelines that feed ARISE's machine-learning models.
Interested in training opportunities with ARISE?
Get in touch →Outreach
Taking the lab to the field.
ARISE's research only matters if it reaches the breeders, producers, and students it's built for — outreach is how we keep that loop closed.
Follow along
Field updates, trial photos, and announcements, posted as the season happens.
Field Days
OngoingOn-farm and research-station plot tours of SDSU winter wheat trials — most recently the 2026 Dakota Lakes Research Farm Field Day, June 26, 2026.
Stakeholder Meetings
OngoingRegular check-ins with producers, seed companies, and commodity boards — most recently the 37th Annual Draper Winter Wheat Meeting, Aug 2026.
Workshops
UpcomingHands-on sessions on AI-assisted phenotyping, trial design, and tool adoption for breeders, students, and extension staff.
Want ARISE at your field day or meeting?
Get in touch →Gallery
The trials, from above.
Drone footage from SDSU Winter wheat trial — the same fields behind the data on every other page.
Early Observation Trial (EOT)
The first trial where the SDSU winter wheat breeding program gets an early read on experimental lines' yield potential and resistance to disease and insect pests.
Aerial View of Brookings Location in 2026
Drone footage over SDSU Winter wheat trial plots, showing the field-level scale this research runs at.
Want to see the trials in person?
See upcoming field days →