Research Project: Expanding Resiliency and Utility of Alfalfa in Agroecosystems

Location: Plant Science Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Comparison of genetic linkage maps constructed using three reference genomes in autotetraploid alfalfa - (Peer Reviewed Journal)

Unlocking alfalfa’s potential as a viable source of protein: Improving protein extraction and characterizing the isolate protein - (Peer Reviewed Journal)
Mor, S., Heuschele, D.J., Saeidy, S., Ismail, B.P. 2026. Unlocking alfalfa’s potential as a viable source of protein: Improving protein extraction and characterizing the isolated protein. Food Research International. https://doi.org/10.1021/acsfoodscitech.6c00462.

Haplotype-resolved genome of autotetraploid alfalfa (Medicago sativa) Regen-SY27x uncovers large scale structural variation and resistance gene dynamics - (Pre-print Publication)
Kaur, H., Connor, C., Gomez, A., Mudge, J., Farmer, A., Shannon, L.M., Samac, D.A. 2026. Haplotype-resolved genome of autotetraploid alfalfa (Medicago sativa) Regen-SY27x uncovers large scale structural variation and resistance gene dynamics. bioRxiv. https://doi.org/10.64898/2026.05.01.722254.

Identification of race-specific QTL and candidate genes for Aphanomyces root rot resistance in alfalfa (Medicago sativa L.) - (Peer Reviewed Journal)
Lin, M., Tang, X., Zhao, D., Medina, C.A., Dornbusch, M.R., Beil, C.T., Sheehan, M.J., Samac, D.A. 2026. Identification of race-specific QTL and candidate genes for Aphanomyces root rot resistance in alfalfa (Medicago sativa L.). G3: Genes, Genomes, Genetics. Article: jkag131. https://doi.org/10.1093/g3journal/jkag131.

Development and deployment of a universal training population system (TPS) for accelerating alfalfa genomic selection - (Abstract Only)
Medina, C.A., Samac, D.A., Xu, Z. 2026. Development and deployment of a universal training population system (TPS) for accelerating alfalfa genomic selection. North American Alfalfa Improvement Conference. North American Alfalfa Improvement Conference. Stillwater, MN. July 14-16, 2026.

Establishment-year forage yield and nutritive value of alfalfa in northern U.S. enviro - (Abstract Only)
Grijalba Sierra, M., Berti, M.T., Morocho, M., Muleya, P., Lindell, H., Gartenberg, M., Gasch, C., Samac, D.A. 2026. Establishment-year forage yield and nutritive value of alfalfa in northern U.S. enviro. North American Alfalfa Improvement Conference. Stillwater, MN. July 14-16, 2026.

From the gene to the field: A retrospective summary of alfalfa research by the USDA-ARS-Plant Science Research Unit - (Abstract Only)
Samac, D.A. 2026. From the gene to the field: A retrospective summary of alfalfa research by the USDA-ARS-Plant Science Research Unit. North American Alfalfa Improvement Conference. North American Alfalfa Improvement Conference. Stillwater, MN July 14-16, 2026.

Refining the root-associated microbial consortia for enhanced biocontrol of the root-rot pathogen of corn - (Peer Reviewed Journal)
Kaki, P., Schlatter, D.C., Khokhani, D. 2026. Refining the root-associated microbial consortia for enhanced biocontrol of the root-rot pathogen of corn. Frontiers in Microbiology. 17. Article 1714069. https://doi.org/10.3389/fmicb.2026.1714069.

Overcoming acid soil sensitivity in alfalfa - (Trade Journal)
Samac, D.A., Missaoui, A. 2026. Overcoming acid soil sensitivity in alfalfa. Forage Focus. March 2026:16-17.

Temporal variability of soil health indicators under annual and perennial continuous living cover: Effects of annual weather and management - (Peer Reviewed Journal)
Kundert, J., Jungers, J., Gamble, J.D., Bergquist, G., Gutknecht, J. 2026. Temporal variability of soil health indicators under annual and perennial continuous living cover: Effects of annual weather and management. Soil Science Society of America Journal. 90(2). Article e70229. https://doi.org/10.1002/saj2.70229.

Canola alters rhizosphere and root microbiome of following wheat crops - (Peer Reviewed Journal)
Schlatter, D.C., Yin, C., Hansen, J.C., Schillinger, W.F., Paulitz, T.C. 2025. Canola alters rhizosphere and root microbiome of following wheat crops. Applied Soil Ecology. 218. Article 106694. https://doi.org/10.1016/j.apsoil.2025.106694.

Betalain synthesis in alfalfa impacts fiber digestion and enteric methane production - (Peer Reviewed Journal)
Heuschele, D.J., Nimpoeno, J., Curtin, S.J., Samac, D.A. 2026. Betalain synthesis in alfalfa impacts fiber digestion and enteric methane production. Crop Science. 66(1). Article e70226. https://doi.org/10.1002/csc2.70226.

First US alfalfa reference genome sequence completed - (Trade Journal)
Samac, D.A., Kaur, H. 2025. First US alfalfa reference genome sequence completed. Forage Focus. December 2025:8.

Evaluation of 30 novel plant secondary compounds for gas production, methane concentration, nutrient digestibility, and volatile fatty acid concentrations using in vitro batch culture fermentation - (Peer Reviewed Journal)
Stypinski, J.D., Heuschele, D.J., Salfer, I.J. 2026. Evaluation of 30 novel plant secondary compounds for gas production, methane concentration, nutrient digestibility, and volatile fatty acid concentrations using in vitro batch culture fermentation. The Journal of Agricultural Science. 164. Article e13. https://doi.org/10.1017/S0021859626100537.

No more laborious stem counting: AI-powered computer vision enables identification and quantification of solid and hollow alfalfa stems at the pixel level - (Peer Reviewed Journal)
Weihs, B.J., Tang, Z., Roy, S., Tian, Z., Heuschele, D.J., Zhang, Z., Williams, C., Zhang, Z., Heineck, G.C., Saha, S., Xu, Z. 2025. No more laborious stem counting: AI-powered computer vision enables identification and quantification of solid and hollow alfalfa stems at the pixel level. Smart Agricultural Technology. 12. Article 101278. https://doi.org/10.1016/j.atech.2025.101278.

A 3D printed grinder adaptor for streamlined sample processing - (Peer Reviewed Journal)
Heuschele, O.L., Jeo, R.T., Heuschele, D.J. 2025. A 3D printed grinder adaptor for streamlined sample processing. HardwareX. 24. Article e00699. https://doi.org/10.1016/j.ohx.2025.e00699.

Toward the development and validation of diagnostic assays for fungal pathogens of Northern wild rice (Zizania palustris L.) in North America - (Abstract Only)

Conquering the devastating diseases of alfalfa - (Trade Journal)
Samac, D.A. 2025. Conquering the devastating diseases of alfalfa. Forage Focus. May 2025:16-17.

Assessment of seed treatments for management of pathogens causing seed rot, seedling damping-off, and seedling root rot in alfalfa (Medicago sativa) - (Peer Reviewed Journal)
Larsen, L., Dornbusch, M.R., Hines-Snider, C., Samac, D.A. 2026. Assessment of seed treatments for management of pathogens causing seed rot, seedling damping-off, and seedling root rot in alfalfa (Medicago sativa). Plant Disease. 110(1):113-121. https://doi.org/10.1094/PDIS-05-24-1147-RE.

Perspective: Impacts of dairy forage management on soil carbon change and net zero accounting - (Peer Reviewed Journal)
Gamble, J.D., Alexander, J.R. 2025. Perspective: Impacts of dairy forage management on soil carbon change and net zero accounting. Journal of Dairy Science. 108(5):4479-4484. https://doi.org/10.3168/jds.2024-25796.

Foliar fungi-imposed costs to plant productivity moderate shifts in composition of the rhizosphere microbiome - (Peer Reviewed Journal)
Lane, B.R., Kuhs, M.A., Zaret, M.M., Song, Z., Borer, E.T., Seabloom, E.W., Schlatter, D.C., Kinkel, L.L. 2025. Foliar fungi-imposed costs to plant productivity moderate shifts in composition of the rhizosphere microbiome. Frontiers in Plant Science. 16. Article 1558191. https://doi.org/10.3389/fpls.2025.1558191.

SNPs vs. microhaplotypes: challenges and advantages in alfalfa breeding - (Abstract Only)
Medina, C.M., Heuschele, D.J., Zhao, D., Lin, M., Beil, C.T., Sheehan, M.J., Xu, Z. 2025. SNPs vs. microhaplotypes: challenges and advantages in alfalfa breeding. Plant and Animal Genome Conference. San Diego, California, January 10-15, 2025.

Confluence between association mapping and genomic selection to increase stem digestibility in alfalfa - (Abstract Only)
Medina, C.M., Heuschele, D.J., Zhao, D., Lin, M., Beil, C.T., Sheehan, M.J., Xu, Z. 2025. Confluence between association mapping and genomic selection to increase stem digestibility in alfalfa. Plant and Animal Genome Conference. San Diego, California, January 10-15, 2025.

Seasonal nonstructural carbohydrates in the crowns and rhizomes of in situ populations of Japanese knotweed (Fallopia japonica) and the hybrid Bohemian knotweed (F. x bohemica) - (Peer Reviewed Journal)
Becker, R.L., Mentz, R.S., Smith, A.G., Annor, G.G., Singh, N., Sarangi, D., Anderson, N.O., Heuschele, D.J., Katovich, J., Clark, M.D. 2025. Seasonal nonstructural carbohydrates in the crowns and rhizomes of in situ populations of Japanese knotweed (Fallopia japonica) and the hybrid Bohemian knotweed (F. x bohemica). Weed Science. 73. Article e73. https://doi.org/10.1017/wsc.2025.11.

Stabilization and extraction of alfalfa (Medicago sativa) protein following multiple post-harvest processing techniques coupled with protease inactivation - (Peer Reviewed Journal)
Smovzhenko, A., Heuschele, D.J., Ismail, P.B. 2025. Stabilization and extraction of alfalfa (Medicago sativa) protein following multiple postharvest processing techniques coupled with protease inactivation. Food Research International. 201. Article 115588. https://doi.org/10.1016/j.foodres.2024.115588.

First report of Bipolaris zeicola causing leaf spot on Northern Wild Rice (Zizania palustris L.) in Minnesota - (Research Notes)
Castell-Miller, C.V., Samac, D.A., Kimball, J.A. 2025. First report of Bipolaris zeicola causing leaf spot on Northern Wild Rice (Zizania palustris L.) in Minnesota. Plant Disease. 109(3):720. https://doi.org/10.1094/PDIS-10-24-2252-PDN.

Quantifying potassium requirement and removal across crop species - (Peer Reviewed Journal)
Carciochi, W.D., Dobermann, A., Menza, N., Brouder, S.M., Donough, C., Heuschele, D.J., Oberthur, T., Sandana, P., Shehu, B.M., Pereira, J.S., Soratto, R.P., Volenec, J.J., Wandri, R., Wang, Y., Win, S., He, P., Grassini, P. 2025. Quantifying potassium requirement and removal across crop species. Field Crops Research. 322. Article 109717. https://doi.org/10.1016/j.fcr.2024.109717.

Constructing the alfalfa pangenome: Insights into structural variation and genomic complexity in an autopolyploid crop - (Abstract Only)
Kaur, H., Shannon, L.M., Samac, D.A. 2025. Constructing the alfalfa pangenome: Insights into structural variation and genomic complexity in an autopolyploid crop. Plant and Animal Genome Conference Proceedings. Plant and Animal Genome Conference, January 10-15, 2025, San Diego, California.

A stepwise guide for pangenome development in crop plants: An alfalfa (Medicago sativa) case study - (Review Article)
Kaur, H., Shannon, L.M., Samac, D.A. 2024. A stepwise guide for pangenome development in crop plants: An alfalfa (Medicago sativa) case study. BMC Genomics. 25. Article 1022. https://doi.org/10.1186/s12864-024-10931-w.

Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes - (Peer Reviewed Journal)
Michalska-Smith, M., Schlatter, D.C., Pombubpa, N., Castle, S.C., Grandy, S., Borer, E.T., Seabloom, E.W., Kinkel, L.L. 2024. Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes. Frontiers in Microbiology. 15. Article 1452534. https://doi.org/10.3389/fmicb.2024.1452534.

Development of universal DaRTag markers for alfalfa (Medicago sativa) and use in mapping resistance to Aphanomyces root rot - (Abstract Only)

Phenotyping alfalfa (Medicago sativa L.) root structure architecture via integrating confident machine learning with ResNet-18 - (Peer Reviewed Journal)
Weihs, B.J., Tang, Z., Tian, Z., Heuschele, D.J., Siddique, A., Terrill, T., Zhang, Z., York, L., Zhang, Z., Xu, Z. 2024. Phenotyping alfalfa (Medicago sativa L.) root structure architecture via integrating confident machine learning with ResNet-18. Plant Phenomics. https://doi.org/10.34133/plantphenomics.0251.

Multi-trait modeling and machine learning discover new markers associated with stem traits in alfalfa - (Peer Reviewed Journal)
Medina, C.A., Heuschele, D.J., Zhao, D., Lin, M., Beil, C., Sheehan, M.J., Xu, Z. 2024. Multi-trait modeling and machine learning discover new markers associated with stem traits in alfalfa. Frontiers in Plant Science. 15. Article 1429976. https://doi.org/10.3389/fpls.2024.1429976.

Bacterial Stem Blight: A re-emerging disease of alfalfa caused by Pseudomonas syringae phylogroup (PG) 2b and PG7a - (Abstract Only)
Samac, D.A., Lipps, S.M., Morris, C.E., Ishii, S. 2024. Bacterial Stem Blight: A re-emerging disease of alfalfa caused by Pseudomonas syringae phylogroup (PG) 2b and PG7a. Plant Pathogenic Bacteria International Conference, July 8-12, 2024, Blacksburg, Virginia.

Genome-wide association and genomic prediction of root system architecture in alfalfa - (Abstract Only)
Medina, C., Zhao, D., Lin, M., Beil, C., Sheehan, M., Irish, B.M., Yu, L., Smith, K., Samac, D.A., Xu, Z. 2024. Genome-wide association and genomic prediction of root system architecture in alfalfa. North American Alfalfa Improvement Conference. Pasco, Washington. June 24-26, 2024.

Plasticity in root attributes and belowground interactions between a perennial legume and a grass companion - (Abstract Only)
Nosshi, M., Gamble, J.D., Russelle, M., Samac, D.A. 2024. Plasticity in root attributes and belowground interactions between a perennial legume and a grass companion. Ecological Society of America, August 4-9, 2024, Long Beach, California.

Alfalfa nutrient concentrate provides benefits to diets for rainbow trout - (Trade Journal)
Deng, D.F., Samac, D.A. 2024. Alfalfa nutrient concentrate provides benefits to diets for rainbow trout. Forage Focus (May 2024):8-9.

Identification of SNP markers associated with resistance to Aphanomyces root rot race 2 - (Abstract Only)
Samac, D.A., Lin, M., Zhao, D., Tang, X., Yu, L., Beil, C., Sheehan, M. 2024. Identification of SNP markers associated with resistance to Aphanomyces root rot race 2. North American Alfalfa Improvement Conference, June 24-26, 2024, Pasco, Washington.