Research Project: Enabling Mechanistic Allele Mining to Accelerate Genomic Selection for New Agro-Ecosystems

Location: Plant, Soil and Nutrition Research

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

AI Agents for Plant Genomics Research via Model Context Protocol Integration with Gramene and Complementary Biological Databases - (Abstract Only)
Olson, A., Chougule, K., Gladman, N.P., Kumari, S., Lu, Z., Wei, S., Ware, D. 2026. AI Agents for Plant Genomics Research via Model Context Protocol Integration with Gramene and Complementary Biological Databases. Cold Spring Harbor Meeting. 90th Cold Spring Harbor Laboratory Symposium on Quantitative Biology: AI in Biology.

Extensive modulation of a conserved cis-regulatory code across 589 grass species - (Peer Reviewed Journal)
Hale, C.O., Hsu, S., Zhai, J., Schulz, A.J., Aubuchon-Elder, T., Costa-Neto, G., Gelford, A., El-Walid, M., Hufford, M., Kellog, E.A., La, T., Marand, A.P., Seetharam, A.S., Scheben, A., Stitzer, M., Wrightsman, T., Romay, M., Buckler Iv, E.S. 2025. Extensive modulation of a conserved cis-regulatory code across 589 grass species. Molecular Biology and Evolution. 43(1):1-15. https://doi.org/10.1093/molbev/msaf324.

Environmental data provide marginal benefit for predicting climate adaptation. - (Peer Reviewed Journal)
Li, F., Gates, D.J., Buckler Iv, E.S., Hufford, M.B., Janzen, G.M., Rellan-Alvarez, R., Rodriguez-Zapata, F., Romero Navarro, J., Sawers, R.J., Snodgrass, S.J., Sonder, K., Wilcox, M.C., Hearne, S.J., Ross-Ibarra, J., Runcie, D. 2025. Environmental data provide marginal benefit for predicting climate adaptation.. PLoS Genetics. https://doi.org/10.1371/journal.pgen.1011714.

Extensive modulation of a conserved cis-regulatory code across 589 grass species - (Pre-print Publication)
Hale, C.O., Hsu, S., Zhai, J., Schulz, A.J., Aubuchon-Elder, T., Costa-Neto, G., Gelford, A., El-Walid, M., Hufford, M., Kellog, E.A., La, T., Marand, A.P., Seetharam, A.S., Scheben, A., Stitzer, M., Wrightsman, T., Romay, M., Buckler Iv, E.S. 2025. Extensive modulation of a conserved cis-regulatory code across 589 grass species. bioRxiv. https://doi.org/10.1101/2025.04.23.650228.

Higher order repeat structures reflect diverging evolutionary paths in maize centromeres and knobs - (Other)
Piri, R.D., Romay, M., Buckler Iv, E.S., Dawe, R. 2025. Higher order repeat structures reflect diverging evolutionary paths in maize centromeres and knobs. bioRxiv. https://doi.org/10.1101/2025.01.31.635908.

Maize inbreds show allelic variation for diel transcription patterns - (Other)
Gage, J., Romay, M., Buckler Iv, E.S. 2024. Maize inbreds show allelic variation for diel transcription patterns. bioRxiv. https://doi.org/10.1101/2024.12.16.628400.

Evolutionary signatures of the erosion of sexual reproduction genes in domesticated cassava (Manihot esculenta) - (Peer Reviewed Journal)
Long, E.M., Stitzer, M.C., Monier, B., Schulz, A.J., Romay, M., Robbins, K.R., Buckler Iv, E.S. 2024. Evolutionary signatures of the erosion of sexual reproduction genes in domesticated cassava (Manihot esculenta). G3: Genes, Genomes, Genetics. 15(2), jkae282. https://doi.org/10.1093/g3journal/jkae282.

The maize recombination landscape evolved during domestication - (Other)

Fishing for a reelGene: evaluating gene models with evolution and machine learning - (Pre-print Publication)
Schulz, A.J., Zhai, J., Aubuchon-Elder, T., El-Walid, M., Ferebee, T.H., Gilmore, E.H., Hufford, M.B., Johnson, L.C., Kellogg, E.A., La, T., Long, E., Miller, Z.R., Romay, M., Seetharam, A.S., Stitzer, M.C., Wrightsman, T., Buckler Iv, E.S., Monier, B., Hsu, S. 2024. Fishing for a reelGene: evaluating gene models with evolution and machine learning. bioRxiv. https://doi.org/10.1101/2023.09.19.558246.

Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability - (Peer Reviewed Journal)
Gorjifard, S., Jores, T., Tonnies, J., Mueth, N.A., Bubb, K., Wrightsman, T., Buckler Iv, E.S., Fields, S., Cuperus, J.T., Queitsch, C. 2024. Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability. Nature Communications. 15. Article 5868. https://doi.org/10.1038/s41467-024-50174-7.

Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model - (Pre-print Publication)
Zhai, J., Gokaslan, A., Schiff, Y., Berthel, A., Liu, Z., Miller, Z.R., Scheben, A., Stitzer, M.C., Romay, M., Buckler Iv, E.S., Kuleshov, V. 2024. Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model. bioRxiv. https://doi.org/10.1101/2024.06.04.596709.

Current genomic deep learning architectures generalize across grass species but not alleles - (Pre-print Publication)
Wrightsman, T., Ferebee, T.H., Romay, M., Aubuchon-Elder, T., Phillips, A.R., Syring, M., Kellogg, E.A., Buckler Iv, E.S. 2024. Current genomic deep learning architectures generalize across grass species but not alleles. bioRxiv. https://doi.org/10.1101/2024.04.11.589024.

Spatio-temporal modeling of high-throughput multispectral aerial images improves agronomic trait genomic prediction in hybrid maize - (Peer Reviewed Journal)
Morales, N., Anche, M.T., Kaczmar, N.S., Lepak, N.K., Ni, P., Romay, M., Santantonio, N., Buckler Iv, E.S., Gore, M.A., Mueller, L.A., Robbins, K.R. 2024. Spatio-temporal modeling of high-throughput multispectral aerial images improves agronomic trait genomic prediction in hybrid maize. Genetics. 227(1):iyae037. https://doi.org/10.1093/genetics/iyae037.

Muller’s Ratchet in Action: The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta) - (Pre-print Publication)
Long, E.M., Stitzer, M., Schulz, A.J., Romay, M., Robbins, K.R., Buckler Iv, E.S. 2024. Muller’s Ratchet in Action: The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta). bioRxiv. https://doi.org/10.1101/2024.02.14.580345.

Reinstatement and expansion of the genus Anatherum (Andropogoneae, Panicoideae, Poaceae) - (Peer Reviewed Journal)
Vorontsova, M.S., Peterson, K.B., Minx, P., Aubuchon-Elder, T.M., Romay, M., Buckler Iv, E.S., Kellogg, E.A. 2023. Reinstatement and expansion of the genus Anatherum (Andropogoneae, Panicoideae, Poaceae). Systematics and Biodiversity. 21(1). https://doi.org/10.1080/14772000.2023.2274386.

Synergizing Proximal Remote Sensing Modalities for Enhanced Prediction of Key Agronomic Crop Traits - (Other)
Farmer, E., Michael, P., Yan, R., Lepak, N.K., Romay, M., Buckler Iv, E.S., Snavely, N., Sun, Y., Gage, J.L., Davis, A., Gore, M.A. 2023. Synergizing Proximal Remote Sensing Modalities for Enhanced Prediction of Key Agronomic Crop Traits. North American Plant Phenotyping Network Meeting. https://doi.org/10.22541/essoar.169871639.93497349/v1.

New whole-genome alignment tools are needed for tapping into plant diversity - (Peer Reviewed Journal)
Song, B., Buckler Iv, E.S., Stitzer, M.C. 2023. New whole-genome alignment tools are needed for tapping into plant diversity. Trends in Plant Science. 29(3):355. https://doi.org/10.1016/j.tplants.2023.08.013.

Transposable element abundance subtly contributes to lower fitness in maize - (Pre-print Publication)
Stitzer, M.C., Khaipho-Burch, M.B., Hudson, A.L., Song, B., Valdez-Franco, J., Ramstein, G., Feschotte, C., Buckler Iv, E.S. 2023. Transposable element abundance subtly contributes to lower fitness in maize. bioRxiv. https://doi.org/10.1101/2023.09.18.557618.