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.)

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. Vol 15; p.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.