Research Project: Improving Crop Efficiency Using Genomic Diversity and Computational Modeling

Location: Plant, Soil and Nutrition Research

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

Features that govern terminator strength in plants - (Pre-print Publication)
Gorjifard, S., Jores, T., Tonnies, J., Mueth, N.A., Bubb, K., Wrightsman, T., Buckler IV, E.S., Fields, S., Cuperus, J.T., Queitsch, C. 2023. Features that Govern Terminator Strength in Plants. bioRxiv. https://doi.org/10.1101/2023.06.16.545379.

Exploring the utility of regulatory network-based machine learning for gene expression prediction in maize - (Pre-print Publication)
Ferebee, T.H., Buckler IV, E.S. 2023. Exploring the utility of regulatory network-based machine learning for gene expression prediction in maize. bioRxiv. 05/14/2023. https://doi.org/10.1101/2023.05.11.540406.

Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding - (Peer Reviewed Journal)
Wu, Y., Li, D., Hu, Y., Li, H., Ramstein, G.P., Zhou, S., Zhang, X., Bao, Z., Zhang, Y., Song, B., Zhou, Y., Zhou, Y., Gagnon, E., Sarkinen, T., Knaap, S., Zhang, C., Stadler, T., Buckler IV, E.S., Huang, S. 2023. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell. 186(11):2313-2328. https://doi.org/10.1016/j.cell.2023.04.008.

A happy accident: a novel turfgrass reference genome - (Peer Reviewed Journal)
Phillips, A.R., Seetharam, A.S., Albert, P.S., Aubuchon-Elder, T., Birchler, J.A., Buckler IV, E.S., Gillespie, L.J., Hufford, M.B., Romay, M., Soreng, R.J., Kellogg, E.A., Ross-Ibarra, J. 2023. A happy accident: a novel turfgrass reference genome. Genes, Genomes, Genetics. 13(6). Article jkad073. https://doi.org/10.1093/g3journal/jkad073.

Genome-wide association study for root morphology and phosphorus acquisition efficiency in diverse maize panels - (Peer Reviewed Journal)
Ribeiro, C.R., Tinoco, S.E., De Soouza, V., Negri, B., Gault, C., Pastina, M., Magalhaes, J., Guimaraes, L.I., De Barros, E.V., Buckler IV, E.S., Guimaraes, C.A. 2023. Genome-wide association study for root morphology and phosphorus acquisition efficiency in diverse maize panels. International Journal of Molecular Sciences. 24(7). Article 6233. https://doi.org/10.3390/ijms24076233.

Loss of OPT3 function decreases phloem copper levels and impairs crosstalk between copper and iron homeostasis and shoot-to-root signaling in Arabidopsis thaliana - (Peer Reviewed Journal)
Chia, J., Yan, J., Ishka, M.R., Faulkner, M.M., Huang, R., Smieska, L., Woll, A., Tappero, R., Kiss, A., Jiao, C., Fei, Z., Pineros, M., Kochian, L., Walker, E., Vatamaniuk, O.K. 2023. Loss of OPT3 function decreases phloem copper levels and impairs crosstalk between copper and iron homeostasis and shoot-to-root signaling in Arabidopsis thaliana. The Plant Cell. 35(6):2157-2185. https://doi.org/10.1093/plcell/koad053.

Elucidating the patterns of pleiotropy and its biological relevance in maize - (Peer Reviewed Journal)
Khaipho-Burch, M., Ferebee, T., Giri, A., Ramstein, G., Monier, B., Yi, E., Romay, M., Buckler IV, E.S. 2023. Elucidating the patterns of pleiotropy and its biological relevance in maize. PLoS Genetics. PLoS Genet 19(3): e1010664. https://doi.org/10.1371/journal.pgen.1010664.

Cross-species predictive modeling reveals conserved drought responses between maize and sorghum - (Peer Reviewed Journal)
Pardo, J., Wai, C., Harman, M., Nguyen, A., Kremling, K.A., Romay, M., Lepak, N.K., Bauerle, T.L., Buckler IV, E.S., Thompson, A.M., Vanburen, R.M. 2023. Cross-species predictive modeling reveals conserved drought responses between maize and sorghum. Proceedings of the National Academy of Sciences (PNAS). 120(10). Article e2216894120. https://doi.org/10.1073/pnas.2216894120.

Utilizing evolutionary conservation to detect deleterious mutations and improve genomic prediction in cassava - (Peer Reviewed Journal)
Long, E.K., Romay, M., Ramstein, G., Buckler IV, E.S., Robbins, K.R. 2023. Utilizing evolutionary conservation to detect deleterious mutations and improve genomic prediction in cassava. Frontiers in Plant Science. 13:1041925. https://doi.org/10.3389/fpls.2022.1041925.

Scale up trials to validate modified crops' benefits - (Peer Reviewed Journal)
Khaipho-Burch, M., Cooper, M., Crossa, J., De Leon, N., Holland, J.B., Lewis, R., Mccouch, S., Murray, S., Rabbi, I., Ronald, P., Ross-Ibarra, J., Weigel, D., Buckler IV, E.S. 2023. Scale up trials to validate modified crops' benefits. Nature. 621:470-473. https://doi.org/10.1038/d41586-023-02895-w.

Spatio-temporal modeling of high-throughput multi-spectral aerial images improves agronomic trait genomic prediction in hybrid maize - (Pre-print Publication)
Morales, N., Anche, M.T., Kaczmar, N., Lepak, N.K., Ni, P., Romay, M., Santantonio, N., Buckler IV, E.S., Gore, M.A., Mueller, L.A., Robbins, K.R. 2022. Spatio-temporal modeling of high-throughput multi-spectral aerial images improves agronomic trait genomic prediction in hybrid maize. bioRxiv. https://doi.org/10.1101/2022.10.18.512728.

Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize - (Peer Reviewed Journal)
Ramstein, G.P., Buckler IV, E.S. 2022. Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize. Genome Biology. 23. Article 183. https://doi.org/10.1186/s13059-022-02747-2.

Elucidating the patterns of pleiotropy and its biological relevance in maize - (Pre-print Publication)
Khaipho-Burch, M., Ferebee, T., Giri, A., Ramstein, G., Monier, B., Yi, E., Romay, M.C., Buckler IV, E.S. 2022. Elucidating the patterns of pleiotropy and its biological relevance in maize. bioRxiv. https://doi.org/10.1101/2022.07.20.500810.

The practical haplotype graph, a platform for storing and using pangenomes for imputation - (Peer Reviewed Journal)
Bradbury, P.J., Casstevens, T., Jensen, S.E., Johnson, L.E., Miller, Z.R., Monier, B., Romay, M., Song, B., Buckler IV, E.S. 2022. The practical haplotype graph, a platform for storing and using pangenomes for imputation. Bioinformatics. 38(15):3698-3702. https://doi.org/10.1093/bioinformatics/btac410.

The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. - (Peer Reviewed Journal)
Bradbury, P.J., Casstevens, T., Jensen, S.E., Johnson, L.C., Miller, Z.R., Monier, B., Romay, M.C., Song, B., Buckler IV, E.S. 2022. The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac410.

rTASSEL: An R interface to TASSEL for analyzing genomic diversity - (Peer Reviewed Journal)
Monier, B., Casstevens, T.M., Bradbury, P., Buckler IV, E.S. 2022. rTASSEL: An R interface to TASSEL for analyzing genomic diversity. Journal of Open Source Software. https://doi.org/10.21105/joss.04530.

Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks - (Peer Reviewed Journal)
Wrightsman, T., Marand, A.P., Crisp, P.A., Springer, N.M., Buckler IV, E.S. 2022. Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks. The Plant Genome. 15(3):e20249. https://doi.org/10.1002/tpg2.20249.

An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time - (Peer Reviewed Journal)
Barnes, A.C., Rodríguez-Zapata, F., Juárez-Núñez, K.A., Gates, D.J., Janzen, G.M., Kur, A., Wang, L., Jensen, S.J., Estévez-Palmas, J.M., Crow, T.M., Kavi, H.S., Pil, H.D., Stokes, R.L., Knizner, K.T., Aguilar-Rangel, M.R., Demesa-Arévalo, E., Skopelitis, T., Pérez-Limón, S., Stutts, W.L., Thompson, P., Chiu, Y., Jackson, D., Muddiman, D.C., Fiehn, O., Runcie, D., Buckler Iv, E.S., Ross-Ibarra, J., Hufford, M.B., Sawers, R.J., Rellán-Álvarez, R. 2022. An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time. Proceedings of the National Academy of Sciences (PNAS). 119(27). Article e2100036119. https://doi.org/10.1073/pnas.2100036119.

A happy accident: a novel turfgrass reference genome - (Pre-print Publication)
Phillips, A.R., Seetharam, A.S., Aubuchon-Elder, T., Buckler IV, E.S., Gillespie, L.J., Hufford, M.B., Llaca, V., Romay, M.C., Soreng, R.J., Kellogg, E.A., Ross-Ibarra, J. 2022. A happy accident: a novel turfgrass reference genome. bioRxiv. https://doi.org/10.1101/2022.03.08.483531.

Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance - (Peer Reviewed Journal)
Gage, J.L., Mali, S., McLoughlin, F., Khaipho-Burch, M., Monier, B., Bailey-Serres, J., Vierstra, R.D., Buckler IV, E.S. 2022. Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance. Proceedings of the National Academy of Sciences (PNAS). 119(14). Article e2112516119. https://doi.org/10.1073/pnas.2112516119.

AnchorWave: sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication - (Peer Reviewed Journal)
Song, B., Marco-Sola, S., Moreto, M., Johnson, L., Buckler IV, E.S., Stitzer, M.C. 2021. AnchorWave: sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication. Proceedings of the National Academy of Sciences (PNAS). 119(1). Article e2113075119. https://doi.org/10.1073/pnas.2113075119.

Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks - (Pre-print Publication)
Wrightsman, T., Marand, A.P., Crisp, P.A., Springer, N.M., Buckler IV, E.S. 2021. Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks. bioRxiv. https://doi.org/10.1101/2021.11.11.468292.

QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes - (Peer Reviewed Journal)
Oren, E., Tzuri, G., Dafna, A., Reese, E.R., Song, B., Freilich, S., Elkind, Y., Isaacson, T., Schaffer, A.A., Tadmor, Y., Burger, J., Buckler IV, E.S., Gur, A. 2022. QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes. Horticulture Research. https://doi.org/10.1093/hr/uhab081.

Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava - (Peer Reviewed Journal)
Long, E.M., Bradbury, P., Romay, C.M., Buckler IV, E.S., Robbins, K.R. 2021. Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava. G3, Genes/Genomes/Genetics. 12(1):jkab383. https://doi.org/10.1093/g3journal/jkab383.

Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact - (Peer Reviewed Journal)
Zhang, X., Zhu, Y., Kremling, K.A., Romay, C., Bukowski, R., Sun, Q., Gao, S., Buckler Iv, E.S., Lu, F. 2021. Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-021-03965-1.

Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize - (Peer Reviewed Journal)
Giri, A., Khaipho-Burch, M., Buckler IV, E.S., Ramstein, G.P. 2021. Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize. PLoS Genetics. https://doi.org/10.1371/journal.pgen.1009568.

Prediction of evolutionary constraint by genomic annotations improves prioritization of causal variants in maize - (Pre-print Publication)
Ramstein, G.P., Buckler IV, E.S. 2021. Prediction of evolutionary constraint by genomic annotations improves prioritization of causal variants in maize. bioRxiv. 2021.09.03.458856. https://doi.org/10.1101/2021.09.03.458856.

The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation - (Pre-print Publication)
Bradbury, P., Casstevens, T., Jensen, S.E., Johnson, L.C., Miller, Z.R., Monier, B., Romay, M.C., Song, B., Buckler IV, E.S. 2021. The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. bioRxiv. 2021.08.27.457652. https://doi.org/10.1101/2021.08.27.457652.

AnchorWave: sensitive alignment of genomes with high diversity, structural polymorphism and whole-genome duplication variation - (Pre-print Publication)
Song, B., Marco-Sola, S., Moreto, M., Johnson, L., Buckler IV, E.S., Stitzer, M.C. 2021. AnchorWave: sensitive alignment of genomes with high diversity, structural polymorphism and whole-genome duplication variation. bioRxiv. 2021.07.29.454331. https://doi.org/10.1101/2021.07.29.454331.

Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes - (Peer Reviewed Journal)
Pignon, C.P., Fernandes, S.B., Valluru, R., Bandillo, N., Lozano, R., Buckler IV, E.S., Gore, M.A., Long, S.P., Brown, P.J., Leakey, A. 2021. Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes. Plant Physiology. 184(4):2544-2562. https://doi.org/10.1093/plphys/kiab395.

Pfam domain adaptation profiles reflect plant species’ evolutionary history - (Pre-print Publication)
Jensen, S.E., Buckler IV, E.S. 2021. Pfam domain adaptation profiles reflect plant species’ evolutionary history. bioRxiv. https://doi.org/10.1101/2021.07.13.452250.

Predicting protein domain temperature adaptation across the prokaryote-eukaryote divide - (Pre-print Publication)
Jensen, S.E., Johnson, L.C., Casstevens, T., Buckler IV, E.S. 2021. Predicting protein domain temperature adaptation across the prokaryote-eukaryote divide. bioRxiv. 2021.07.13.452245. https://doi.org/10.1101/2021.07.13.452245.

RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants - (Peer Reviewed Journal)
Lozano, R., Booth, G.T., Omar, B., Li, B., Buckler IV, E.S., Lis, J.T., Pino Del Carpio, D., Jannink, J. 2021. RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants. Genes, Genomes, Genetics. jkab273. https://doi.org/10.1093/g3journal/jkab273.

Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions - (Peer Reviewed Journal)
Ferguson, J.N., Fernandes, S.B., Monier, B., Miller, N.D., Allan, D., Dmitrieva, A., Schmuker, P., Lozano, R., Valluru, R., Buckler IV, E.S., Gore, M.A., Brown, P.J., Spalding, E.P., Leakey, A.D. 2021. Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. Plant Physiology. 187(3):1481-1500. https://doi.org/10.1093/plphys/kiab346.

A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants - (Other)
Wu, Y., Johnson, L., Song, B., Romay, M., Stitzer, M., Siepel, A., Buckler IV, E.S., Scheben, A. 2021. A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants. bioRxiv. https://doi.org/10.1101/2021.06.01.446647.

Variation in upstream open reading frames contributes to allelic diversity in protein abundance - (Other)
Gage, J.L., Mali, S., Mcloughlin, F., Khaipho-Burch, M., Monier, B., Bailey-Serres, J., Vierstra, R.D., Buckler IV, E.S. 2021. Variation in upstream open reading frames contributes to allelic diversity in protein abundance. bioRxiv. https://doi.org/10.1101/2021.05.25.445499.

Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels - (Peer Reviewed Journal)
Baseggio, M., Murray, M., Wu, D., Ziegler, G., Kaczmar, N., Chamness, J., Hamilton, J.P., Buell, R.C., Vatamaniuk, O.K., Buckler IV, E.S., Smith, M.E., Baxter, I., Tracy, W.F., Gore, M.A. 2021. Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels. G3, Genes/Genomes/Genetics. 11(8). https://doi.org/10.1093/g3journal/jkab186.

Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize - (Peer Reviewed Journal)
Song, B., Buckler IV, E.S., Wang, H., Wu, Y., Rees, E., Kellogg, E.A., Gates, D.J., Khaipho-Burch, M., Bradbury, P., Ross-Ibarra, J., Hufford, M.B., Romay, M. 2021. Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize. Genome Research. 31:1245-1257. https://doi.org/10.1101/gr.266528.120.

Underground heterosis for yield improvement in melon - (Peer Reviewed Journal)
Dafna, A., Halperin, I., Oren, E., Isaacson, T., Tzuri, G., Meir, A., Schaffer, A.A., Burger, J., Tadmor, Y., Buckler IV, E.S., Gur, A. 2021. Underground heterosis for yield improvement in melon. Journal of Experimental Botany. 72(18):6205-6218. https://doi.org/10.1093/jxb/erab219.

Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava - (Other)
Long, E.M., Bradbury, P., Romay, M., Buckler IV, E.S., Robbins, K.R. 2021. Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava. bioRxiv. https://doi.org/10.1101/2021.05.12.443913.

Somatic variations led to the selection of acidic and acidless orange cultivars - (Peer Reviewed Journal)
Wang, L., Huang, Y., Liu, Z., He, J., Jiang, X., He, F., Lu, Z., Yang, S., Chen, P., Yu, H., Zeng, B., Ke, L., Xie, Z., Larkin, R., Jiang, D., Ming, R., Buckler IV, E.S., Xu, Q. 2021. Somatic variations led to the selection of acidic and acidless orange cultivars. Nature Plants. https://doi.org/10.1038/s41477-021-00941-x.

Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance - (Peer Reviewed Journal)
Wu, X., Feng, H., Wu, D., Yan, S., Zhang, P., Wang, W., Zhang, J., Ye, J., Dai, G., Fan, Y., Li, W., Song, B., Geng, Z., Yang, W., Chen, G., Qin, F., Terzaghi, W., Stitzer, M., Li, L., Xiong, L., Yan, J., Buckler IV, E.S., Dai, M. 2021. Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance. Genome Biology. 22(185):1-26. https://doi.org/10.1186/s13059-021-02377-0.

Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize - (Pre-print Publication)
Giri, A., Khaipho-Burch, M., Buckler IV, E.S., Ramstein, G.P. 2021. Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize. bioRxiv. https://doi.org/10.1101/2021.04.30.442099.

Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters - (Peer Reviewed Journal)
Jores, T., Tonnies, J., Wrightsman, T., Buckler IV, E.S., Cuperus, J.T., Fields, S., Queitsch, C. 2021. Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. Nature Plants. 7:842-855. https://doi.org/10.1038/s41477-021-00932-y.

Underground heterosis for melons yield - (Pre-print Publication)
Dafna, A., Halperin, I., Oren, E., Isaacson, T., Tzuri, G., Meir, A., Schaffer, A., Burger, J., Tadmor, Y., Buckler IV, E.S., Gur, A. 2021. Underground heterosis for melons yield. bioRxiv. https://doi.org/10.1101/2021.03.04.434025.

Joint analysis of days to flowering reveals independent temperate adaptations in maize - (Peer Reviewed Journal)
Swarts, K., Bauer, E., Glaubitz, J.C., Ho, T., Johnson, L., Li, Y., Li, Y., Miller, Z., Schon, C., Wang, T., Zhang, Z., Buckler Iv, E.S., Bradbury, P. 2021. Joint analysis of days to flowering reveals independent temperate adaptations in maize. Heredity. 126:929-941. https://doi.org/10.1038/s41437-021-00422-z.

A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants - (Peer Reviewed Journal)
Wu, Y., Johnson, L., Song, B., Romay, M.C., Stitzer, M., Siepel, A., Buckler IV, E.S., Scheben, A. 2022. A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants. The Plant Genome. 15(2). Article e20204. https://doi.org/10.1002/tpg2.20204.

Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain - (Peer Reviewed Journal)
Diepenbrock, C.H., Ilut, D.C., Magallanes-Lundback, M., Kandianis, C.B., Lipka, A.E., Bradbury, P., Holland, J.B., Hamilton, J.P., Wooldridge, E., Vaillancourt, B., Góngora-Castillo, E., Wallace, J.G., Cepela, J., Mateos-Hernandez, M., Owens, B.F., Tiede, T., Buckler IV, E.S., Rocheford, T., Buell, C., Gore, M.A., Dellapenna, D. 2021. Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain. The Plant Cell. 33(4):882–900. https://doi.org/10.1093/plcell/koab032.

Teosinte introgression modulates phosphatidylcholine levels and induces early maize flowering time - (Pre-print Publication)
Rodriguez-Zapata, F., Barnes, A.C., Blocker-Juarez, K.A., Gates, D., Kur, A., Wang, L., Janzen, G.M., Jensen, S., Estevez-Palmas, J.M., Crow, T., Aguilar-Rangel, R., Demesa-Arevalo, E., Skopelitis, T., Perez-Limon, S., Stutts, W., Thompson, P., Chiu, Y., Jackson, D., Fiehn, O., Runcie, D., Buckler IV, E.S., Ross-Ibarra, J., Hufford, M.B., Sawers, R., Rellan-Alvarez, R. 2021. Teosinte introgression modulates phosphatidylcholine levels and induces early maize flowering time. bioRxiv. https://doi.org/10.1101/2021.01.25.426574.

Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters - (Pre-print Publication)
Jores, T., Tonnies, J., Wrightsman, T., Buckler IV, E.S., Cuperus, J.T., Fields, S., Queitsch, C. 2021. Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. bioRxiv. https://doi.org/10.1101/2021.01.07.425784.

Utility of climatic information via combining ability models to improve genomic prediction for yield within the genomes to fields maize project - (Peer Reviewed Journal)
Jarquin, D., De Leon, N., Romay, M., Bohn, M., Buckler IV, E.S., Ciampitti, I., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gore, M.A., Graham, C., Hirsch, C.N., Holland, J.B., Hooker, D., Kaeppler, S.M., Knoll, J.E., Lee, E.S., Lawrence-Dill, C.J., Lynch, J.P., Moose, S.P., Murray, S.C., Nelson, R., Rocheford, T., Schnable, J.C., Schnable, P.S., Smith, M., Springer, N., Thomison, P., Tuinstra, M., Wisser, R.J., Xu, W., Lorenz, A. 2021. Utility of climatic information via combining ability models to improve genomic prediction for yield within the genomes to fields maize project. Frontiers in Genetics. 11:592769. https://doi.org/10.3389/fgene.2020.592769.

Local adaptation contributes to gene expression divergence in maize - (Peer Reviewed Journal)
Blanc, J., Kremling, K., Buckler IV, E.S., Josephs, E. 2021. Local adaptation contributes to gene expression divergence in maize. Genes, Genomes, Genetics. 11(2):jkab004. https://doi.org/10.1093/g3journal/jkab004.

Decoding the regulatory architecture of the maize leaf - (Pre-print Publication)
Tu, X., Mejia-Guerra, M.K., Valdes Franco, J.A., Tzeng, D., Chu, P., Dai, X., Li, P., Buckler IV, E.S., Zhong, S. 2020. Decoding the regulatory architecture of the maize leaf. bioRxiv. 54:34-41. https://doi.org/10.1101/2020.01.07.898056.

Comparative evolutionary genetics of deleterious load in sorghum and maize - (Peer Reviewed Journal)
Lozano, R., Gazave, E., Dos Santos, J., Valluru, R., Bandillo, N., Fernandes, S., Brown, P.J., Shakoor, N., Mockler, T., Ross-Ibarra, J., Buckler IV, E.S., Gore, M.A. 2021. Comparative evolutionary genetics of deleterious load in sorghum and maize. Nature Plants. (7):17-24. https://doi.org/10.1038/s41477-020-00834-5.

Comparative evolutionary genetics of deleterious load in sorghum and maize - (Peer Reviewed Journal)
Lozano, R., Gazave, E., Dos Santos, J., Stetter, M.G., Valluru, R., Bandillo, N., Fernandes, S., Brown, P.J., Shakoor, N., Mockler, T., Cooper, E., Perkins, T., Buckler IV, E.S., Ross-Ibarra, J., Gore, M.A. 2021. Comparative evolutionary genetics of deleterious load in sorghum and maize. Nature Plants. 7:17-24. https://doi.org/10.1038/s41477-020-00834-5.

The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment - (Peer Reviewed Journal)
Rogers, A.R., Dunne, J.C., Romay, M.C., Bohn, M., Buckler IV, E.S., Ciampitti, I.C., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gore, M.A., Graham, C., Hirsch, C.N., Hood, E.C., Hooker, D., Knoll, J.E., Lee, E.C., Lorenz, A., Lynch, J.P., Mckay, J., Moose, S.P., Murray, S.C., Nelson, R., Rocheford, T., Schnable, J.C., Schnable, P.S., Sekhon, R., Singh, M., Smith, M., Springer, N., Thelen, K., Thomison, P., Thompson, A., Tuinstra, M., Wallace, J., Wisser, R., Xu, W., Gilmour, A., Kaeppler, S.M., Deleon, N., Holland, J.B. 2021. The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment. Genes, Genomes, Genetics. 11(2):jkaa050. https://doi.org/10.1093/g3journal/jkaa050.

The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment - (Peer Reviewed Journal)
Rogers, A.R., Dunne, J.C., Romay, C., Bohn, M., Buckler IV, E.S., Ciampitti, I.C., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gore, M.A., Graham, C., Hirsch, C.N., Hood, E., Hooker, D.C., Knoll, J.E., Lee, E.C., Lorenz, A., Lynch, J.P., Mckay, J., Moose, S.P., Murray, S.C., Nelson, R., Rocheford, T., Schnable, J.C., Schnable, P.S., Sekhon, R., Singh, M., Smith, M., Springer, N., Thelen, K., Thomison, P., Thompson, A., Tuinstra, M., Wallace, J., Wisser, R.J., Xu, W., Gilmour, A., Kaeppler, S.M., Deleon, N., Holland, J.B. 2021. The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment. Genes, Genomes, Genetics. https://doi.org/10.1093/g3journal/jkaa050.

Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions - (Pre-print Publication)
Ferguson, J.N., Fernandes, S.B., Monier, B., Miller, N.D., Allan, D., Dmitrieva, A., Schmuker, P., Lozano, R., Valluru, R., Buckler IV, E.S., Gore, M.A., Brown, P., Spalding, E.P., Leakey, A. 2020. Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. bioRxiv. https://doi.org/10.1101/2020.11.02.365213.

Building a tRNA thermometer to estimate microbial adaptation to temperature - (Peer Reviewed Journal)
Cimen, E., Jensen, S., Buckler IV, E.S. 2020. Building a tRNA thermometer to estimate microbial adaptation to temperature. Nucleic Acids Research. 48(21):12004-12045. https://doi.org/10.1093/nar/gkaa1030.

Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors - (Peer Reviewed Journal)
Tu, X., Majia-Guerra, M., Valdes Franco, J.A., Tzeng, D., Chu, P., Shen, W., Wei, Y., Dai, X., Li, P., Buckler IV, E.S., Zhong, S. 2020. Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors. Nature Communications. (11):5089. https://doi.org/10.1038/s41467-020-18832-8.

Identification of miRNA-eQTLs in maize mature leaf by GWAS - (Peer Reviewed Journal)
Chen, S., Mei-Hsiu, S., Kremling, K.A., Lepak, N.K., Romay, M.C., Sun, Q., Bradbury, P., Buckler IV, E.S., Ku, H. 2020. Identification of miRNA-eQTLs in maize mature leaf by GWAS. Biomed Central (BMC) Genomics. 21(689). https://doi.org/10.1186/s12864-020-07073-0.

Genetic elucidation of interconnected antibiotic pathways mediating maize innate immunity - (Peer Reviewed Journal)
Ding, Y., Weckwerth, P.R., Poretsky, E., Murphy, K.M., Sims, J., Saldivar, E., Christensen, S.A., Char, S., Yang, B., Tong, A., Shen, Z., Kremling, K.A., Buckler IV, E.S., Kono, T., Nelson, D.R., Bohlmann, J., Bakker, M.G., Vaughan, M.M., Khalil, A.S., Betsiashvili, M., Briggs, S.P., Zerbe, P., Schmelz, E.A., Huffaker, A. 2020. Genetic elucidation of interconnected antibiotic pathways mediating maize innate immunity. Nature Plants. (6):1375-1388. https://doi.org/10.1038/s41477-020-00787-9.

A maize practical haplotype graph leverages diverse NAM assemblies - (Other)
Valdes Franco, J.A., Gage, J.L., Bradbury, P., Johnson, L.C., Miller, Z.R., Buckler IV, E.S., Romay, M. 2020. A maize practical haplotype graph leverages diverse NAM assemblies. bioRxiv. https://doi.org/10.1101/2020.08.31.268425.

Local adaptation contributes to gene expression divergence in maize - (Other)
Blanc, J., Kremling, K.A., Buckler IV, E.S., Josephs, E.B. 2020. Local adaptation contributes to gene expression divergence in maize. bioRxiv. https://doi.org/10.1101/2020.08.01.231217.

rTASSEL: an R interface to TASSEL for association mapping of complex traits - (Other)
Monier, B., Casstevens, T.M., Buckler IV, E.S. 2020. rTASSEL: an R interface to TASSEL for association mapping of complex traits. bioRxiv. https://doi.org/10.1101/2020.07.21.209114.

Maize introgression library provides evidence for the involvement of liguleless1 in resistance to northern leaf blight - (Peer Reviewed Journal)
Kolkman, J.M., Strable, J., Harline, K., Kroon, D.E., Wiesner-Hanks, T., Bradbury, P., Nelson, R.J. 2020. Maize introgression library provides evidence for the involvement of liguleless1 in resistance to northern leaf blight. Genes, Genomes, Genetics. https://doi.org/10.1534/g3.120.401500.

Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain - (Pre-print Publication)
Diepenbrock, C.H., Llut, D.C., Magallanes-Lundback, M., Kandianis, C.B., Lipka, A.E., Bradbury, P., Holland, J.B., Hamilton, J.P., Wooldridge, E., Vaillancourt, B., Gongora-Castillo, E., Wallace, J.G., Capela, J., Mateos-Hernandez, M. 2020. Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain. bioRxiv. https://doi.org/10.1101/2020.07.15.203448.

Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize - (Other)
Song, B., Wang, H., Wu, Y., Rees, E., Gates, D.J., Burch, M., Bradbury, P., Ross-Ibarra, J., Kellogg, E.A., Hufford, M.B., Romay, C., Buckler IV, E.S. 2020. Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize. bioRxiv. https://doi.org/10.1101/2020.07.11.192575.

Ten years of the maize Nested Association Mapping population: impact, limitations, and future directions - (Peer Reviewed Journal)
Gage, J., Monier, B., Giri, A., Buckler IV, E.S. 2020. Ten years of the maize Nested Association Mapping population: impact, limitations, and future directions. The Plant Cell. https://doi.org/10.1105/tpc.19.00951.

Genetic elucidation of complex biochemical traits mediating maize innate immunity - (Pre-print Publication)
Ding, Y., Weckwerth, P., Poretsky, E., Murphy, K., Sims, J., Saldivar, E., Christensen, S.A., Char, S., Yang, B., Tong, A., Shen, Z., Kremling, K., Buckler IV, E.S., Kono, T., Nelson, D., Bohlmann, J., Bakker, M.G., Vaughan, M.M., Khalil, A., Betsiashvili, M., Briggs, S., Zerbe, P., Schmelz, E., Huffaker, A. 2020. Genetic elucidation of complex biochemical traits mediating maize innate immunity. bioRxiv. https://doi.org/10.1101/2020.03.04.977355.

Deep learning for plant genomics and crop improvement - (Peer Reviewed Journal)
Wang, H., Cimen, E., Singh, N., Buckler IV, E.S. 2020. Deep learning for plant genomics and crop improvement. Current Opinion in Plant Biology. 54:34-41. https://doi.org/10.1016/j.pbi.2019.12.010.

A sorghum practical haplotype graph facilitates genome-wide imputation and cost effective genomic prediction - (Peer Reviewed Journal)
Jensen, S., Charles, J., Muleta, K., Bradbury, P., Casstevens, T., Deshpande, S.P., Gore, M.A., Gupta, R., Johnson, L., Lozano, R., Miller, Z., Ramu, P., Rathore, A., Upadhyaya, H.D., Varshney, R., Morris, G.P., Pressoir, G., Buckler IV, E.S., Ramstein, G. 2020. A sorghum practical haplotype graph facilitates genome-wide imputation and cost effective genomic prediction. The Plant Genome. 13(1). Article e20009. https://doi.org/10.1002/tpg2.20009.

Novel bayesian networks for genomic prediction of developmental traits in biomass sorghum - (Peer Reviewed Journal)
Dos Santos, J.P., Fernandes, S.B., Mccoy, S., Lozano, R., Brown, P.J., Leakey, A.D., Buckler IV, E.S., Garcia, A.A., Gore, M.A. 2020. Novel bayesian networks for genomic prediction of developmental traits in biomass sorghum. Genes, Genomes, Genetics. 10(2):769-781. https://doi.org/10.1534/g3.119.400759.

Maize genomes to fields (G2F): 2014 –2017 field seasons: genotype, phenotype, climatic, soil and inbred ear image datasets - (Peer Reviewed Journal)
Mcfarland, B.A., Alkhalifah, N., Bohn, M., Bubert, J., Buckler IV, E.S., Ciampitti, I., Edwards, J.W., Ertl, D., Gage, J.L., Falcon, C.M., Flint Garcia, S.A., Gore, M., Graham, C., Hirsch, C., Holland, J.B., Hood, E., Hooker, D., Jarquin, D., Kaeppler, S., Knoll, J.E., Kruger, G., Lauter, N.C., Lee, E.C., Lima, D.C., Lorenz, A., Lynch, J.P., Mckay, J., Miller, N.D., Moose, S.P., Murray, S.C., Nelson, R., Poudyal, C., Rocheford, T., Rodriguez, O., Romay, M., Schnable, J.C., Schnable, P.S., Scully, B.T., Sekhon, R., Silverstein, K., Singh, M., Smith, M., Spalding, E.P., Springer, N., Thelen, K., Thomison, P., Tuinstra, M., Wallace, J., Walls, R., Wills, D., Wisser, R.J., Xu, W., Yeh, C., De Leon, N. Maize genomes to fields (G2F): 2014 –2017 field seasons: genotype, phenotype, climatic, soil and inbred ear image datasets. BMC Research Notes. 13,71 (2020). https://doi.org/10.1186/s13104-020-4922-8.

In-field whole plant maize architecture characterized by Subcanopy Rovers and Latent Space Phenotyping - (Peer Reviewed Journal)
Gage, J.L., Richards, E., Lepak, N.K., Kaczmar, N., Soman, C., Chowdhary, G., Gore, M.A., Buckler IV, E.S. 2019. In-field whole plant maize architecture characterized by Subcanopy Rovers and Latent Space Phenotyping. The Plant Phenome Journal. 2(1):1-11. https://doi.org/10.1101/763342.

Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn - (Peer Reviewed Journal)
Baseggio, M., Murray, M., Magallanes-Lundback, M., Kaczmar, N., Chamness, J., Buckler IV, E.S., Smith, M.E., Dellapenna, D., Tracy, W.F., Gore, M.A. 2020. Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn. The Plant Genome. https://doi.org/10.1002/tpg2.20008.

A strategy for building and using a human reference pangenome - (Other)
Llamas, B., Narzisi, G., Schneider, V., Audano, P.A., Biederstedt, E., Blauvelt, L., Bradbury, P., Chang, X., Chin, C., Fungtammasan, A., Clarke, W.E., Cleary, A., Ebler, J., Eizenga, J.M., Sibbesen, J.A., Markello, C.J., Garrison, E., Lazo, G.R., Lin, M.F., Mahmoud, M., Marschall, T., Minkin, L., Monlong, J., Musunuri, R.L., Sagayaradj, S., Novak, A.M., Rautiainen, M., Regier, A., Sedlazeck, F.J., Siren, J., Souilmi, Y., Souilmi, Y., Wrightsman, T., Yokoyama, T., Zeng, Q., Zook, J.M., Paten, B., Busby, B. 2019. A strategy for building and using a human reference pangenome. F1000Research. 8:1751. https://doi.org/10.12688/f1000research.19630.1.

Widespread long-range cis-regulatory elements in the maize genome - (Peer Reviewed Journal)
Ricci, W.A., Lu, Z., Ji, L., Marand, A.P., Ethridge, C.L., Murphy, N.G., Noshay, J.M., Galli, M., Mejia-Guerra, M.K., Colome-Tatche, M., Johannes, F., Rowley, M., Corces, V.G., Zhai, J., Scanlon, M.J., Buckler IV, E.S., Gallavotti, A., Springer, N.M., Schmitz, R.J., Zhang, X. 2019. Widespread long-range cis-regulatory elements in the maize genome. Nature Plants. 5:1237-1249. https://doi.org/10.1038/s41477-019-0547-0.

Relative utility of agronomic, phenological, and morphological traits for assessing genotype-by-environment interaction in maize inbreds - (Peer Reviewed Journal)
Falcon, C.M., Kaeppler, S.M., Spalding, E.P., Miller, N.D., Haase, N., Alkhalifah, N., Bohn, M., Buckler IV, E.S., Campbell, D.A., Ciampitti, I., Coffey, L., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gore, M.A., Graham, C., Hirsch, C.N., Holland, J.B., Jarquin, D., Knoll, J.E., Lauter, N.C., Lawrence-Dill, C.J., Lee, E.C., Lorenz, A., Lynch, J.P., Murray, S.C., Nelson, R., Romay, M., Rocheford, T., Schnable, P., Scully, B.T., Smith, M.C., Springer, N., Tuinstra, M., Walton, R., Weldekidan, T., Wisser, R.J., Xu, W., De Leon, N. Relative utility of agronomic, phenological, and morphological traits for assessing genotype-by-environment interaction in maize inbreds. Crop Science. 2020; 60:62-81. https://doi.org/10.1002/csc2.20035

Multiple genes recruited from hormone pathways partition maize diterpenoid defences - (Peer Reviewed Journal)
Ding, Y., Murphy, K., Poretsky, E., Mafu, S., Yang, B., Char, S., Christensen, S.A., Saldivar, E., Wu, M., Wang, Q., Ji, L., Schmitz, R., Kremling, K., Buckler IV, E.S., Shen, Z., Briggs, S., Bohlmann, J., Sher, A., Castro-Falcon, G., Hughes, C., Huffaker, A., Zerbe, P., Schmelz, E. 2019. Multiple genes recruited from hormone pathways partition maize diterpenoid defences. Nature Plants. https://doi.org/10.1038/s41477-019-0509-6.

Single-gene resolution of locally adaptive genetic variation in Mexican maize - (Other)
Gates, D., Runcie, D., Janzen, G., Romero Navarro, A., Willcox, M., Sonder, K., Snodgrass, S., Rodriqyez-Zapata, F., J.H. Sawers, R., Buckler IV, E.S., Hearne, S., Hufford, M., Ross-Ibarra, J. 2019. Single-gene resolution of locally adaptive genetic variation in Mexican maize. bioRxiv. https://doi.org/10.1101/706739.

Transcriptome-wide association supplements genome-wide association in Zea mays - (Peer Reviewed Journal)
Kremling, K., Diepenbrock, C., Gore, M., Buckler IV, E.S., Bandillo, N. 2019. Transcriptome-wide association supplements genome-wide association in Zea mays. Genes, Genomes, Genetics. 9(9):3023-3033. https://doi.org/10.1534/g3.119.400549.

Novel bayesian networks for genomic prediction of developmental traits in biomass sorghum - (Peer Reviewed Journal)
Dos Santos, J.P., Fernandes, S.B., Lozano, R., Brown, P.K., Buckler IV, E.S., Garcia, A.A., Gore, M.A. 2019. Novel bayesian networks for genomic prediction of developmental traits in biomass sorghum. bioRxiv. https://doi.org/10.1101/677179.

Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites - (Review Article)
Shaoqun, Z., Kremling, K.A., Bandillo, N., Richter, A., Zhang, Y.K., Ahern, K.R., Artyukhin, A.B., Hui, J.X., Younkin, G.C., Schroeder, F.C., Buckler IV, E.S., Jander, G. 2019. Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites. The Plant Cell. 31:937-955. https://doi.org/10.1105/tpc.18.00772.

k-mer grammar uncovers maize regulatory architecture - (Review Article)
Mejia-Guerra, M., Buckler IV, E.S. 2019. k-mer grammar uncovers maize regulatory architecture. Biomed Central (BMC) Plant Biology. 19:103. https://doi.org/10.1186/s12870-019-1693-2.

Multiple maize reference genomes impact the identification of variants by genome-wide association study in a diverse inbred panel - (Peer Reviewed Journal)
Gage, J.L., Vaillancourt, B., Hamilton, J.P., Manrique-Carpintero, N.C., Gustafson, T.J., Barry, K., Lipzen, A., Tracy, W.F., Mikel, M.A., Kaeppler, S.M., Buell, R.C., De Leon, N. 2019. Multiple maize reference genomes impact the identification of variants by genome-wide association study in a diverse inbred panel. The Plant Genome. 12:2. https://doi.org/10.3835/plantgenome2018.09.0069.

Evolutionarily informed deep learning methods: Predicting transcript abundance from DNA sequence - (Review Article)
Washburn, J.D., Mejia Guerra, M., Ramstein, G., Kremling, K., Valluru, R., Buckler IV, E.S., Wang, H. 2019. Evolutionarily informed deep learning methods: Predicting transcript abundance from DNA sequence. Proceedings of the National Academy of Sciences. 116(12):5542-5549. https://doi.org/10.1073/pnas.1814551116.

Deleterious mutation burden and its association with complex traits in sorghum (sorghum bicolor) - (Peer Reviewed Journal)
Valluru, R., Gazave, E., Fernandes, S., Ferguson, J., Lazano, R., Hirannaiah, P., Zuo, T., Brown, P., Leakey, A., Gore, M., Buckler IV, E.S., Bandillo, N. 2019. Deleterious mutation burden and its association with complex traits in sorghum (sorghum bicolor). Genetics. 211(3):1075-1087. https://doi.org/10.25386/genetics.7638122.

Breaking the curse of dimensionality to identify causal variants in Breeding 4 - (Review Article)
Ramstein, G.P., Jensen, S.E., Buckler IV, E.S. 2019. Breaking the curse of dimensionality to identify causal variants in Breeding 4. Theoretical and Applied Genetics. 132(3):559-567. https://doi.org/10.1007/s00122-018-3267-3.

On the road to breeding 4.0: unraveling the good, the bad, and the boring of crop quantitative genomics - (Peer Reviewed Journal)
Wallace, J.G., Rodgers-Melnick, E., Buckler IV, E.S. 2018. On the road to breeding 4.0: unraveling the good, the bad, and the boring of crop quantitative genomics. Annual Review of Genetics. 52(1)421-444. https://doi.org/10.1146/annurev-genet-120116-024846.

Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots - (Review Article)
Zhou, S., Zhang, Y., Kremling, K., Ding, Y., Bennett, J., Bae, J., Kim, D., Kolomiets, M., Schmelz, E., Schroeder, F., Buckler Iv, E.S., Jander, G. 2018. Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots. New Phytologist. 221(4):2096-2111. https://doi.org/10.1111/nph.15520.

Co-regulation of ribosomal RNA with hundreds of genes contributes to phenotypic variations - (Peer Reviewed Journal)
Li, B., Kremling, K., Wu, P., Bukowski, R., Romay, M., Xie, E., Buckler IV, E.S., Chen, M. 2018. Co-regulation of ribosomal RNA with hundreds of genes contributes to phenotypic variations. Genome Research. https://doi.org/10.1101/gr.229716.117.

Quantitative genetics of the maize leaf microbiome - (Review Article)
Wallace, J., Kremling, K., Buckler IV, E.S. 2019. Quantitative genetic analysis of the maize leaf microbiome. Phytobiomes Journal. 2(4):208-224. https://doi.org/10.1094/PBIOMES-02-18-0008-R.

Genome-wide association and genomic prediction models of tocochromanols in fresh sweet corn kernels - (Review Article)
Baseggio, M., Murray, M., Magallanes-Lundback, M., Kaczmar, N., Chamness, J., Buckler IV, E.S., Smith, M.E., Dellapenna, D., Tracy, W.F., Gore, M.A. 2018. Genome-wide association and genomic prediction models of tocochromanols in fresh sweet corn kernels. The Plant Genome. 12:180038. https://doi.org/10.3835/plantgenome2018.06.0038.

RNA polymerase mapping in plants identifies enhancers enriched in causal variants - (Review Article)
Lozano, R., Booth, G.T., Omar, B.Y., Li, B., Buckler IV, E.S., Lis, J.T., Jannink, J., Pino Del Carpio, D. 2018. RNA polymerase mapping in plants identifies enhancers enriched in causal variants. bioRxiv. https://doi.org/10.1101/376640.

Leveraging mutational burden for complex trait prediction in sorghum - (Review Article)
Valluru, R., Gazave, E.E., Fernandes, S.B., Ferguson, J.N., Lozano, R., Hirannaiah, P., Zuo, T., Brown, P.J., Leakey, A.D., Gore, M., Buckler IV, E.S., Bandillo, N. 2018. Leveraging mutational burden for complex trait prediction in sorghum. bioRxiv. https://doi.org/10.1101/357418.

Maize genomes to fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets - (Peer Reviewed Journal)
Alkhalifah, N., Campbell, D., Falcon, C., Miller, N., Romay, M., Walls, R., Walton, R., Yeh, C., Bohn, M., Buckler IV, E.S., Ciampitti, I., Flint Garcia, S.A., Gore, M., Graham, C., Hirsch, C., Holland, J.B., Hooker, D., Kaeppler, S., Knoll, J.E., Lauter, N.C., Lee, E., Lorenz, A., Lynch, J., Moose, S., Murray, S., Nelson, R., Rocheford, T., Rodriguez, O., Schnable, J., Scully, B.T., Smith, M., Springer, N., Thomison, P., Tuinstra, M., Wisser, R., Xu, W., Ertl, D., Schnable, P., De Leon, N., Spalding, E., Edwards, J.W., Lawrence-Dill, C. 2018. Maize genomes to fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. Biomed Central (BMC) Plant Biology. 11:452. https://doi.org/10.1186/s13104-018-3508-1.

Large-scale replicated field study of maize rhizosphere identifies heritable microbes - (Peer Reviewed Journal)
Walters, W.A., Jin, Z., Youngblut, N., Wallace, J.G., Sutter, J., Zhang, W., González-Peña, A., Peiffer, J., Koren, O., Shi, Q., Knight, R., Glavina Del Rio, T., Tringe, S.G., Buckler IV, E.S., Dangl, J.L., Ley, R.E. 2018. Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proceedings of the National Academy of Sciences. 115(28):7368-7373.

Predicting gene structure changes resulting from genetic variants via exon definition features - (Peer Reviewed Journal)
Majoros, W., Holt, C., Campbell, M., Ware, D., Yandell, M., Reddy, T. 2018. Predicting gene structure changes resulting from genetic variants via exon definition features. Bioinformatics. 34(21):3616-3623.

Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize - (Peer Reviewed Journal)
Li, Y., Chen, L., Bradbury, P., Shi, Y., Song, Y., Zhang, D., Zhang, Z., Buckler IV, E.S., Li, Y., Wang, T. 2018. Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize. Nature Scientific Reports. (8):6848. https://doi.org/10.1038/s41598-018-25304-z.

Construction of the third generation Zea mays haplotype map - (Peer Reviewed Journal)
Bukowski, R., Guo, X., Lu, Y., Zou, C., He, B., Rong, Z., Yang, B., Wang, B., Xu, D., Xie, C., Fan, L., Gao, S., Xy, X., Zhang, G., Li, Y., Jiao, Y., Doebley, J., Ross-Ibarra, J., Buffalo, V., Romay, C., Buckler IV, E.S., Wu, Y., Lai, J., Ware, D., Sun, Q. 2018. Construction of the third generation Zea mays haplotype map. Gigascience. 7(4):1-12.

Expanding the BLUP alphabet for genomic prediction adaptable to the genetic architectures of complex traits - (Peer Reviewed Journal)
Wang, J., Zhou, Z., Li, H., Liu, D., Zhang, Q., Bradbury, P., Buckler IV, E.S., Zhang, Z. 2018. Expanding the BLUP alphabet for genomic prediction adaptable to the genetic architectures of complex traits. Heredity. https://doi.org/10.1038/s41437-018-0075-0.

Novel loci underlie natural variation in vitamin E levels in maize grain - (Peer Reviewed Journal)
Diepenbrock, C., Kandianis, C., Lipka, A., Magallanes-Lundback, M., Vaillancourt, B., Gongora-Castillo, E., Wallace, J., Cepela, J., Mesberg, A., Bradbury, P., Ilut, D., Mateos-Hernandez, M., Hamilton, J., Owens, B., Tiede, T., Buckler IV, E.S., Rocheford, T., Buell, R., Gore, M., Dellapenna, D. 2017. Novel loci underlie natural variation in vitamin E levels in maize grain. The Plant Cell. 29(10):2374-2392. DOI: https://doi.org/10.1105/tpc.17.00475

Non-mendelian single-nucleotide polymorphism inheritance and atypical meiotic configurations are prevalent in hop - (Peer Reviewed Journal)
Zhang, D., Easterling, K., Pitra, N., Coles, M., Buckler IV, E.S., Bass, H., Matthews, P. 2017. Non-mendelian single-nucleotide polymorphism inheritance and atypical meiotic configurations are prevalent in hop. The Plant Genome. 10(3). https://doi.org/10.3835/plantgenome2017.04.0032.

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize - (Peer Reviewed Journal)
Yang, J., Mezmouk, S., Baumgarten, A., Buckler IV, E.S., Guill, K.E., McMullen, M., Mumm, R., Ross-Ibarra, J. 2017. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS Genetics. https://doi.org/10.1371/journal.pgen.1007019.

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments - (Peer Reviewed Journal)
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Development of a high-density linkage map and tagging leaf spot resistance in pearl millet uysing genotyping-by-sequencing markers - (Peer Reviewed Journal)
Punnuri, S.M., Wallace, J.G., Knoll, J.E., Hyma, K.E., Mitchell, S.E., Buckler IV, E.S., Varshney, R.K., Singh, B.P. 2016. Development of a high-density linkage map and tagging leaf spot resistance in pearl millet uysing genotyping-by-sequencing markers. The Plant Genome. 9(2):1-13.

Expanding maize genetic resources with predomestication alleles: Maize–teosinte introgression populations - (Peer Reviewed Journal)
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