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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Research Project #434435

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

Location: Plant, Soil and Nutrition Research

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

Elucidating the patterns of pleiotropy and its biological relevance in maize Reprint Icon - (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. Reprint Icon - (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.

An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.

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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.

Underground heterosis for yield improvement in melon Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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) Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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)
Varshney, R., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S., Wang, H., Jiang, Y., Couderc, M., Katta, M., Paudel, D., Mungra, K., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N., Conner, J., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H., Cubry, P., Rhoné, B., Gueye, M., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R., Singh, B., Yadav, R., Lyons, E., Datta, S., Hash, C., Devos, K., Buckler IV, E.S., Bennetzen, J., Paterson, A.H., Ozias-Akins, P., Grando, S., Wang, J., Mohapatra, T., Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y., Xu, X. 2017. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Communications. 35(10):969.

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)
Liu, Z., Cook, J., Melia-Hancock, S., Guill, K.E., Bottoms, C., Garcia, A., Ott, O., Nelson, R., Reckerd, J., Balint Kurti, P.J., Larsson, S., Lepak, N.K., Buckler IV, E.S., Trimble, L., Tracy, W., McMullen, M.D., Flint Garcia, S.A. 2016. Expanding maize genetic resources with predomestication alleles: Maize–teosinte introgression populations. The Plant Genome. (9):1.