Publications

2025

• The relationships among alkaloid concentration, endophyte mycelial concentration and host genetics in the tall fescue-Epichloë symbiosis
  Talamantes DR, Phillips C, Young C, Wallace JG: . BMC Genomics 2025, doi:10.1186/s12864-025-12331-0.
• Gene-by-environment interaction significantly drives bacterial endophyte communities in maize stalks (PREPRINT)
  Li H, Griffis HK, Edwards J, Flint-Garcia S, Hirsch CN, Holland JB, Knoll JE, Lima DC, Leon N de, Murray SC, et al. 2025, doi:10.64898/2025.12.23.696053.
• Identification of candidate genes for stigma color using a genome-wide association study in centipedegrass
  Harris-Shultz K, Wallace J, Sapkota S, Schwartz B, Read QD, Peterson J, Santana AL, Smolensky D, Coffin A: . Crop Science 2025, 65. doi: 10.1002/csc2.70185.
• Aerial root formation in oaxacan maize (Zea mays) landraces persists into the adult phase and is minimally affected by soil nitrogen and ambient humidity
  Venado RE, Wilker J, Infante V, McLimans C, Robbins F, Phillips C, Calderón CI, Wallace JG, Ané J-M. Frontiers in Plant Science 2025, 16. doi: 10.3389/fpls.2025.1607733
• Identifying associations between maize leaf transcriptome and bacteriome during different diurnal periods (PREPRINT)
  Santos RAC dos, Hidalgo-Martinez K, Muñoz Perez JM, Laspisa DJ, Li C, Mendes LW, Riaño-Pachón DM, Wallace JG, 2025, doi: 10.1101/2025.07.11.664371.
• Mapping QTLs for pyricularia leaf spot, nematode resistance, and yield related traits in pearl millet [Cenchrus americanus (l.) morrone]
  Vutla S, Knoll JE, Sankuratri A, Nayak RG, Liu L, Chee PW, Karthikeyan R, Fakrudin B, Thudi M, Timper P, et al.: Frontiers in Plant Science 2025, 16. doi: 10.3389/fpls.2025.1588485
• Genetic dissection of lint percentage and seed cotton yield in exotic x elite upland cotton crosses using population-specific and joint population analysis
  Mangla H, Liu M, Vitrakoti D, Shehzad T, Chandnani R, Das S, Wallace JG, Snider JL, Jones DC, Chee PW, et al. Euphytica 2025, 221. doi: 10.1007/s10681-025-03549-w
• Genetic determinants of aerial root traits that support biological nitrogen fixation in maize (PREPRINT)
  Laspisa D, Venado R, Diogo R, Ané J-M, Wallace JG, 2025, doi: 10.1101/2025.05.30.657053.
• Identification of favorable alleles from exotic upland cotton lines for fiber quality improvement using multiple association models
  Mangla H, Liu M, Vitrakoti D, Somala RV, Shehzad T, Chandnani R, Das S, Wallace JG, Snider JL, Jones DC, et al., Frontiers in Plant Science 2025, 16. doi: 10.3389/fpls.2025.1553514

2024

• Sampling and analysis of the maize microbiome
  Wallace JG, Favela A, Raglin S. Cold Spring Harbor Protocols 2024, doi:10.1101/pdb.top108463.
  • Sampling root-associated microbiome communities of maize (zea mays)
    Favela A, Raglin S, Wallace JG. Cold Spring Harbor Protocols 2024, doi:10.1101/pdb.prot108580.
  • Sampling the maize (Zea mays) leaf microbiome
    Wallace JG. Cold Spring Harbor Protocols 2024, doi:10.1101/pdb.prot108581.
  • Sampling maize (Zea mays) seed endophytes
    Wallace JG, Laspisa D. Cold Spring Harbor Protocols 2024, doi:10.1101/pdb.prot108582.
  • Preparation of illumina 16s amplicon sequencing libraries with peptide nucleic acids (PNAs) for the analysis of maize-associated microbiomes
    Wallace JG, Griffis H. Cold Spring Harbor Protocols 2024, doi:10.1101/pdb.prot108583.
  • Manipulating the maize (Zea mays) microbiome
    Raglin SS, Favela A, Laspisa D, Wallace JG. Cold Spring Harbor Protocols 2024, doi:10.1101/pdb.prot108584.
• Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (panicum miliaceum l.)
  Vetriventhan M, Upadhyaya HD, Deshpande S, Johnson MS, Wallace JG, Victor A, Naresh D, Rayaprolu L, Singh K, Mayes S. Scientific Reports 2024, 14.
• Metagenomic analysis of a glacial ice core record from the contiguous United States.
  Kvitko B, Wallace J, Desai HV, Lavender HF, Mijatovic J, Techtmann S, Christner BC, Smith A. 2024, doi:10.21203/rs.3.rs-5045654/v1.
• Data-driven identification of environmental variables influencing phenotypic plasticity to facilitate breeding for future climates
  Kusmec A, Yeh C ‘Eddy’, Schnable PS., Genomes to Fields. New Phytologist 2024, 244:618–634.
• Soybean microbiome composition and the impact of host plant resistance
  Tran DT, Mitchum MG, Zhang S, Wallace JG, Li Z. Frontiers in Plant Science 2024, 14.
• Genomic selection as an approach to select for reduced aflatoxin contamination in peanut under terminal drought stress
  Gimode D, Wallace J, Holbrook C, Isleib TG, Chu Y, Virk S, Porter W, Ozias-Akins P. Peanut Science 2024, 51:18–31.
• High-density genotyping for pearl millet linkage map improvement with next-generation sequencing data
  Punnuri S, Wallace J, Knoll J. The pearl millet genome 2024, doi:10.1007/978-3-031-56976-0_7.
• Developing robust quantitative PCR primers for comparative biomass analysis of tall fescue (Festuca arundinacea) and its Epichloë endophyte
  Talamantes D, Kirkpatrick C, Wallace J. microPublication Biology 2024, doi:10.17912/micropub.biology.001275.

2023

• kGWASflow: a modular, flexible, and reproducible Snakemake workflow for k-mers-based GWAS.
  Corut, Adnan Kivanc; Wallace, Jason G. G3: Genes, Genomes, Genetics 14 (1) DOI: 10.1093/g3journal/jkad246.
• Mining the Utricularia gibba genome for insulator-like elements for genetic engineering.
  Laspisa, Daniel; llla-Berenguer, Eudald; Bang, Sohyun; Schmitz, Robert J.; Parrott, Wayne et al. Frontiers in Plant Science 14 DOI: 10.3389/fpls.2023.1279231.
• 2020-2021 field seasons of Maize GxE project within the Genomes to Fields Initiative.
  Lima, Dayane Cristina; Aviles, Alejandro Castro; Alpers, Ryan Timothy; Perkins, Alden; Schoemaker, Dylan L et al. BMC Research Notes 16 (1) DOI: 10.1186/s13104-023-06430-y.
• Genomes to Fields 2022 Maize genotype by Environment Prediction Competition.
  Dayane Cristina Lima; Jacob D. Washburn; José Ignacio Varela; Qiuyue Chen; Joseph L. Gage et al. BMC Research Notes 16 (1) DOI: 10.1186/s13104-023-06421-z.
• A perennial living mulch system fosters a more diverse and balanced soil bacterial community. Hanxia Li, Nicholas Hill, Jason G. Wallace. PLoS ONE 18(8): e0290608. DOI: 10.1371/journal.pone.0290608
• Genetic mapping and prediction for novel lesion mimic in maize demonstrates quantitative effects from genetic background, environment and epistasis.
  Alper Adak; Seth C. Murray; Claudia Irene Calderon; Valentina Infante; Jennifer Wilker et al. Theoretical and Applied Genetics 136 (7) DOI: 10.1007/s00122-023-04394-y.
• 2018-2019 field seasons of the Maize Genomes to Fields (G2F) G x E project.
  Dayane Cristina Lima; Alejandro Castro Aviles; Ryan Timothy Alpers; Bridget A. McFarland; Shawn Kaeppler et al. BMC Genomic Data 24 (1) DOI: 10.1186/s12863-023-01129-2.
• Effects of Inbreeding on Microbial Community Diversity of Zea mays.
  Corey R. Schultz; Matthew Johnson; Jason G. Wallace. Microorganisms 11 (4): 879. DOI: 10.3390/microorganisms11040879.
• Yield prediction through integration of genetic, environment, and management data through deep learning.
  Daniel R Kick; Jason G Wallace; James C Schnable; Judith M Kolkman; Barış Alaca et al. G3 Genes|Genomes|Genetics 13 (4) DOI: 10.1093/g3journal/jkad006.

2022

• Maize seed endophytes. 
  Jason G. Wallace. Molecular Plant Pathology DOI: 10.1111/mpp.13278.
• Identification of small effect quantitative trait loci of plant architectural, flowering, and early maturity traits in reciprocal interspecific introgression population in cotton. 
  Rahul Chandnani; Changsoo Kim; Jinesh D. Patel; Hui Guo; Tariq Shehzad et al. Frontiers in Plant Science 13 DOI: 10.3389/fpls.2022.981682.
• Genome-wide association mapping of resistance to the sorghum aphid in Sorghum bicolor. 
  Somashekhar M. Punnuri; Addissu G. Ayele; Karen R. Harris-Shultz; Joseph E. Knoll; Alisa W. Coffin et al. Genomics 114 (4): 110408. DOI: 10.1016/j.ygeno.2022.110408.
• The role of genetic variation in Zea mays response to beneficial endophytes. 
  Corey R. Schultz; Kamaya M. Brantley; Jason G. Wallace. Plant Growth Regulation 98 (1): 167–177. DOI: 10.1007/s10725-022-00842-9.

2021

• Genetic diversity assessment of Georgia peanut cultivars developed during ninety years of breeding. 
  Nino Brown; William D. Branch; Matthew Johnson; Jason Wallace. The Plant Genome 14 (3) DOI: 10.1002/tpg2.20141.
• White clover living mulch enhances soil health vs. annual cover crops. 
  Nicholas S. Hill; Matthew Levi; Nicholas Basinger; Aaron Thompson; Miguel Cabrera et al. Agronomy Journal 113 (4): 3697–3707. DOI: 10.1002/agj2.20768.
• Comparing DNA Extraction and 16S rRNA Gene Amplification Methods for Plant-Associated Bacterial Communities. 
  Giangacomo, Cecelia; Mohseni, Mohsen; Kovar, Lynsey L; Wallace, Jason. Phytobiomes Journal 0 (ja): null. DOI: 10.1094/PBIOMES-07-20-0055-R.
• Genomic and Chemical Diversity of Commercially Available High-CBD Industrial Hemp Accessions. 
  Johnson, Matthew S.; Wallace, Jason G. Frontiers in Genetics 12: 1160. DOI: 10.3389/fgene.2021.682475.
• Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis). 
  Xuewen Wang; Shiyu Chen; Xiao Ma; Anna E J Yssel; Srinivasa R Chaluvadi et al. GigaScience 10 (3) DOI: 10.1093/gigascience/giab013.

2020

• Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain. 
  Christine H Diepenbrock; Daniel C Ilut; Maria Magallanes-Lundback; Catherine B Kandianis; Alexander E Lipka et al. The Plant Cell 33 (4): 882–900. DOI: 10.1093/plcell/koab032.
• Maize genomes to fields (G2F): 2014-2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets. 
  McFarland, Bridget A.; AlKhalifah, Naser; Bohn, Martin; Bubert, Jessica; Buckler, Edward S. et al. BMC Research Notes 13 (1): 71. DOI: 10.1186/s13104-020-4922-8.

2019

• Genome-Wide Population Structure Analyses of Three Minor Millets: Kodo Millet, Little Millet, and Proso Millet. 
  Johnson, Matthew; Deshpande, Santosh; Vetriventhan, Mani; Upadhyaya, Hari D; Wallace, Jason G. The Plant Genome 12 (3): 1-9. DOI: 10.3835/plantgenome2019.03.0021.
• A Novel QTL for Root-Knot Nematode Resistance is Identified from a South African Sweet Sorghum Line. 
  Harris-Shultz, Karen R.; Davis, Richard F.; Wallace, Jason; Knoll, Joseph E.; Wang, Hongliang. Phytopathology 109 (6): 1011-1017. DOI: 10.1094/PHYTO-11-18-0433-R.

2018

• Deep Learning at the Edge.
  Sahar Voghoei; N. H. Tonekaboni; Jason G. Wallace; Hamid R. Arabnia. Proceedings of the 2018 International Conference on Computational Science and Computational Intelligence (): . DOI: 10.1109/CSCI.2018.00176.
• On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics. 
  Jason G. Wallace; Eli Rodgers-Melnick; Edward S. Buckler. Annual Review of Genetics 52 (1): 421–444. DOI: 10.1146/annurev-genet-120116-024846.
• Quantitative Genetics of the Maize Leaf Microbiome. 
  Jason Wallace; Karl A. Kremling; Lynsey L Kovar; Edward S Buckler. Phytobiomes Journal DOI: 10.1094/pbiomes-02-18-0008-r.
• Genetic Analysis of Fiber Quality Traits in Reciprocal Advanced Backcross Populations. 
  Rahul Chandnani; Changsoo Kim; Hui Guo; Tariq Shehzad; Jason G. Wallace et al. The Plant Genome 11 (1): 0. DOI: 10.3835/plantgenome2017.06.0057.
• Endophytes: The Other Maize Genome.
  Jason G. Wallace; Georgiana May. : 213–246. DOI: 10.1007/978-3-319-97427-9_14.
• Large-scale replicated field study of maize rhizosphere identifies heritable microbes. 
  William A. Walters; Zhao Jin; Nicholas Youngblut; Jason G. Wallace; Jessica Sutter et al. Proceedings of the National Academy of Sciences 115 (28): 7368–7373. DOI: 10.1073/pnas.1800918115.
• A Kinesin-14 Motor Activates Neocentromeres to Promote Meiotic Drive in Maize. 
  R. Kelly Dawe; Elizabeth G. Lowry; Jonathan I. Gent; Michelle C. Stitzer; Kyle W. Swentowsky et al. Cell 173 (4): 839–850.e18. DOI: 10.1016/j.cell.2018.03.009.
• Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map.
  Anna Pucher; C. Tom Hash; Jason G. Wallace; Sen Han; Willmar L. Leiser et al. BMC Plant Biology 18 (1) DOI: 10.1186/s12870-018-1267-8.

2017

• Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. 
  Rajeev K Varshney; Chengcheng Shi; Mahendar Thudi; Cedric Mariac; Jason Wallace et al. Nature Biotechnology 35 (10): 969–976. DOI: 10.1038/nbt.3943.
• Maize YABBY Genes drooping leaf1 and drooping leaf2 Regulate Plant Architecture . 
  Josh Strable; Jason G. Wallace; Erica Unger-Wallace; Sarah Briggs; Peter J. Bradbury et al. The Plant Cell 29 (7): 1622–1641. DOI: 10.1105/tpc.16.00477.
• Genotyping-by-Sequencing.
  Wallace, Jason G.; Mitchell, Sharon E. Current Protocols in Plant Biology2 (1): 64-77. DOI: 10.1002/cppb.20042 .
  • Preprint
  • Supplemental Data
• Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain. 
  Diepenbrock, Christine H.; Kandianis, Catherine B.; Lipka, Alexander E.; Magallanes-Lundback, Maria; Vaillancourt, Brieanne et al. The Plant Cell 29 (10): 2374–2392. DOI: 10.1105/tpc.17.00475.

2016

• Fast-Flowering Mini-Maize: Seed to Seed in 60 Days. 
  Morgan E. McCaw; Jason G. Wallace; Patrice S. Albert; Edward S. Buckler; James A. Birchler. Genetics 204 (1): 35–42. DOI: 10.1534/genetics.116.191726.
• Genome-wide Association for Plant Height and Flowering Time across 15 Tropical Maize Populations under Managed Drought Stress and Well-Watered Conditions in Sub-Saharan Africa. 
  Jason G. Wallace; Xuecai Zhang; Yoseph Beyene; Kassa Semagn; Michael Olsen et al. Crop Science 56 (5): 2365. DOI: 10.2135/cropsci2015.10.0632.
• Development of a High-Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping-by-Sequencing Markers. 
  Somashekhar M. Punnuri; Jason G. Wallace; Joseph E. Knoll; Katie E. Hyma; Sharon E. Mitchell et al. The Plant Genome 9 (2): 0. DOI: 10.3835/plantgenome2015.10.0106.

2015

• Population Genetics and Structure of a Global Foxtail Millet Germplasm Collection. 
  Hari D. Upadhyaya; Mani Vetriventhan; Santosh P. Deshpande; Selvanayagam Sivasubramani; Jason G. Wallace et al. The Plant Genome 8 (3): 0. DOI: 10.3835/plantgenome2015.07.0054.
• The Genetic Makeup of a Global Barnyard Millet Germplasm Collection.
  Jason G. Wallace; Hari D. Upadhyaya; M. Vetriventhan; Edward S. Buckler; C. Tom Hash et al. The Plant Genome 8 (1): 0. DOI: 10.3835/plantgenome2014.10.0067.
• Genome-Wide Association of Carbon and Nitrogen Metabolism in the Maize Nested Association Mapping Population. 
  Zhang, Nengyi; Gibon, Yves; Wallace, Jason G.; Lepak, Nicholas; Li, Pinghua et al. Plant Physiology 168 (2): 575–583. DOI: 10.1104/pp.15.00025.

2014 and prior

• Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize. 
  Wallace, Jason G.; Bradbury, Peter J.; Zhang, Nengyi; Gibon, Yves; Stitt, Mark et al. PLoS Genet 10 (12): e1004845. DOI: 10.1371/journal.pgen.1004845.
• Entering the second century of maize quantitative genetics. 
  J G Wallace; S J Larsson; E S Buckler. Heredity 112 (1): 30–38. DOI: 10.1038/hdy.2013.6.
• OLE RNA protects extremophilic bacteria from alcohol toxicity. 
  Wallace, Jason G.; Zhou, Zhiyuan; Breaker, Ronald R. Nucleic Acids Research 40 (14): 6898-6907. DOI: 10.1093/nar/gks352.
• Association of OLE RNA with bacterial membranes via an RNA–protein interaction. 
  Block, Kirsten F.; Puerta-Fernandez, Elena; Wallace, Jason G.; Breaker, Ronald R. Molecular Microbiology 79 (1): 21–34. DOI: 10.1111/j.1365-2958.2010.07439.x.
• Improved genetic transformation methods for the model alkaliphile Bacillus halodurans C-125.
  Wallace, J.G.; Breaker, R.R. Letters in Applied Microbiology 52 (4): 430–432. DOI: 10.1111/j.1472-765X.2011.03017.x.