Publications

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.