@article{barnes_myers_surber_liang_mower_schnable_roston_2023, title={Oligogalactolipid production during cold challenge is conserved in early diverging lineages}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/erad241}, abstractNote={Severe cold, defined as a damaging cold beyond acclimation temperatures, has unique responses, but the signaling and evolution of these responses are not well understood. Production of oligogalactolipids, which is triggered by cytosolic acidification in Arabidopsis (Arabidopsis thaliana), contributes to survival in severe cold. Here, we investigated oligogalactolipid production in species from bryophytes to angiosperms. Production of oligogalactolipids differed within each clade, suggesting multiple evolutionary origins of severe cold tolerance. We also observed greater oligogalactolipid production in control samples instead of temperature-challenged samples of some species. Further examination of representative species revealed a tight association between temperature, damage, and oligogalactolipid production that scaled with the cold tolerance of each species. Based on oligogalactolipid production and transcript changes, multiple angiosperm species share a signal of oligogalactolipid production initially described in Arabidopsis, cytosolic acidification. Together, these data suggest that oligogalactolipid production is a severe cold response that originated from an ancestral damage response that remains in many land plant lineages and that cytosolic acidification may be a common signaling mechanism for its activation.}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Barnes, Allison C. and Myers, Jennifer L. and Surber, Samantha M. and Liang, Zhikai and Mower, Jeffrey P. and Schnable, James C. and Roston, Rebecca L.}, year={2023}, month={Jun} }
 @article{barnes_rodriguez-zapata_juarez-nunez_gates_janzen_kur_wang_jensen_estevez-palmas_crow_et al._2022, title={An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time}, volume={119}, ISSN={["1091-6490"]}, url={http://dx.doi.org/10.1073/pnas.2100036119}, DOI={10.1073/pnas.2100036119}, abstractNote={Native Americans domesticated maize ( Zea mays ssp. mays ) from lowland teosinte parviglumis ( Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 ( HPC1 ), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.}, number={27}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Barnes, Allison C. and Rodriguez-Zapata, Fausto and Juarez-Nunez, Karla A. and Gates, Daniel J. and Janzen, Garrett M. and Kur, Andi and Wang, Li and Jensen, Sarah E. and Estevez-Palmas, Juan M. and Crow, Taylor M. and et al.}, year={2022}, month={Jul} }
 @misc{abraham-juarez_barnes_aragon-raygoza_tyson_kur_strable_rellan-alvarez_2021, title={The arches and spandrels of maize domestication, adaptation, and improvement}, volume={64}, ISSN={["1879-0356"]}, url={https://doi.org/10.1016/j.pbi.2021.102124}, DOI={10.1016/j.pbi.2021.102124}, abstractNote={People living in the Balsas River basin in southwest México domesticated maize from the bushy grass teosinte. Nine thousand years later, in 2021, Ms. Deb Haaland - a member of the Pueblo of Laguna tribe of New Mexico - wore a dress adorned with a cornstalk when she was sworn in as the Secretary of Interior of the United States of America. This choice of garment highlights the importance of the coevolution of maize and the farmers who, through careful selection over thousands of years, domesticated maize and adapted the physiology and shoot architecture of maize to fit local environments and growth habits. Some traits such as tillering were directly selected on (arches), and others such as tassel size are the by-products (spandrels) of maize evolution. Here, we review current knowledge of the underlying cellular, developmental, physiological, and metabolic processes that were selected by farmers and breeders, which have positioned maize as a top global staple crop.}, journal={CURRENT OPINION IN PLANT BIOLOGY}, publisher={Elsevier BV}, author={Abraham-Juarez, Maria Jazmin and Barnes, Allison C. and Aragon-Raygoza, Alejandro and Tyson, Destiny and Kur, Andi and Strable, Josh and Rellan-Alvarez, Ruben}, year={2021}, month={Dec} }
 @article{barnes_barnes_knezevic_lawrence_jhala_2020, title={Risk assessment of pollen-mediated gene flow from Ga1-m field corn to dent-sterile Ga1-s popcorn}, volume={60}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20254}, abstractNote={1 Dep. of Agronomy and Horticulture, Univ. of Nebraska‒Lincoln, Lincoln, NE 68583, USA 2 Biology Data Management Scientist, GreenLight Biosciences, Research Triangle Park, NC 27709, USA 3 Dep. of Biochemistry, Univ. of Nebraska‒Lincoln, Lincoln, NE 68588, USA 4 Molecular and Structural Biochemistry, North Carolina State Univ., Raleigh, NC 27695, USA 5 Northeast Research and Extension Center, Haskell Agricultural Lab., Univ. of Nebraska‒Lincoln, Concord, NE 68728, USA 6 Panhandle Research and Extension Center, Univ. of Nebraska‒Lincoln, Scottsbluff, NE 69361, USA}, number={6}, journal={CROP SCIENCE}, author={Barnes, Ethann R. and Barnes, Allison C. and Knezevic, Stevan Z. and Lawrence, Nevin C. and Jhala, Amit J.}, year={2020}, pages={3278–3290} }