@article{naveed_gandhi_billings_jones_campbell_jones_rustgi_2023, title={Alterations in Growth Habit to Channel End-of-Season Perennial Reserves towards Increased Yield and Reduced Regrowth after Defoliation in Upland Cotton (<i>Gossypium hirsutum</i> L.)}, volume={24}, ISSN={["1422-0067"]}, DOI={10.3390/ijms241814174}, abstractNote={Cotton (Gossypium spp.) is the primary source of natural textile fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an Upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time, and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified molecular markers associated with the gene expression traits via genome-wide association analysis using a 63 K SNP Array. Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed associations with expression traits. Of these 396 markers, 159 were mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated.}, number={18}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Naveed, Salman and Gandhi, Nitant and Billings, Grant and Jones, Zachary and Campbell, B. Todd and Jones, Michael and Rustgi, Sachin}, year={2023}, month={Sep} }
 @article{graham_park_billings_hulse-kemp_haigler_lobaton_2022, title={Efficient imaging and computer vision detection of two cell shapes in young cotton fibers}, volume={11}, ISSN={["2168-0450"]}, url={https://doi.org/10.1002/aps3.11503}, DOI={10.1002/aps3.11503}, abstractNote={Abstract}, journal={APPLICATIONS IN PLANT SCIENCES}, author={Graham, Benjamin P. and Park, Jeremy and Billings, Grant T. and Hulse-Kemp, Amanda M. and Haigler, Candace H. and Lobaton, Edgar}, year={2022}, month={Nov} }
 @article{billings_jones_rustgi_bridges_holland_hulse-kemp_campbell_2022, title={Outlook for Implementation of Genomics-Based Selection in Public Cotton Breeding Programs}, volume={11}, ISSN={["2223-7747"]}, url={https://doi.org/10.3390/plants11111446}, DOI={10.3390/plants11111446}, abstractNote={Researchers have used quantitative genetics to map cotton fiber quality and agronomic performance loci, but many alleles may be population or environment-specific, limiting their usefulness in a pedigree selection, inbreeding-based system. Here, we utilized genotypic and phenotypic data on a panel of 80 important historical Upland cotton (Gossypium hirsutum L.) lines to investigate the potential for genomics-based selection within a cotton breeding program’s relatively closed gene pool. We performed a genome-wide association study (GWAS) to identify alleles correlated to 20 fiber quality, seed composition, and yield traits and looked for a consistent detection of GWAS hits across 14 individual field trials. We also explored the potential for genomic prediction to capture genotypic variation for these quantitative traits and tested the incorporation of GWAS hits into the prediction model. Overall, we found that genomic selection programs for fiber quality can begin immediately, and the prediction ability for most other traits is lower but commensurate with heritability. Stably detected GWAS hits can improve prediction accuracy, although a significance threshold must be carefully chosen to include a marker as a fixed effect. We place these results in the context of modern public cotton line-breeding and highlight the need for a community-based approach to amass the data and expertise necessary to launch US public-sector cotton breeders into the genomics-based selection era.}, number={11}, journal={PLANTS-BASEL}, author={Billings, Grant T. and Jones, Michael A. and Rustgi, Sachin and Bridges, William C. and Holland, James B. and Hulse-Kemp, Amanda M. and Campbell, B. Todd}, year={2022}, month={Jun} }
 @article{brocke_billings_taft-benz_alexis_heise_jaspers_2022, title={Woodsmoke particle exposure prior to SARS-CoV-2 infection alters antiviral response gene expression in human nasal epithelial cells in a sex-dependent manner}, volume={322}, ISSN={["1522-1504"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85126152415&partnerID=MN8TOARS}, DOI={10.1152/ajplung.00362.2021}, abstractNote={ Inhalational exposure to particulate matter (PM) derived from natural or anthropogenic sources alters gene expression in the airways and increases susceptibility to respiratory viral infection. Woodsmoke-derived ambient PM from wildfire events during 2020 was associated with higher COVID-19 case rates in the western United States. We hypothesized that exposure to suspensions of woodsmoke particles (WSPs) or diesel exhaust particles (DEPs) prior to SARS-CoV-2 infection would alter host immune gene expression at the transcript level. Primary human nasal epithelial cells (hNECs) from both sexes were exposed to WSPs or DEPs (22 μg/cm2) for 2 h, followed by infection with SARS-CoV-2 at a multiplicity of infection of 0.5. Forty-six genes related to SARS-CoV-2 entry and host response were assessed. Particle exposure alone minimally affected gene expression, whereas SARS-CoV-2 infection alone induced a robust transcriptional response in hNECs, upregulating type I and III interferons, interferon-stimulated genes, and chemokines by 72 h postinfection (p.i.). This upregulation was higher overall in cells from male donors. However, exposure to WSPs prior to infection dampened expression of antiviral, interferon, and chemokine mRNAs. Sex stratification of these results revealed that WSP exposure downregulated gene expression in cells from females more so than males. We next hypothesized that hNECs exposed to particles would have increased apical viral loads compared with unexposed cells. Although apical viral load was correlated to expression of host response genes, viral titer did not differ between groups. These data indicate that WSPs alter epithelial immune responses in a sex-dependent manner, potentially suppressing host defense to SARS-CoV-2 infection. }, number={3}, journal={AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY}, author={Brocke, Stephanie A. and Billings, Grant T. and Taft-Benz, Sharon and Alexis, Neil E. and Heise, Mark T. and Jaspers, Ilona}, year={2022}, month={Mar}, pages={L479–L494} }
 @article{billings_jones_rustgi_hulse-kemp_campbell_2021, title={Population structure and genetic diversity of the Pee Dee cotton breeding program}, volume={11}, ISSN={["2160-1836"]}, url={https://doi.org/10.1093/g3journal/jkab145}, DOI={10.1093/g3journal/jkab145}, abstractNote={Abstract}, number={7}, journal={G3-GENES GENOMES GENETICS}, publisher={Oxford University Press (OUP)}, author={Billings, Grant T. and Jones, Michael A. and Rustgi, Sachin and Hulse-Kemp, Amanda M. and Campbell, B. Todd}, year={2021}, month={Jul} }
 @article{kaiser_billings_coombs_buell_enciso-rodriguez_douches_2021, title={Self-fertility and resistance to the Colorado potato beetle (Leptinotarsa decemlineata) in a diploid Solanum chacoense recombinant inbred line population}, volume={7}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85111138436&partnerID=MN8TOARS}, DOI={10.1002/csc2.20534}, abstractNote={Abstract}, number={5}, journal={CROP SCIENCE}, author={Kaiser, Natalie R. and Billings, Grant and Coombs, Joseph and Buell, C. Robin and Enciso-Rodriguez, Felix and Douches, David S.}, year={2021}, month={Jul} }
 @article{brocke_billings_taft-benz_alexis_heise_jaspers_2021, title={Woodsmoke particulates alter expression of antiviral host response genes in human nasal epithelial cells infected with SARS-CoV-2 in a sex-dependent manner}, volume={8}, url={https://doi.org/10.1101/2021.08.23.457411}, DOI={10.1101/2021.08.23.457411}, abstractNote={Abstract}, journal={bioRxiv}, publisher={Cold Spring Harbor Laboratory}, author={Brocke, Stephanie A. and Billings, Grant T. and Taft-Benz, Sharon and Alexis, Neil E. and Heise, Mark T. and Jaspers, Ilona}, year={2021}, month={Aug} }