@article{hislop_luby_loarca_humann_hummer_bassil_zhao_sheehan_casa_billings_et al._2024, title={A Blueberry (<i> Vaccinium</i> L.) Crop Ontology to Enable Standardized Phenotyping for Blueberry Breeding and Research}, volume={59}, ISSN={["2327-9834"]}, DOI={10.21273/HORTSCI17676-23}, abstractNote={Breeding programs around the world continually collect data on large numbers of individuals. To be able to combine data collected across regions, years, and experiments, research communities develop standard operating procedures for data collection and measurement. One such method is a crop ontology, or a standardized vocabulary for collecting data on commonly measured traits. The ontology is also computer readable to facilitate the use of data management systems such as databases. Blueberry breeders and researchers across the United States have come together to develop the first standardized crop ontology in blueberry ( Vaccinium spp.). We provide an overview and report on the construction of the first blueberry crop ontology and the 178 traits and methods included within. Researchers of Vaccinium species—such as other blueberry species, cranberry, lingonberry, and bilberry—can use the described crop ontology to collect phenotypic data of greater quality and consistency, interoperability, and computer readability. Crop ontologies, as a shared data language, benefit the entire worldwide research community by enabling collaborative meta-analyses that can be used with genomic data for quantitative trait loci, genome-wide association studies, and genomic selection analysis.}, number={10}, journal={HORTSCIENCE}, author={Hislop, Lillian M. and Luby, Claire H. and Loarca, Jenyne and Humann, Jodi and Hummer, Kim E. and Bassil, Nahla and Zhao, Dongyan and Sheehan, Moira J. and Casa, Alexandra M. and Billings, Grant T. and et al.}, year={2024}, month={Oct}, pages={1433–1442} }
 @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={AbstractPremiseThe shape of young cotton (Gossypium) fibers varies within and between commercial cotton species, as revealed by previous detailed analyses of one cultivar of G. hirsutum and one of G. barbadense. Both narrow and wide fibers exist in G. hirsutum cv. Deltapine 90, which may impact the quality of our most abundant renewable textile material. More efficient cellular phenotyping methods are needed to empower future research efforts.MethodsWe developed semi‐automated imaging methods for young cotton fibers and a novel machine learning algorithm for the rapid detection of tapered (narrow) or hemisphere (wide) fibers in homogeneous or mixed populations.ResultsThe new methods were accurate for diverse accessions of G. hirsutum and G. barbadense and at least eight times more efficient than manual methods. Narrow fibers dominated in the three G. barbadense accessions analyzed, whereas the three G. hirsutum accessions showed a mixture of tapered and hemisphere fibers in varying proportions.DiscussionThe use or adaptation of these improved methods will facilitate experiments with higher throughput to understand the biological factors controlling the variable shapes of young cotton fibers or other elongating single cells. This research also enables the exploration of links between early cell shape and mature cotton fiber quality in diverse field‐grown cotton accessions.}, 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
               Accelerated marker-assisted selection and genomic selection breeding systems require genotyping data to select the best parents for combining beneficial traits. Since 1935, the Pee Dee (PD) cotton germplasm enhancement program has developed an important genetic resource for upland cotton (Gossypium hirsutum L.), contributing alleles for improved fiber quality, agronomic performance, and genetic diversity. To date, a detailed genetic survey of the program’s eight historical breeding cycles has yet to be undertaken. The objectives of this study were to evaluate genetic diversity across and within-breeding groups, examine population structure, and contextualize these findings relative to the global upland cotton gene pool. The CottonSNP63K array was used to identify 17,441 polymorphic markers in a panel of 114 diverse PD genotypes. A subset of 4597 markers was selected to decrease marker density bias. Identity-by-state pairwise distance varied substantially, ranging from 0.55 to 0.97. Pedigree-based estimates of relatedness were not very predictive of observed genetic similarities. Few rare alleles were present, with 99.1% of SNP alleles appearing within the first four breeding cycles. Population structure analysis with principal component analysis, discriminant analysis of principal components, fastSTRUCTURE, and a phylogenetic approach revealed an admixed population with moderate substructure. A small core collection (n < 20) captured 99% of the program’s allelic diversity. Allele frequency analysis indicated potential selection signatures associated with stress resistance and fiber cell growth. The results of this study will steer future utilization of the program’s germplasm resources and aid in combining program-specific beneficial alleles and maintaining genetic diversity.}, 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={AbstractA diploid potato (Solanum tuberosum L.) recombinant inbred line population was derived from a cross between Solanum chacoense inbred line M6 and S. chacoense accession USDA8380‐1 (80‐1) to identify loci associated with self‐compatibility and Colorado potato beetle resistance. Individuals from the F4 and F5 generations were genotyped on the Illumina Infinium V3 22K Single Nucleotide Polymorphism (SNP) Array and a genetic map constructed. All F5 individuals contain at least one copy of the dominant S‐locus inhibitor (Sli) haplotype; however, not all F5 individuals set fruit. Pollen tubes reached the ovaries of both self‐fruitful and self‐unfruitful plants, indicating that the presence of the dominant Sli allele is not sufficient for selfed fruit and seed production. Loci on chromosomes 3, 5, 6, and 12 were identified as novel targets for self‐fertility improvement. Evaluation of fruit and seed set upon selfing in the F4 generation over two greenhouse seasons revealed environmental influence on self‐fertility. Loci exhibiting residual heterozygosity were found on all chromosomes except chromosomes 3 and 11 in F5 inbreds, but none of the measured self‐fertility traits were correlated with the level of heterozygosity based on SNP genotyping. Four SNPs on chromosome 2 between 22,151,711 and 22,381,719 bp were associated with foliar leptine glycoalkaloid synthesis and Colorado potato beetle resistance in the recombinant inbred line population. Robust inbred lines carrying Colorado potato beetle resistance were developed without field selection during the inbreeding process and beetle resistance was introgressed into diploid breeding lines.}, 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={AbstractWe have previously shown that exposure to particulate air pollution, both from natural and anthropogenic sources, alters gene expression in the airways and increases susceptibility to respiratory viral infection. Additionally, we have shown that woodsmoke particulates (WSP) affect responses to influenza in a sex-dependent manner. In the present study, we used human nasal epithelial cells (hNECs) from both sexes to investigate how particulate exposure could modulate gene expression in the context of SARS-CoV-2 infection. We used diesel exhaust particulate (DEP) as well as WSP derived from eucalyptus or red oak wood. HNECs were exposed to particulates at a concentration of 22 μg/cm2 for 2 h then immediately infected with SARS-CoV-2 at a MOI (multiplicity of infection) of 0.5. Exposure to particulates had no significant effects on viral load recovered from infected cells. Without particulate exposure, hNECs from both sexes displayed a robust upregulation of antiviral host response genes, though the response was greater in males. However, WSP exposure before infection dampened expression of genes related to the antiviral host response by 72 h post infection. Specifically, red oak WSP downregulated IFIT1, IFITM3, IFNB1, MX1, CCL3, CCL5, CXCL11, CXCL10, and DDX58, among others. After sex stratification of these results, we found that exposure to WSP prior to SARS-CoV-2 infection downregulated anti-viral gene expression in hNECs from females more so than males. These data indicate that WSP, specifically from red oak, alter virus-induced gene expression in a sex-dependent manner and potentially suppress antiviral host defense responses following SARS-CoV-2 infection.}, 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} }