@article{knight_doherty_nielsen_2022, title={Assessing the Nucleotide-Level Impact of Spaceflight Stress using RNA-Sequencing Data}, url={https://doi.org/10.1101/2022.12.01.518235}, DOI={10.1101/2022.12.01.518235}, abstractNote={Understanding the effects of space radiation and microgravity on DNA integrity is critical to assess the impact of long-term spaceflight. However, studying spaceflight’s effect on terrestrial life is difficult. NASA created GeneLab, a public Omics database for spaceflight-related data, to help combat these limitations. While GeneLab has very few DNA-based data sets, transcriptome information is abundant. This study used RNA-Seq data from GeneLab to examine DNA sequence variants linked to spaceflight stress exposure. More mutations were observed in spaceflight samples than in the ground control samples. This increase in variants was not reduced in samples grown under artificial gravity in space, suggesting that microgravity did not significantly affect the amount of DNA damage in this experiment. There was also an increase in transversion mutations, consistent with known forms of radiation-induced damage. This work demonstrates that RNA-Seq data is a useful resource for evaluating DNA damage from spaceflight and provides a baseline for the types of mutations that could be detected.}, author={Knight, Montana S. and Doherty, Colleen J. and Nielsen, Dahlia M.}, year={2022}, month={Dec} }
 @article{bheemanahalli_knight_quinones_doherty_jagadish_2021, title={Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice}, volume={11}, ISSN={["2045-2322"]}, url={https://doi.org/10.1038/s41598-021-85921-z}, DOI={10.1038/s41598-021-85921-z}, abstractNote={High night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Bheemanahalli, Raju and Knight, Montana and Quinones, Cherryl and Doherty, Colleen J. and Jagadish, S. V. Krishna}, year={2021}, month={Mar} }