Network Inference of Transcriptional Regulation in Germinating Low Phytic Acid Soybean Seeds

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dc.contributor.authorDeMers, Lindsay C.en
dc.contributor.authorRaboy, Victoren
dc.contributor.authorLi, Songen
dc.contributor.authorSaghai-Maroof, Mohammad A.en
dc.date.accessioned2021-11-12T15:35:20Zen
dc.date.available2021-11-12T15:35:20Zen
dc.date.issued2021-08-31en
dc.description.abstractThe low phytic acid (lpa) trait in soybeans can be conferred by loss-of-function mutations in genes encoding myo-inositol phosphate synthase and two epistatically interacting genes encoding multidrug-resistance protein ATP-binding cassette (ABC) transporters. However, perturbations in phytic acid biosynthesis are associated with poor seed vigor. Since the benefits of the lpa trait, in terms of end-use quality and sustainability, far outweigh the negatives associated with poor seed performance, a fuller understanding of the molecular basis behind the negatives will assist crop breeders and engineers in producing variates with lpa and better germination rate. The gene regulatory network (GRN) for developing low and normal phytic acid soybean seeds was previously constructed, with genes modulating a variety of processes pertinent to phytic acid metabolism and seed viability being identified. In this study, a comparative time series analysis of low and normal phytic acid soybeans was carried out to investigate the transcriptional regulatory elements governing the transitional dynamics from dry seed to germinated seed. GRNs were reverse engineered from time series transcriptomic data of three distinct genotypic subsets composed of lpa soybean lines and their normal phytic acid sibling lines. Using a robust unsupervised network inference scheme, putative regulatory interactions were inferred for each subset of genotypes. These interactions were further validated by published regulatory interactions found in Arabidopsis thaliana and motif sequence analysis. Results indicate that lpa seeds have increased sensitivity to stress, which could be due to changes in phytic acid levels, disrupted inositol phosphate signaling, disrupted phosphate ion (Pi) homeostasis, and altered myo-inositol metabolism. Putative regulatory interactions were identified for the latter two processes. Changes in abscisic acid (ABA) signaling candidate transcription factors (TFs) putatively regulating genes in this process were identified as well. Analysis of the GRNs reveal altered regulation in processes that may be affecting the germination of lpa soybean seeds. Therefore, this work contributes to the ongoing effort to elucidate molecular mechanisms underlying altered seed viability, germination and field emergence of lpa crops, understanding of which is necessary in order to mitigate these problems.</p>en
dc.description.notesThis project was funded in part by the Virginia Soybean Board projects 630, 719, and 783. Additional funding was provided by the Agricultural Experiment Station Hatch Program and Open Access Subvention Fund - both at Virginia Tech. LD was funded in part by the John Lee Pratt Fellowship Program at Virginia Tech.en
dc.description.sponsorshipVirginia Soybean Board projects [630, 719, 783]; Agricultural Experiment Station Hatch Program at Virginia Tech; Open Access Subvention Fund at Virginia Tech; John Lee Pratt Fellowship Program at Virginia Techen
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.3389/fpls.2021.708286en
dc.identifier.issn1664-462Xen
dc.identifier.other708286en
dc.identifier.pmid34531883en
dc.identifier.urihttp://hdl.handle.net/10919/106630en
dc.identifier.volume12en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectphytic aciden
dc.subjectmyo-inositol phosphate synthaseen
dc.subjectmultidrug-resistance protein ABC transporteren
dc.subjectseed germinationen
dc.subjectgene regulatory networken
dc.subjectunsupervised machine learningen
dc.subjectabscisic acid signalingen
dc.subjectphosphate homeostasisen
dc.titleNetwork Inference of Transcriptional Regulation in Germinating Low Phytic Acid Soybean Seedsen
dc.title.serialFrontiers in Plant Scienceen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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