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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #365660
Research Project: Database Tools for Managing and Analyzing Big Data Sets to Enhance Small Grains Breeding

Location: Plant, Soil and Nutrition Research

Title: A new oat seed transcriptome identifies heritable temporal gene expression patterns in developing seeds of hexaploid oat

Author
item HU, HAIXIAO - Cornell University
item GUTIERREZ-GONZALEZ, JUAN - University Of Minnesota
item LIU, XINFANG - Liaoning Research Institute Of Pomology
item YEATS, TREVOR - Cornell University
item Garvin, David
item HOEKENGA, OWEN - Cayuga Genetics Consulting Group, Llc
item SORRELS, MARK - Cornell University
item GORE, MICHAEL - Cornell University
item Jannink, Jean-Luc

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/26/2019
Publication Date: 5/1/2020
Citation: Hu, H., Gutierrez-Gonzalez, J.L., Liu, X., Yeats, T.H., Garvin, D.F., Hoekenga, O.A., Sorrels, M.E., Gore, M.A., Jannink, J. 2020. A new oat seed transcriptome identifies heritable temporal gene expression patterns in developing seeds of hexaploid oat. Plant Biotechnology Journal. 18(5):1211-1222. https://doi.org/10.1111/pbi.13286.
DOI: https://doi.org/10.1111/pbi.13286

Interpretive Summary: Which genes are expressed at what time points in the developing oat seed is not known. We measured gene expression during seed development in 22 diverse oat lines grown in two environments at six time points. We showed that there is significant genetic variation in gene expression levels. This study extended understanding of physiological processes occurring during oat seed development and will provide oat breeders with the means to change seed composition.

Technical Abstract: Oat ranks sixth in world cereal production and has a higher content of health-promoting compounds compared to other cereals. However, there is neither a robust oat reference genome available nor detailed transcriptomes. Using deeply sequenced full-length mRNA libraries of oat cultivar Ogle-C from both Illumina HiSeq 2000 and MiSeq platforms, a de novo, high-quality and comprehensive oat seed transcriptome was assembled. With this reference and QuantSeq 3’ mRNA sequencing technology, gene expression was quantified during seed development from 22 diverse oat lines grown in two environments across six time points. Transcript expression showed higher correlations between adjacent time points. Based on differentially expressed genes between adjacent time points, we identified 22 major temporal patterns of gene expression in developing seeds and revealed enriched gene ontology biological processes. Within each temporal expression set, highly correlated transcripts that putatively belong to the same genetic background were clustered, and 17 of the 22 temporal expression sets whose subclusters with median heritabilities higher than 0.50. These heritability estimates were much higher than that estimated from permutation analysis, and there was no divergence observed in subcluster sizes between permutation and non-permutation analyses. Temporal expression patterns of oat avenanthramides and lipid biosynthetic genes were characterized validating previous studies on avenanthramide biosynthetic enzyme activities and lipid accumulation. This study extended the understanding of physiological processes occurring during oat seed maturation and provides plant breeders the means to change oat seed composition through targeted manipulation of key pathways.