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Title: Exploring the fate of mRNA in aging seeds: protection, destruction, or slow decay?

Author
item Fleming, Margaret
item PATTERSON, ERIC - Colorado State University
item Reeves, Patrick
item Richards, Christopher
item GAINES, TODD - Colorado State University
item Walters, Christina

Submitted to: Journal of Experimental Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/18/2018
Publication Date: 6/12/2018
Citation: Fleming, M.B., Patterson, E., Reeves, P.A., Richards, C.M., Gaines, T., Walters, C.T. 2018. Exploring the fate of mRNA in aging seeds: protection, destruction, or slow decay? Journal of Experimental Botany. 69(18):4309-4321. https://doi.org/10.1093/jxb/ery215.
DOI: https://doi.org/10.1093/jxb/ery215

Interpretive Summary: A chemical test of seed aging would save millions of dollars a year for agriculture by obviating expensive viability monitoring tests and avoiding unscheduled losses in seed quality. This kind of test has been elusive because all molecules within the cell degrade with time and so there is no particular chemical signal. Our work here focuses on mRNA, which is the intermediary molecule used by cells to translate genetic code from DNA into proteins that carry out metabolism. The mRNA transcripts degrade during seed aging like other molecules. We discovered here that degradation of mRNA results in molecular fissures, and these can be detected using tiny amounts of seed or seed parts, automated sequencing techniques, and standardized comparisons to reference sequences in genomic libraries. This approach brings us a new capacity to detect chemical change while seeds are dying, and future pursuits may reveal the breaking point of seed aging that limits a seed’s ability to germinate.

Technical Abstract: Chemical degradation of dry seeds is slow, and aging processes eventually result in seed death. Extant hypotheses of aging mechanisms involve all classes of biological molecules, but, to date, only degradation of total RNA has been detected in dry seeds contemporaneously with viability loss. Therefore, an analysis of the soybean seed transcriptome was undertaken to quantify changes specific to mRNAs. Up- and down-regulation of transcripts does not occur in dry seeds because they lack integrated metabolism. However, we detected strong evidence of fragmented molecules, compared to reference transcripts, using new, whole-molecule sequencing techniques. Molecules of mRNA broke at non-specific positions all along the transcript and greater fragmentation occurred in longer transcripts, consistent with proposed mechanisms of molecular fission by free radical attack at random bases. This study provides an approach to identify markers of aging that have been elusive in the past, potentially by comparing distribution of transcript lengths relative to reference lengths as a function of storage time. Highest incidence of intact mRNAs was observed in the shortest transcripts, which might suggest these are the most protected and essential for germination. Yet, seeds died despite high integrity of these mRNAs, suggesting they are not the factor limiting germination.