| Abstract |
- In the study of any developmental process, whether in plants, animals, or other models, it is prudent to consider the developmental position of the subjects being measured. This is generally not taken into consideration in grapevine studies despite a growing body of literature documenting that fruits within clusters develop and ripen non-uniformly. What complicates such accounting is that grape berries develop and ripen within a complex, extensively branched panicle. In the studies that follow, a tagging strategy was deployed in which fruits were labeled on their dates of anthesis or developmental position at véraison (when 50% of a cluster has initiated ripening) and subsequently sampled. Using this approach, why fruits initiate ripening unevenly and how much variation persists late in the ripening process were explored. The ripening onset for individual berries and the hormonal shifts characteristic of the ripening onset were best associated with their seed content, with flowering time playing an inconsistent and small role. Late in ripening, the abundance of enologically meaningful metabolites were still able to distinguish berries based on their developmental position at véraison.Grape Leafroll-associated Virus 3 (GLRaV3) is the most consequential virus that affects grapevine globally, with reports showing infected vines yield less and produce poorer quality fruit. Furthermore, GLRaV3 is reported to affect grapevines in a developmentally specific way. Given the developmental heterogeneity within clusters and that viral symptoms in the fruit occur in a developmentally-sensitive manner, the aforementioned tagging strategy was used to study the impact of GLRaV3 in berries during ripening. RNA sequencing and small RNA sequencing libraries were constructed to capture transcriptome-wide changes in gene expression, small RNAs, and the production of viral small interfering RNAs, as well as to identify novel micro and other small RNAs abundant during ripening and affected by GLRaV3. The effects of GLRaV3 in terms of gene expression and small RNA abundance were most numerous at véraison and included ordered and disordered responses. Most modules of co-expressed genes exhibited ordered responses, with groups of genes becoming differentially expressed while remaining co-expressed. However, disordered responses were observed as well. Various regulatory strategies were indicted in the orchestration of GLRaV3 responses, as were genes involved in the crosstalk between metabolite biosynthetic pathways and hormone signaling pathways.
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| Additional Information |
- description.provenance : Submitted by Amanda Vondras (vondrasa) on 2017-09-18T15:44:23ZNo. of bitstreams: 7Supplemental File. DCeN scores.xlsx: 1362671 bytes, checksum: c43d06e251a67a475f0c6f30860d438a (MD5)Supplemental File. Differentially abundant sRNA and targets.xlsx: 1617358 bytes, checksum: 3937f0d57568503cea730efd728a326f (MD5)Supplemental File. miRNA Hairpin Key and Annotation.xlsx: 132596 bytes, checksum: 5e653f0a829395a65ca70e8af41d08cd (MD5)Supplemental File. miRNA Hairpins.pdf: 23132455 bytes, checksum: 1bb94a8e23296d9a3d2b82dfaa0cb57d (MD5)Supplemental File. miRNA targets.txt: 55899 bytes, checksum: 4ca0969cd2b7b89726d89183f529884f (MD5)Supplemental File. Next-generation sequencing.xlsx: 67020 bytes, checksum: d977cd2a881c0163675fb2ca8d2ff6a4 (MD5)VondrasAmandaM2017.pdf: 64881077 bytes, checksum: 8a0e9131f1d953a1f0ef0ae40ce4b048 (MD5)
- description.provenance : Rejected by Julie Kurtz(julie.kurtz@oregonstate.edu), reason: Hi Amanda,Everything looks good except there is a problem with the page numbers. After page 140 the next page is 145, so 4 pages are either missing or they are mis-numbered.Everything else looks good. Once revised, log back into ScholarsArchive and go to the upload page. Replace the attached file with the revised PDF and resubmit.Thanks,Julie on 2017-09-06T20:58:02Z (GMT)
- description.provenance : Approved for entry into archive by Julie Kurtz(julie.kurtz@oregonstate.edu) on 2017-09-18T16:46:49Z (GMT) No. of bitstreams: 7Supplemental File. DCeN scores.xlsx: 1362671 bytes, checksum: c43d06e251a67a475f0c6f30860d438a (MD5)Supplemental File. Differentially abundant sRNA and targets.xlsx: 1617358 bytes, checksum: 3937f0d57568503cea730efd728a326f (MD5)Supplemental File. miRNA Hairpin Key and Annotation.xlsx: 132596 bytes, checksum: 5e653f0a829395a65ca70e8af41d08cd (MD5)Supplemental File. miRNA Hairpins.pdf: 23132455 bytes, checksum: 1bb94a8e23296d9a3d2b82dfaa0cb57d (MD5)Supplemental File. miRNA targets.txt: 55899 bytes, checksum: 4ca0969cd2b7b89726d89183f529884f (MD5)Supplemental File. Next-generation sequencing.xlsx: 67020 bytes, checksum: d977cd2a881c0163675fb2ca8d2ff6a4 (MD5)VondrasAmandaM2017.pdf: 64881077 bytes, checksum: 8a0e9131f1d953a1f0ef0ae40ce4b048 (MD5)
- description.provenance : Approved for entry into archive by Julie Kurtz(julie.kurtz@oregonstate.edu) on 2017-09-08T15:49:13Z (GMT) No. of bitstreams: 7Supplemental File. DCeN scores.xlsx: 1362671 bytes, checksum: c43d06e251a67a475f0c6f30860d438a (MD5)Supplemental File. Differentially abundant sRNA and targets.xlsx: 1617358 bytes, checksum: 3937f0d57568503cea730efd728a326f (MD5)Supplemental File. miRNA Hairpin Key and Annotation.xlsx: 132596 bytes, checksum: 5e653f0a829395a65ca70e8af41d08cd (MD5)Supplemental File. miRNA Hairpins.pdf: 23132455 bytes, checksum: 1bb94a8e23296d9a3d2b82dfaa0cb57d (MD5)Supplemental File. miRNA targets.txt: 55899 bytes, checksum: 4ca0969cd2b7b89726d89183f529884f (MD5)Supplemental File. Next-generation sequencing.xlsx: 67020 bytes, checksum: d977cd2a881c0163675fb2ca8d2ff6a4 (MD5)VondrasAmandaM2017.pdf: 64899438 bytes, checksum: bc9e4b0d00f78cadbe91c46dfd1b40f8 (MD5)
- description.provenance : Submitted by Amanda Vondras (vondrasa) on 2017-09-08T05:24:13ZNo. of bitstreams: 7Supplemental File. DCeN scores.xlsx: 1362671 bytes, checksum: c43d06e251a67a475f0c6f30860d438a (MD5)Supplemental File. Differentially abundant sRNA and targets.xlsx: 1617358 bytes, checksum: 3937f0d57568503cea730efd728a326f (MD5)Supplemental File. miRNA Hairpin Key and Annotation.xlsx: 132596 bytes, checksum: 5e653f0a829395a65ca70e8af41d08cd (MD5)Supplemental File. miRNA Hairpins.pdf: 23132455 bytes, checksum: 1bb94a8e23296d9a3d2b82dfaa0cb57d (MD5)Supplemental File. miRNA targets.txt: 55899 bytes, checksum: 4ca0969cd2b7b89726d89183f529884f (MD5)Supplemental File. Next-generation sequencing.xlsx: 67020 bytes, checksum: d977cd2a881c0163675fb2ca8d2ff6a4 (MD5)VondrasAmandaM2017.pdf: 64899438 bytes, checksum: bc9e4b0d00f78cadbe91c46dfd1b40f8 (MD5)
- description.provenance : Submitted by Amanda Vondras (vondrasa) on 2017-09-03T07:17:48ZNo. of bitstreams: 7VondrasAmandaM2017.pdf: 64869697 bytes, checksum: a7556b7d8880d8ba90f9469507b90917 (MD5)Supplemental File. DCeN scores.xlsx: 1362671 bytes, checksum: c43d06e251a67a475f0c6f30860d438a (MD5)Supplemental File. Differentially abundant sRNA and targets.xlsx: 1617358 bytes, checksum: 3937f0d57568503cea730efd728a326f (MD5)Supplemental File. miRNA Hairpin Key and Annotation.xlsx: 132596 bytes, checksum: 5e653f0a829395a65ca70e8af41d08cd (MD5)Supplemental File. miRNA Hairpins.pdf: 23132455 bytes, checksum: 1bb94a8e23296d9a3d2b82dfaa0cb57d (MD5)Supplemental File. miRNA targets.txt: 55899 bytes, checksum: 4ca0969cd2b7b89726d89183f529884f (MD5)Supplemental File. Next-generation sequencing.xlsx: 67020 bytes, checksum: d977cd2a881c0163675fb2ca8d2ff6a4 (MD5)
- description.provenance : Approved for entry into archive by Steven Van Tuyl(steve.vantuyl@oregonstate.edu) on 2017-09-20T21:37:45Z (GMT) No. of bitstreams: 7Supplemental File. DCeN scores.xlsx: 1362671 bytes, checksum: c43d06e251a67a475f0c6f30860d438a (MD5)Supplemental File. Differentially abundant sRNA and targets.xlsx: 1617358 bytes, checksum: 3937f0d57568503cea730efd728a326f (MD5)Supplemental File. miRNA Hairpin Key and Annotation.xlsx: 132596 bytes, checksum: 5e653f0a829395a65ca70e8af41d08cd (MD5)Supplemental File. miRNA Hairpins.pdf: 23132455 bytes, checksum: 1bb94a8e23296d9a3d2b82dfaa0cb57d (MD5)Supplemental File. miRNA targets.txt: 55899 bytes, checksum: 4ca0969cd2b7b89726d89183f529884f (MD5)Supplemental File. Next-generation sequencing.xlsx: 67020 bytes, checksum: d977cd2a881c0163675fb2ca8d2ff6a4 (MD5)VondrasAmandaM2017.pdf: 64881077 bytes, checksum: 8a0e9131f1d953a1f0ef0ae40ce4b048 (MD5)
- description.provenance : Made available in DSpace on 2017-09-20T21:37:45Z (GMT). No. of bitstreams: 7Supplemental File. DCeN scores.xlsx: 1362671 bytes, checksum: c43d06e251a67a475f0c6f30860d438a (MD5)Supplemental File. Differentially abundant sRNA and targets.xlsx: 1617358 bytes, checksum: 3937f0d57568503cea730efd728a326f (MD5)Supplemental File. miRNA Hairpin Key and Annotation.xlsx: 132596 bytes, checksum: 5e653f0a829395a65ca70e8af41d08cd (MD5)Supplemental File. miRNA Hairpins.pdf: 23132455 bytes, checksum: 1bb94a8e23296d9a3d2b82dfaa0cb57d (MD5)Supplemental File. miRNA targets.txt: 55899 bytes, checksum: 4ca0969cd2b7b89726d89183f529884f (MD5)Supplemental File. Next-generation sequencing.xlsx: 67020 bytes, checksum: d977cd2a881c0163675fb2ca8d2ff6a4 (MD5)VondrasAmandaM2017.pdf: 64881077 bytes, checksum: 8a0e9131f1d953a1f0ef0ae40ce4b048 (MD5) Previous issue date: 2017-08-02
- description.provenance : Rejected by Julie Kurtz(julie.kurtz@oregonstate.edu), reason: Rejecting per your request.Thanks,Julie on 2017-09-15T23:40:10Z (GMT)
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