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Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.)
BACKGROUND: Drought is an important constraint on grapevine sustainability. Vitis riparia, widely used in rootstock and scion breeding, has been studied in isolated leaf drying response studies; however, it is essential to identify key root and shoot water deficit signaling traits in intact plants....
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375209/ https://www.ncbi.nlm.nih.gov/pubmed/30760212 http://dx.doi.org/10.1186/s12870-019-1664-7 |
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author | Khadka, Vedbar Singh Vaughn, Kimberley Xie, Juan Swaminathan, Padmapriya Ma, Qin Cramer, Grant R. Fennell, Anne Y. |
author_facet | Khadka, Vedbar Singh Vaughn, Kimberley Xie, Juan Swaminathan, Padmapriya Ma, Qin Cramer, Grant R. Fennell, Anne Y. |
author_sort | Khadka, Vedbar Singh |
collection | PubMed |
description | BACKGROUND: Drought is an important constraint on grapevine sustainability. Vitis riparia, widely used in rootstock and scion breeding, has been studied in isolated leaf drying response studies; however, it is essential to identify key root and shoot water deficit signaling traits in intact plants. This information will aid improved scion and rootstock selection and management practices in grapevine. RNAseq data were generated from V. riparia roots and shoots under water deficit and well-watered conditions to determine root signaling and shoot responses to water deficit. RESULTS: Shoot elongation, photosynthetic rate, and stomatal conductance were significantly reduced in water deficit (WD) treated than in well-watered grapevines. RNAseq analysis indicated greater transcriptional differences in shoots than in roots under WD, with 6925 and 1395 genes differentially expressed, respectively (q-value < 0.05). There were 50 and 25 VitisNet pathways significantly enriched in WD relative to well-watered treatments in grapevine shoots and roots, respectively. The ABA biosynthesis genes beta-carotene hydroxylase, zeaxanthin epoxidase, and 9-cis-epoxycarotenoid dioxygenases were up-regulated in WD root and WD shoot. A positive enrichment of ABA biosynthesis genes and signaling pathways in WD grapevine roots indicated enhanced root signaling to the shoot. An increased frequency of differentially expressed reactive oxygen species scavenging (ROS) genes were found in the WD shoot. Analyses of hormone signaling genes indicated a strong ABA, auxin, and ethylene network and an ABA, cytokinin, and circadian rhythm network in both WD shoot and WD root. CONCLUSIONS: This work supports previous findings in detached leaf studies suggesting ABA-responsive binding factor 2 (ABF2) is a central regulator in ABA signaling in the WD shoot. Likewise, ABF2 may have a key role in V. riparia WD shoot and WD root. A role for ABF3 was indicated only in WD root. WD shoot and WD root hormone expression analysis identified strong ABA, auxin, ethylene, cytokinin, and circadian rhythm signaling networks. These results present the first ABA, cytokinin, and circadian rhythm signaling network in roots under water deficit. These networks point to organ specific regulators that should be explored to further define the communication network from soil to shoot. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1664-7) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6375209 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-63752092019-02-26 Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.) Khadka, Vedbar Singh Vaughn, Kimberley Xie, Juan Swaminathan, Padmapriya Ma, Qin Cramer, Grant R. Fennell, Anne Y. BMC Plant Biol Research Article BACKGROUND: Drought is an important constraint on grapevine sustainability. Vitis riparia, widely used in rootstock and scion breeding, has been studied in isolated leaf drying response studies; however, it is essential to identify key root and shoot water deficit signaling traits in intact plants. This information will aid improved scion and rootstock selection and management practices in grapevine. RNAseq data were generated from V. riparia roots and shoots under water deficit and well-watered conditions to determine root signaling and shoot responses to water deficit. RESULTS: Shoot elongation, photosynthetic rate, and stomatal conductance were significantly reduced in water deficit (WD) treated than in well-watered grapevines. RNAseq analysis indicated greater transcriptional differences in shoots than in roots under WD, with 6925 and 1395 genes differentially expressed, respectively (q-value < 0.05). There were 50 and 25 VitisNet pathways significantly enriched in WD relative to well-watered treatments in grapevine shoots and roots, respectively. The ABA biosynthesis genes beta-carotene hydroxylase, zeaxanthin epoxidase, and 9-cis-epoxycarotenoid dioxygenases were up-regulated in WD root and WD shoot. A positive enrichment of ABA biosynthesis genes and signaling pathways in WD grapevine roots indicated enhanced root signaling to the shoot. An increased frequency of differentially expressed reactive oxygen species scavenging (ROS) genes were found in the WD shoot. Analyses of hormone signaling genes indicated a strong ABA, auxin, and ethylene network and an ABA, cytokinin, and circadian rhythm network in both WD shoot and WD root. CONCLUSIONS: This work supports previous findings in detached leaf studies suggesting ABA-responsive binding factor 2 (ABF2) is a central regulator in ABA signaling in the WD shoot. Likewise, ABF2 may have a key role in V. riparia WD shoot and WD root. A role for ABF3 was indicated only in WD root. WD shoot and WD root hormone expression analysis identified strong ABA, auxin, ethylene, cytokinin, and circadian rhythm signaling networks. These results present the first ABA, cytokinin, and circadian rhythm signaling network in roots under water deficit. These networks point to organ specific regulators that should be explored to further define the communication network from soil to shoot. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1664-7) contains supplementary material, which is available to authorized users. BioMed Central 2019-02-13 /pmc/articles/PMC6375209/ /pubmed/30760212 http://dx.doi.org/10.1186/s12870-019-1664-7 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Khadka, Vedbar Singh Vaughn, Kimberley Xie, Juan Swaminathan, Padmapriya Ma, Qin Cramer, Grant R. Fennell, Anne Y. Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.) |
title | Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.) |
title_full | Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.) |
title_fullStr | Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.) |
title_full_unstemmed | Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.) |
title_short | Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.) |
title_sort | transcriptomic response is more sensitive to water deficit in shoots than roots of vitis riparia (michx.) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375209/ https://www.ncbi.nlm.nih.gov/pubmed/30760212 http://dx.doi.org/10.1186/s12870-019-1664-7 |
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