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Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds

BACKGROUND: Ramet propagation in strawberry (Fragaria × ananassa) is the most effective way in production. However, the lack of systematically phenotypic observations and high-throughput methods limits our ability to analyze the key factors regulating the heterogeneity in strawberry stolon buds. RES...

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Autores principales: Guan, Ling, Zhao, Mizhen, Qian, Yaming, Yu, Hongmei, Xia, Jin, Wu, Ejiao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862844/
https://www.ncbi.nlm.nih.gov/pubmed/31744478
http://dx.doi.org/10.1186/s12870-019-2096-0
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author Guan, Ling
Zhao, Mizhen
Qian, Yaming
Yu, Hongmei
Xia, Jin
Wu, Ejiao
author_facet Guan, Ling
Zhao, Mizhen
Qian, Yaming
Yu, Hongmei
Xia, Jin
Wu, Ejiao
author_sort Guan, Ling
collection PubMed
description BACKGROUND: Ramet propagation in strawberry (Fragaria × ananassa) is the most effective way in production. However, the lack of systematically phenotypic observations and high-throughput methods limits our ability to analyze the key factors regulating the heterogeneity in strawberry stolon buds. RESULTS: From observation, we found that the axillary bud located in the first node quickly stepped into dormancy (DSB), after several bract and leaf buds were differentiated. The stolon apical meristem (SAM) degenerated as the new ramet leaf buds (RLB), and the new active axillary stolon buds (ASB) differentiated continually after the differentiation of the first leaf. Using the tandem mass tags (TMT) labeling method, a total of 7271 strawberry proteins were identified. Between ASB and DSB, the spliceosome DEPs, such as Ser/Arg-rich (SR) and heterogeneous nuclear ribonucleoprotein particle (hnRNP), showed the highest enrichment and high PPI connectivity. This indicated that the differences in DEPs (e.g., SF-3A and PK) at the transcriptional level may be causing the differences between the physiological statuses of ASB and DSB. As expected, the photosynthetic pre-form RLB mainly differentiated from ASB and DSB judging by the DEP enrichment of photosynthesis. However, there are still other specialized features of DEPs between RLB and DSB and between ASB and DSB. The DEPs relative to DNA duplication [e.g., minichromosome maintenance protein (MCM 2, 3, 4, 7)], provide a strong hint of functional gene duplication leading the bud heterogeneity between RLB and DSB. In addition, the top fold change DEP of LSH 10-like might be involved in the degeneration of SAM into RLBs, based on its significant function in modulating the plant shoot initiation. As for RLB/ASB, the phenylpropanoid biosynthesis pathway probably regulates the ramet axillary bud specialization, and further promotes the differentiation of xylem when ASB develops into a new stolon [e.g., cinnamyl alcohol dehydrogenase 1 (CAD1) and phenylalanine ammonia-lyase 1 (PAL1)]. CONCLUSIONS: By using phenotypic observation combined with proteomic networks with different types of strawberry stolon buds, the definite dormancy phase of DSB was identified, and the biological pathways and gene networks that might be responsible for heterogeneity among different stolon buds in strawberry were also revealed.
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spelling pubmed-68628442019-12-11 Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds Guan, Ling Zhao, Mizhen Qian, Yaming Yu, Hongmei Xia, Jin Wu, Ejiao BMC Plant Biol Research Article BACKGROUND: Ramet propagation in strawberry (Fragaria × ananassa) is the most effective way in production. However, the lack of systematically phenotypic observations and high-throughput methods limits our ability to analyze the key factors regulating the heterogeneity in strawberry stolon buds. RESULTS: From observation, we found that the axillary bud located in the first node quickly stepped into dormancy (DSB), after several bract and leaf buds were differentiated. The stolon apical meristem (SAM) degenerated as the new ramet leaf buds (RLB), and the new active axillary stolon buds (ASB) differentiated continually after the differentiation of the first leaf. Using the tandem mass tags (TMT) labeling method, a total of 7271 strawberry proteins were identified. Between ASB and DSB, the spliceosome DEPs, such as Ser/Arg-rich (SR) and heterogeneous nuclear ribonucleoprotein particle (hnRNP), showed the highest enrichment and high PPI connectivity. This indicated that the differences in DEPs (e.g., SF-3A and PK) at the transcriptional level may be causing the differences between the physiological statuses of ASB and DSB. As expected, the photosynthetic pre-form RLB mainly differentiated from ASB and DSB judging by the DEP enrichment of photosynthesis. However, there are still other specialized features of DEPs between RLB and DSB and between ASB and DSB. The DEPs relative to DNA duplication [e.g., minichromosome maintenance protein (MCM 2, 3, 4, 7)], provide a strong hint of functional gene duplication leading the bud heterogeneity between RLB and DSB. In addition, the top fold change DEP of LSH 10-like might be involved in the degeneration of SAM into RLBs, based on its significant function in modulating the plant shoot initiation. As for RLB/ASB, the phenylpropanoid biosynthesis pathway probably regulates the ramet axillary bud specialization, and further promotes the differentiation of xylem when ASB develops into a new stolon [e.g., cinnamyl alcohol dehydrogenase 1 (CAD1) and phenylalanine ammonia-lyase 1 (PAL1)]. CONCLUSIONS: By using phenotypic observation combined with proteomic networks with different types of strawberry stolon buds, the definite dormancy phase of DSB was identified, and the biological pathways and gene networks that might be responsible for heterogeneity among different stolon buds in strawberry were also revealed. BioMed Central 2019-11-19 /pmc/articles/PMC6862844/ /pubmed/31744478 http://dx.doi.org/10.1186/s12870-019-2096-0 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
Guan, Ling
Zhao, Mizhen
Qian, Yaming
Yu, Hongmei
Xia, Jin
Wu, Ejiao
Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds
title Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds
title_full Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds
title_fullStr Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds
title_full_unstemmed Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds
title_short Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds
title_sort phenotypic analysis combined with tandem mass tags (tmt) labeling reveal the heterogeneity of strawberry stolon buds
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862844/
https://www.ncbi.nlm.nih.gov/pubmed/31744478
http://dx.doi.org/10.1186/s12870-019-2096-0
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