Research on the Molecular Mechanisms and Key Gene Discovery in Quercus variabilis Root Pruning Based on Transcriptomics and Hormone Profiling
( ), a significant broadleaf species used in afforestation across high, sandy, and mountainous regions, presents unique challenges for transplantation. This species is characterized by its slow above-ground growth and rapid taproot development, which suppresses the proliferation of lateral and fibro...
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| Veröffentlicht in: | International journal of molecular sciences 2024-11, Vol.25 (21), p.11541 |
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| creator | Dou, Hao Sun, Jiajia Feng, Xi Lyu, Huyang Qin, Zhen Ni, Ruoyi Wang, Yilin Sun, Huijuan Zhou, Xin Tang, Wu Quan, Jin'e Yang, Xitian |
| description | (
), a significant broadleaf species used in afforestation across high, sandy, and mountainous regions, presents unique challenges for transplantation. This species is characterized by its slow above-ground growth and rapid taproot development, which suppresses the proliferation of lateral and fibrous roots, negatively impacting post-transplant survival. Research indicates that targeted root pruning-specifically, the removal of one-third of the roots-promotes the development of lateral roots in these seedlings. This study involved pruning the root systems of
and assessing the subsequent root development in comparison to an unpruned control group. Our analysis, which included transcriptome sequencing and plant hormone metabolism assays conducted at 2, 12, and 25 days post-pruning, yielded 126.02 Gb of clean data and identified 7662 differentially expressed genes (DEGs). These genes were primarily enriched in the plant hormone signal transduction pathway. Further investigation of this pathway, along with hormone content measurements, elucidated the mechanisms that contribute to enhanced root growth following pruning. Additionally, through a weighted correlation network analysis (WGCNA), we identified 20 key genes that are instrumental in promoting root development in
saplings. This research advances the theoretical framework for forestry seedling production and afforestation, laying the groundwork for scientifically informed vegetation restoration techniques. |
| doi_str_mv | 10.3390/ijms252111541 |
| format | Article |
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), a significant broadleaf species used in afforestation across high, sandy, and mountainous regions, presents unique challenges for transplantation. This species is characterized by its slow above-ground growth and rapid taproot development, which suppresses the proliferation of lateral and fibrous roots, negatively impacting post-transplant survival. Research indicates that targeted root pruning-specifically, the removal of one-third of the roots-promotes the development of lateral roots in these seedlings. This study involved pruning the root systems of
and assessing the subsequent root development in comparison to an unpruned control group. Our analysis, which included transcriptome sequencing and plant hormone metabolism assays conducted at 2, 12, and 25 days post-pruning, yielded 126.02 Gb of clean data and identified 7662 differentially expressed genes (DEGs). These genes were primarily enriched in the plant hormone signal transduction pathway. Further investigation of this pathway, along with hormone content measurements, elucidated the mechanisms that contribute to enhanced root growth following pruning. Additionally, through a weighted correlation network analysis (WGCNA), we identified 20 key genes that are instrumental in promoting root development in
saplings. This research advances the theoretical framework for forestry seedling production and afforestation, laying the groundwork for scientifically informed vegetation restoration techniques.</description><identifier>ISSN: 1422-0067</identifier><identifier>ISSN: 1661-6596</identifier><identifier>EISSN: 1422-0067</identifier><identifier>DOI: 10.3390/ijms252111541</identifier><identifier>PMID: 39519096</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Abscisic acid ; Afforestation ; Analysis ; Cellular signal transduction ; Gene Expression Profiling - methods ; Gene Expression Regulation, Plant ; Genes ; Hormones ; Medical research ; Medicine, Experimental ; Morphology ; Physiological aspects ; Physiology ; Plant Growth Regulators - genetics ; Plant Growth Regulators - metabolism ; Plant hormones ; Plant Roots - genetics ; Plant Roots - growth & development ; Plant Roots - metabolism ; Quercus - genetics ; Quercus - growth & development ; Quercus - metabolism ; Seedlings - genetics ; Seedlings - growth & development ; Seedlings - metabolism ; Signal Transduction - genetics ; Transcriptome</subject><ispartof>International journal of molecular sciences, 2024-11, Vol.25 (21), p.11541</ispartof><rights>COPYRIGHT 2024 MDPI AG</rights><rights>2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2024 by the authors. 2024</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c369t-43f8b7c60e3d51f4fbb8952de75730f76ee968ae94ee25b88035f8655994587c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11546583/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11546583/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39519096$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dou, Hao</creatorcontrib><creatorcontrib>Sun, Jiajia</creatorcontrib><creatorcontrib>Feng, Xi</creatorcontrib><creatorcontrib>Lyu, Huyang</creatorcontrib><creatorcontrib>Qin, Zhen</creatorcontrib><creatorcontrib>Ni, Ruoyi</creatorcontrib><creatorcontrib>Wang, Yilin</creatorcontrib><creatorcontrib>Sun, Huijuan</creatorcontrib><creatorcontrib>Zhou, Xin</creatorcontrib><creatorcontrib>Tang, Wu</creatorcontrib><creatorcontrib>Quan, Jin'e</creatorcontrib><creatorcontrib>Yang, Xitian</creatorcontrib><title>Research on the Molecular Mechanisms and Key Gene Discovery in Quercus variabilis Root Pruning Based on Transcriptomics and Hormone Profiling</title><title>International journal of molecular sciences</title><addtitle>Int J Mol Sci</addtitle><description>(
), a significant broadleaf species used in afforestation across high, sandy, and mountainous regions, presents unique challenges for transplantation. This species is characterized by its slow above-ground growth and rapid taproot development, which suppresses the proliferation of lateral and fibrous roots, negatively impacting post-transplant survival. Research indicates that targeted root pruning-specifically, the removal of one-third of the roots-promotes the development of lateral roots in these seedlings. This study involved pruning the root systems of
and assessing the subsequent root development in comparison to an unpruned control group. Our analysis, which included transcriptome sequencing and plant hormone metabolism assays conducted at 2, 12, and 25 days post-pruning, yielded 126.02 Gb of clean data and identified 7662 differentially expressed genes (DEGs). These genes were primarily enriched in the plant hormone signal transduction pathway. Further investigation of this pathway, along with hormone content measurements, elucidated the mechanisms that contribute to enhanced root growth following pruning. Additionally, through a weighted correlation network analysis (WGCNA), we identified 20 key genes that are instrumental in promoting root development in
saplings. This research advances the theoretical framework for forestry seedling production and afforestation, laying the groundwork for scientifically informed vegetation restoration techniques.</description><subject>Abscisic acid</subject><subject>Afforestation</subject><subject>Analysis</subject><subject>Cellular signal transduction</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genes</subject><subject>Hormones</subject><subject>Medical research</subject><subject>Medicine, Experimental</subject><subject>Morphology</subject><subject>Physiological aspects</subject><subject>Physiology</subject><subject>Plant Growth Regulators - genetics</subject><subject>Plant Growth Regulators - metabolism</subject><subject>Plant hormones</subject><subject>Plant Roots - genetics</subject><subject>Plant Roots - growth & development</subject><subject>Plant Roots - metabolism</subject><subject>Quercus - genetics</subject><subject>Quercus - growth & development</subject><subject>Quercus - metabolism</subject><subject>Seedlings - genetics</subject><subject>Seedlings - growth & development</subject><subject>Seedlings - metabolism</subject><subject>Signal Transduction - genetics</subject><subject>Transcriptome</subject><issn>1422-0067</issn><issn>1661-6596</issn><issn>1422-0067</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNptkk1v1DAQhiMEoh9w5IosceGSYscfsU-oFGgRrShVOVuOM9n1KrG3drLS_oj-ZxxtKV2EfLAlP_OM5tUUxRuCTyhV-INbDaniFSGEM_KsOCSsqkqMRf38yfugOEpphXFFK65eFgdUcaKwEofF_Q0kMNEuUfBoXAK6Cj3YqTcRXYFdGu_SkJDxLfoOW3QOHtBnl2zYQNwi59HPCaKdEtqY6EzjepfQTQgjuo6Td36BPpkE7ey-jcYnG916DIOzO-VFiEPIxusYulzqF6-KF53pE7x-uI-LX1-_3J5dlJc_zr-dnV6Wlgo1lox2sqmtwEBbTjrWNY1UvGqh5jXFXS0AlJAGFAOoeCMlpryTgnOlGJe1pcfFx513PTUDtBb8GE2v19ENJm51ME7v_3i31Iuw0XPKgkuaDe8fDDHcTZBGPeRYoO-NhzAlTUkla8aIVBl99w-6ClP0eb6ZEpgzxuRfamF60M53ITe2s1SfSsIp44ziTJ38h8qnhZxqzjLnCPsF5a7AxpBShO5xSIL1vEB6b4Ey__ZpMo_0n42hvwEINsHK</recordid><startdate>20241101</startdate><enddate>20241101</enddate><creator>Dou, Hao</creator><creator>Sun, Jiajia</creator><creator>Feng, Xi</creator><creator>Lyu, Huyang</creator><creator>Qin, Zhen</creator><creator>Ni, Ruoyi</creator><creator>Wang, Yilin</creator><creator>Sun, Huijuan</creator><creator>Zhou, Xin</creator><creator>Tang, Wu</creator><creator>Quan, Jin'e</creator><creator>Yang, Xitian</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>MBDVC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20241101</creationdate><title>Research on the Molecular Mechanisms and Key Gene Discovery in Quercus variabilis Root Pruning Based on Transcriptomics and Hormone Profiling</title><author>Dou, Hao ; 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), a significant broadleaf species used in afforestation across high, sandy, and mountainous regions, presents unique challenges for transplantation. This species is characterized by its slow above-ground growth and rapid taproot development, which suppresses the proliferation of lateral and fibrous roots, negatively impacting post-transplant survival. Research indicates that targeted root pruning-specifically, the removal of one-third of the roots-promotes the development of lateral roots in these seedlings. This study involved pruning the root systems of
and assessing the subsequent root development in comparison to an unpruned control group. Our analysis, which included transcriptome sequencing and plant hormone metabolism assays conducted at 2, 12, and 25 days post-pruning, yielded 126.02 Gb of clean data and identified 7662 differentially expressed genes (DEGs). These genes were primarily enriched in the plant hormone signal transduction pathway. Further investigation of this pathway, along with hormone content measurements, elucidated the mechanisms that contribute to enhanced root growth following pruning. Additionally, through a weighted correlation network analysis (WGCNA), we identified 20 key genes that are instrumental in promoting root development in
saplings. This research advances the theoretical framework for forestry seedling production and afforestation, laying the groundwork for scientifically informed vegetation restoration techniques.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>39519096</pmid><doi>10.3390/ijms252111541</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Abscisic acid Afforestation Analysis Cellular signal transduction Gene Expression Profiling - methods Gene Expression Regulation, Plant Genes Hormones Medical research Medicine, Experimental Morphology Physiological aspects Physiology Plant Growth Regulators - genetics Plant Growth Regulators - metabolism Plant hormones Plant Roots - genetics Plant Roots - growth & development Plant Roots - metabolism Quercus - genetics Quercus - growth & development Quercus - metabolism Seedlings - genetics Seedlings - growth & development Seedlings - metabolism Signal Transduction - genetics Transcriptome |
| title | Research on the Molecular Mechanisms and Key Gene Discovery in Quercus variabilis Root Pruning Based on Transcriptomics and Hormone Profiling |
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