Genome-wide identification and functional characterization of the LBD transcription factor gene family in Zanthoxylum armatum DC. reveal its potential role in leaf variation
Abstract Background Leaf morphology plays a crucial role in forecasting the productivity and environmental adaptability of economically important trees. Plants with larger leaves usually have higher photosynthesis efficiency and can accumulate more nutrients, thereby increasing yield. In the natural...
Saved in:
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-05-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-025-06727-z |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849705408603619328 |
|---|---|
| author | Yifei Deng Chong Sun Xueqian Fu Yuan Guo Yongxing Zhu Chongyu Liu Ruxin Xu Han Liu Qiang Li Ning Tang Mi Kuang Wenying Yang Xia Liu Zexiong Chen |
| author_facet | Yifei Deng Chong Sun Xueqian Fu Yuan Guo Yongxing Zhu Chongyu Liu Ruxin Xu Han Liu Qiang Li Ning Tang Mi Kuang Wenying Yang Xia Liu Zexiong Chen |
| author_sort | Yifei Deng |
| collection | DOAJ |
| description | Abstract Background Leaf morphology plays a crucial role in forecasting the productivity and environmental adaptability of economically important trees. Plants with larger leaves usually have higher photosynthesis efficiency and can accumulate more nutrients, thereby increasing yield. In the natural population of Z. armatum, due to long-term selection, the leaves size and shape show rich diversity in different latitude regions. This diversity is the result of plants’ adaptation to different environments. However, to date, no studies have systematically revealed the genetic mechanism of Z. armatum leaf variation. In higher plants, lateral organ boundaries domain (LBD) proteins comprise a unique family of transcription factors that play pivotal roles in the establishment of plant leaf polarity and morphogenesis. However, little is currently known regarding the LBD gene family in Z. armatum. Results In this study, we identified 97 members of the LBD gene family within the genome of Z. armatum, which were unevenly distributed among the 33 chromosomes of this species. Physicochemical analysis revealed that these ZaLBDs are hydrophilic proteins with nuclear subcellular localization, whereas phylogenetic analysis of 234 LBD protein from different species indicated that these can be divided into five subfamilies (Ia, Ib, Ic, Id, and II). Furthermore, and analysis of cis-acting regulatory elements revealed that ZaLBDs may play important roles in responses to abiotic stress, hormone signal transduction, and plant growth and development. Transcriptomic data were used to compare the expression of these genes in leaves with differing morphologies collected from Z. armatum plants originating from sites at three different latitudes within the distribution range of this species. These data revealed differences in the expression of 14 genes among Z. armatum populations with different latitudinal distributions, with difference in the expression of the ZaLBD45 gene being the most pronounced, the expression trend of ZaLBD19 was consistent with the trend of leaf size. Moreover, qRT-PCR analysis verified that the relative expression of these genes was highly consistent with the transcriptomic data. Conclusions In this study, we comprehensively analyzed the functional characteristics and expression patterns of genes in the LBD family within the heterophyllous plant Z. armatum distributed at different latitudes. By mediating the regulation of leaf morphology, these genes may play important roles in the response to abiotic stress and adaptation to ecological changes. Our findings will not only enhance our understanding of the genetic mechanisms underlying the adaptive variation in Z. armatum but also provide valuable resources for the genetic improvement of this plant. |
| format | Article |
| id | doaj-art-78a018be505d4e54bd1723decc30670d |
| institution | DOAJ |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-78a018be505d4e54bd1723decc30670d2025-08-20T03:16:29ZengBMCBMC Plant Biology1471-22292025-05-0125111810.1186/s12870-025-06727-zGenome-wide identification and functional characterization of the LBD transcription factor gene family in Zanthoxylum armatum DC. reveal its potential role in leaf variationYifei Deng0Chong Sun1Xueqian Fu2Yuan Guo3Yongxing Zhu4Chongyu Liu5Ruxin Xu6Han Liu7Qiang Li8Ning Tang9Mi Kuang10Wenying Yang11Xia Liu12Zexiong Chen13Chongqing Key Laboratory of Economic Plant Biotechnology/Collaborative Innovation Center of Special Plant Industry in Chongqing/College of Smart Agriculture, Chongqing University of Arts and SciencesChongqing Key Laboratory of Economic Plant Biotechnology/Collaborative Innovation Center of Special Plant Industry in Chongqing/College of Smart Agriculture, Chongqing University of Arts and SciencesChongqing Key Laboratory of Economic Plant Biotechnology/Collaborative Innovation Center of Special Plant Industry in Chongqing/College of Smart Agriculture, Chongqing University of Arts and SciencesChongqing Key Laboratory of Economic Plant Biotechnology/Collaborative Innovation Center of Special Plant Industry in Chongqing/College of Smart Agriculture, Chongqing University of Arts and SciencesHubei Key Laboratory of Spices & Horticultural Plant Germplasm Innovation and Utilization, Yangtze UniversityChongqing Key Laboratory of Economic Plant Biotechnology/Collaborative Innovation Center of Special Plant Industry in Chongqing/College of Smart Agriculture, Chongqing University of Arts and SciencesChongqing Key Laboratory of Economic Plant Biotechnology/Collaborative Innovation Center of Special Plant Industry in Chongqing/College of Smart Agriculture, Chongqing University of Arts and SciencesChongqing Key Laboratory of Economic Plant Biotechnology/Collaborative Innovation Center of Special Plant Industry in Chongqing/College of Smart Agriculture, Chongqing University of Arts and SciencesChongqing Key Laboratory of Economic Plant Biotechnology/Collaborative Innovation Center of Special Plant Industry in Chongqing/College of Smart Agriculture, Chongqing University of Arts and SciencesChongqing Key Laboratory of Economic Plant Biotechnology/Collaborative Innovation Center of Special Plant Industry in Chongqing/College of Smart Agriculture, Chongqing University of Arts and SciencesChongqing Agricultural Technology Promotion General StationRongchang District Forestry Science and Technology Extension Station of ChongqingChongqing Key Laboratory of Economic Plant Biotechnology/Collaborative Innovation Center of Special Plant Industry in Chongqing/College of Smart Agriculture, Chongqing University of Arts and SciencesChongqing Key Laboratory of Economic Plant Biotechnology/Collaborative Innovation Center of Special Plant Industry in Chongqing/College of Smart Agriculture, Chongqing University of Arts and SciencesAbstract Background Leaf morphology plays a crucial role in forecasting the productivity and environmental adaptability of economically important trees. Plants with larger leaves usually have higher photosynthesis efficiency and can accumulate more nutrients, thereby increasing yield. In the natural population of Z. armatum, due to long-term selection, the leaves size and shape show rich diversity in different latitude regions. This diversity is the result of plants’ adaptation to different environments. However, to date, no studies have systematically revealed the genetic mechanism of Z. armatum leaf variation. In higher plants, lateral organ boundaries domain (LBD) proteins comprise a unique family of transcription factors that play pivotal roles in the establishment of plant leaf polarity and morphogenesis. However, little is currently known regarding the LBD gene family in Z. armatum. Results In this study, we identified 97 members of the LBD gene family within the genome of Z. armatum, which were unevenly distributed among the 33 chromosomes of this species. Physicochemical analysis revealed that these ZaLBDs are hydrophilic proteins with nuclear subcellular localization, whereas phylogenetic analysis of 234 LBD protein from different species indicated that these can be divided into five subfamilies (Ia, Ib, Ic, Id, and II). Furthermore, and analysis of cis-acting regulatory elements revealed that ZaLBDs may play important roles in responses to abiotic stress, hormone signal transduction, and plant growth and development. Transcriptomic data were used to compare the expression of these genes in leaves with differing morphologies collected from Z. armatum plants originating from sites at three different latitudes within the distribution range of this species. These data revealed differences in the expression of 14 genes among Z. armatum populations with different latitudinal distributions, with difference in the expression of the ZaLBD45 gene being the most pronounced, the expression trend of ZaLBD19 was consistent with the trend of leaf size. Moreover, qRT-PCR analysis verified that the relative expression of these genes was highly consistent with the transcriptomic data. Conclusions In this study, we comprehensively analyzed the functional characteristics and expression patterns of genes in the LBD family within the heterophyllous plant Z. armatum distributed at different latitudes. By mediating the regulation of leaf morphology, these genes may play important roles in the response to abiotic stress and adaptation to ecological changes. Our findings will not only enhance our understanding of the genetic mechanisms underlying the adaptive variation in Z. armatum but also provide valuable resources for the genetic improvement of this plant.https://doi.org/10.1186/s12870-025-06727-zZanthoxylum armatumZaLBDLeaf variationGene expression |
| spellingShingle | Yifei Deng Chong Sun Xueqian Fu Yuan Guo Yongxing Zhu Chongyu Liu Ruxin Xu Han Liu Qiang Li Ning Tang Mi Kuang Wenying Yang Xia Liu Zexiong Chen Genome-wide identification and functional characterization of the LBD transcription factor gene family in Zanthoxylum armatum DC. reveal its potential role in leaf variation BMC Plant Biology Zanthoxylum armatum ZaLBD Leaf variation Gene expression |
| title | Genome-wide identification and functional characterization of the LBD transcription factor gene family in Zanthoxylum armatum DC. reveal its potential role in leaf variation |
| title_full | Genome-wide identification and functional characterization of the LBD transcription factor gene family in Zanthoxylum armatum DC. reveal its potential role in leaf variation |
| title_fullStr | Genome-wide identification and functional characterization of the LBD transcription factor gene family in Zanthoxylum armatum DC. reveal its potential role in leaf variation |
| title_full_unstemmed | Genome-wide identification and functional characterization of the LBD transcription factor gene family in Zanthoxylum armatum DC. reveal its potential role in leaf variation |
| title_short | Genome-wide identification and functional characterization of the LBD transcription factor gene family in Zanthoxylum armatum DC. reveal its potential role in leaf variation |
| title_sort | genome wide identification and functional characterization of the lbd transcription factor gene family in zanthoxylum armatum dc reveal its potential role in leaf variation |
| topic | Zanthoxylum armatum ZaLBD Leaf variation Gene expression |
| url | https://doi.org/10.1186/s12870-025-06727-z |
| work_keys_str_mv | AT yifeideng genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT chongsun genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT xueqianfu genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT yuanguo genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT yongxingzhu genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT chongyuliu genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT ruxinxu genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT hanliu genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT qiangli genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT ningtang genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT mikuang genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT wenyingyang genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT xialiu genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation AT zexiongchen genomewideidentificationandfunctionalcharacterizationofthelbdtranscriptionfactorgenefamilyinzanthoxylumarmatumdcrevealitspotentialroleinleafvariation |