Combined analysis of lncRNAs and mRNAs associated with coloration and wax formation during ‘Fumei’ Apple development
Abstract ‘Fumei’ apple is characterized by high anthocyanin content and thick wax layer. Long non-coding RNAs (lncRNAs) play essential roles in the growth and development of various plants via regulation of gene expression. This study explored the potential mechanism underlying anthocyanin accumulat...
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| Format: | Article |
| Language: | English |
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BMC
2025-04-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-025-06545-3 |
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| author | Wenping Huo Shasha Liu Xiao Chen Tingting Gu Zhongkang Wang Xiaolong Xu Daliang Liu Yugang Zhang Shenghui Jiang |
| author_facet | Wenping Huo Shasha Liu Xiao Chen Tingting Gu Zhongkang Wang Xiaolong Xu Daliang Liu Yugang Zhang Shenghui Jiang |
| author_sort | Wenping Huo |
| collection | DOAJ |
| description | Abstract ‘Fumei’ apple is characterized by high anthocyanin content and thick wax layer. Long non-coding RNAs (lncRNAs) play essential roles in the growth and development of various plants via regulation of gene expression. This study explored the potential mechanism underlying anthocyanin accumulation and cuticular wax formation during the development of ‘Fumei’ apple fruit. The results demonstrated that anthocyanin accumulation correlates with fruit coloration, while wax content drives wax layer formation. A total of 6039 and 3410 differentially expressed genes (DEGs), as well as 230 and 131 differentially expressed lncRNAs (DELs) were identified in the M1/M2 and M2/M3 pairs, respectively, by using RNA-seq. In the M1/M2 pair, the DEGs were mainly enriched in the ‘photosynthesis’ and ‘flavonoid biosynthesis’ pathways; in the M2/M3 pair, the DEGs were significantly enriched in the ‘photosynthesis’ and ‘cutin, suberine and wax biosynthesis’ pathways. Furthermore, the structural and regulatory genes involved in anthocyanin and cuticular wax biosynthesis were investigated, and the potential lncRNAs and genes that may control the anthocyanin and cuticular wax biosynthesis were identified. This study provides candidate lncRNAs and potential regulatory genes associated with both the regulation of anthocyanins and wax during apple development. |
| format | Article |
| id | doaj-art-225682e3f3874b478dcbe347cbed44b6 |
| institution | OA Journals |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-225682e3f3874b478dcbe347cbed44b62025-08-20T02:30:22ZengBMCBMC Plant Biology1471-22292025-04-0125111410.1186/s12870-025-06545-3Combined analysis of lncRNAs and mRNAs associated with coloration and wax formation during ‘Fumei’ Apple developmentWenping Huo0Shasha Liu1Xiao Chen2Tingting Gu3Zhongkang Wang4Xiaolong Xu5Daliang Liu6Yugang Zhang7Shenghui Jiang8College of Horticulture, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural UniversityCollege of Horticulture, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural UniversityCollege of Agronomy, Qingdao Agricultural UniversityCollege of Agricultural Sciences and Technology, Shandong Agriculture And Engineering UniversityCollege of Horticulture, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural UniversityCollege of Horticulture, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural UniversityCollege of Horticulture, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural UniversityCollege of Horticulture, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural UniversityCollege of Horticulture, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural UniversityAbstract ‘Fumei’ apple is characterized by high anthocyanin content and thick wax layer. Long non-coding RNAs (lncRNAs) play essential roles in the growth and development of various plants via regulation of gene expression. This study explored the potential mechanism underlying anthocyanin accumulation and cuticular wax formation during the development of ‘Fumei’ apple fruit. The results demonstrated that anthocyanin accumulation correlates with fruit coloration, while wax content drives wax layer formation. A total of 6039 and 3410 differentially expressed genes (DEGs), as well as 230 and 131 differentially expressed lncRNAs (DELs) were identified in the M1/M2 and M2/M3 pairs, respectively, by using RNA-seq. In the M1/M2 pair, the DEGs were mainly enriched in the ‘photosynthesis’ and ‘flavonoid biosynthesis’ pathways; in the M2/M3 pair, the DEGs were significantly enriched in the ‘photosynthesis’ and ‘cutin, suberine and wax biosynthesis’ pathways. Furthermore, the structural and regulatory genes involved in anthocyanin and cuticular wax biosynthesis were investigated, and the potential lncRNAs and genes that may control the anthocyanin and cuticular wax biosynthesis were identified. This study provides candidate lncRNAs and potential regulatory genes associated with both the regulation of anthocyanins and wax during apple development.https://doi.org/10.1186/s12870-025-06545-3AppleAnthocyaninWaxlncRNAs |
| spellingShingle | Wenping Huo Shasha Liu Xiao Chen Tingting Gu Zhongkang Wang Xiaolong Xu Daliang Liu Yugang Zhang Shenghui Jiang Combined analysis of lncRNAs and mRNAs associated with coloration and wax formation during ‘Fumei’ Apple development BMC Plant Biology Apple Anthocyanin Wax lncRNAs |
| title | Combined analysis of lncRNAs and mRNAs associated with coloration and wax formation during ‘Fumei’ Apple development |
| title_full | Combined analysis of lncRNAs and mRNAs associated with coloration and wax formation during ‘Fumei’ Apple development |
| title_fullStr | Combined analysis of lncRNAs and mRNAs associated with coloration and wax formation during ‘Fumei’ Apple development |
| title_full_unstemmed | Combined analysis of lncRNAs and mRNAs associated with coloration and wax formation during ‘Fumei’ Apple development |
| title_short | Combined analysis of lncRNAs and mRNAs associated with coloration and wax formation during ‘Fumei’ Apple development |
| title_sort | combined analysis of lncrnas and mrnas associated with coloration and wax formation during fumei apple development |
| topic | Apple Anthocyanin Wax lncRNAs |
| url | https://doi.org/10.1186/s12870-025-06545-3 |
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