Genome-wide transcriptome analysis reveal the molecular mechanism for triggering the formation of purple leaves in rice mutants nip-lpl and nip-dpl
IntroductionThe color of rice leaves are important agronomic traits that directly influence the proportion of sunlight energy utilization and ultimately affect the yield and quality, so it is crucial to excavate the mechanism of regulating rice leave color. MethodsTo investigate the molecular mechan...
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Frontiers Media S.A.
2025-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1584423/full |
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| author | Chengyu Wang Hongyu Zhao Yujie Zhou Haipeng Zhang Xinyu Chen Weifang Liang Han Zheng Fan Hou Junjie Zhang Liujie Xie Mingwei Zhao Bingsong Zheng Jianzhong Li |
| author_facet | Chengyu Wang Hongyu Zhao Yujie Zhou Haipeng Zhang Xinyu Chen Weifang Liang Han Zheng Fan Hou Junjie Zhang Liujie Xie Mingwei Zhao Bingsong Zheng Jianzhong Li |
| author_sort | Chengyu Wang |
| collection | DOAJ |
| description | IntroductionThe color of rice leaves are important agronomic traits that directly influence the proportion of sunlight energy utilization and ultimately affect the yield and quality, so it is crucial to excavate the mechanism of regulating rice leave color. MethodsTo investigate the molecular mechanism that triggers the purple color in rice leaf, phenotypic characterization and genome-wide transcriptome analysis were conducted using the japonica rice cultivar nipponbare (Nip) and its two purple leaf mutants, nip-light purple leaf (nip-lpl) and nip-deep purple leaf (nip-dpl), are rice purple leaf mutants from Nip’s EMS mutant library.ResultsA total of 2247, 5484, 4525, 2103, 4375 and7029DEGs (differentially expressed genes) were identified in nip-a vs nip-lpl-a, nip-a vs nip-dpl-a, nip-c vs nip-dpl-c, nip-c vs nip-lpl-c, nip-lpl-c vs nip-dpl-c, nip-lpl-a vs nip-dpl-a, respectively. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that the DEGs were significantly enriched in phenylalanine biosynthesis, terpenoid backbone biosynthesis, secondary metabolite biosynthesis, and hormones. Additionally, WGCNA (Weighted Gene Co-expression Network Analysis) showed that the darkmagenta module was associated with the purple color mainly due to the accumulation of anthocyanin in the leaves of the mutant rice. This module revealed three pathways for anthocyanin synthesis: phenylalanine could be catalyzed by phenylalanine lyase and cinnamic acid hydroxylase, etc., to generate dihydroxyflavone and ultimately anthocyanin. Furthermore, we speculated that the elevated expression of three hub genes (PAL, CHI and CHS) in nip-lpl/dpl leads to increased anthocyanin content relative to Nip.DiscussionThese results not only revealed the molecular mechanism triggering leaf purple color in the rice mutants nip-lpl/dpl but also contributed greatly to identified potential genetic engineering targets for breeding anthocyanin-rich rice. |
| format | Article |
| id | doaj-art-26550012b7c44e79a098bc702cfa3b9c |
| institution | DOAJ |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-05-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj-art-26550012b7c44e79a098bc702cfa3b9c2025-08-20T03:05:53ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-05-011610.3389/fpls.2025.15844231584423Genome-wide transcriptome analysis reveal the molecular mechanism for triggering the formation of purple leaves in rice mutants nip-lpl and nip-dplChengyu Wang0Hongyu Zhao1Yujie Zhou2Haipeng Zhang3Xinyu Chen4Weifang Liang5Han Zheng6Fan Hou7Junjie Zhang8Liujie Xie9Mingwei Zhao10Bingsong Zheng11Jianzhong Li12College of Agronomy, Anhui Agricultural University, Hefei, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, ChinaZhuji Agricultural Technology Extension Center, Zhuji, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, ChinaCollege of Plant Protection, Shenyang Agricultural University, Shenyang, ChinaCollege of Plant Protection, Yunnan Agricultural University, Kunming, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, ChinaWuwangnong Seed shareholding Co., Ltd., Hangzhou, ChinaGuangzhou Gene Denovo Biotechnology Co., Ltd, Guanzhou, ChinaTaizhou Academy of Agricultural Sciences, Taizhou, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, ChinaNational Key Laboratory for Development and Utilization of Forest Food Resources, Zhejiang A&F University, Hangzhou, ChinaQujiang District Agricultural Technology Extension Center, Quzhou, ChinaIntroductionThe color of rice leaves are important agronomic traits that directly influence the proportion of sunlight energy utilization and ultimately affect the yield and quality, so it is crucial to excavate the mechanism of regulating rice leave color. MethodsTo investigate the molecular mechanism that triggers the purple color in rice leaf, phenotypic characterization and genome-wide transcriptome analysis were conducted using the japonica rice cultivar nipponbare (Nip) and its two purple leaf mutants, nip-light purple leaf (nip-lpl) and nip-deep purple leaf (nip-dpl), are rice purple leaf mutants from Nip’s EMS mutant library.ResultsA total of 2247, 5484, 4525, 2103, 4375 and7029DEGs (differentially expressed genes) were identified in nip-a vs nip-lpl-a, nip-a vs nip-dpl-a, nip-c vs nip-dpl-c, nip-c vs nip-lpl-c, nip-lpl-c vs nip-dpl-c, nip-lpl-a vs nip-dpl-a, respectively. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that the DEGs were significantly enriched in phenylalanine biosynthesis, terpenoid backbone biosynthesis, secondary metabolite biosynthesis, and hormones. Additionally, WGCNA (Weighted Gene Co-expression Network Analysis) showed that the darkmagenta module was associated with the purple color mainly due to the accumulation of anthocyanin in the leaves of the mutant rice. This module revealed three pathways for anthocyanin synthesis: phenylalanine could be catalyzed by phenylalanine lyase and cinnamic acid hydroxylase, etc., to generate dihydroxyflavone and ultimately anthocyanin. Furthermore, we speculated that the elevated expression of three hub genes (PAL, CHI and CHS) in nip-lpl/dpl leads to increased anthocyanin content relative to Nip.DiscussionThese results not only revealed the molecular mechanism triggering leaf purple color in the rice mutants nip-lpl/dpl but also contributed greatly to identified potential genetic engineering targets for breeding anthocyanin-rich rice.https://www.frontiersin.org/articles/10.3389/fpls.2025.1584423/fulltranscriptomeWGCNApurple leaf mutationanthocyaninsecondary metabolism |
| spellingShingle | Chengyu Wang Hongyu Zhao Yujie Zhou Haipeng Zhang Xinyu Chen Weifang Liang Han Zheng Fan Hou Junjie Zhang Liujie Xie Mingwei Zhao Bingsong Zheng Jianzhong Li Genome-wide transcriptome analysis reveal the molecular mechanism for triggering the formation of purple leaves in rice mutants nip-lpl and nip-dpl Frontiers in Plant Science transcriptome WGCNA purple leaf mutation anthocyanin secondary metabolism |
| title | Genome-wide transcriptome analysis reveal the molecular mechanism for triggering the formation of purple leaves in rice mutants nip-lpl and nip-dpl |
| title_full | Genome-wide transcriptome analysis reveal the molecular mechanism for triggering the formation of purple leaves in rice mutants nip-lpl and nip-dpl |
| title_fullStr | Genome-wide transcriptome analysis reveal the molecular mechanism for triggering the formation of purple leaves in rice mutants nip-lpl and nip-dpl |
| title_full_unstemmed | Genome-wide transcriptome analysis reveal the molecular mechanism for triggering the formation of purple leaves in rice mutants nip-lpl and nip-dpl |
| title_short | Genome-wide transcriptome analysis reveal the molecular mechanism for triggering the formation of purple leaves in rice mutants nip-lpl and nip-dpl |
| title_sort | genome wide transcriptome analysis reveal the molecular mechanism for triggering the formation of purple leaves in rice mutants nip lpl and nip dpl |
| topic | transcriptome WGCNA purple leaf mutation anthocyanin secondary metabolism |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1584423/full |
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