Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors
Abstract Background Fruit acidity and color are important quality attributes in peaches. Although there are some exceptions, blood-fleshed peaches typically have a sour taste. However, little is known about the genetic variations linking organic acid and color regulation in peaches. Results Here, we...
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2025-01-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-024-03470-w |
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| author | Wenbo Chen Qi Xie Jia Fu Shaojia Li Yanna Shi Jiao Lu Yuanyuan Zhang Yingjie Zhao Ruijuan Ma Baijun Li Bo Zhang Donald Grierson Mingliang Yu Zhangjun Fei Kunsong Chen |
| author_facet | Wenbo Chen Qi Xie Jia Fu Shaojia Li Yanna Shi Jiao Lu Yuanyuan Zhang Yingjie Zhao Ruijuan Ma Baijun Li Bo Zhang Donald Grierson Mingliang Yu Zhangjun Fei Kunsong Chen |
| author_sort | Wenbo Chen |
| collection | DOAJ |
| description | Abstract Background Fruit acidity and color are important quality attributes in peaches. Although there are some exceptions, blood-fleshed peaches typically have a sour taste. However, little is known about the genetic variations linking organic acid and color regulation in peaches. Results Here, we report a peach graph-based pangenome constructed from sixteen individual genome assemblies, capturing abundant structural variations and 82.3 Mb of sequences absent in the reference genome. Pangenome analysis reveals a long terminal repeat retrotransposon insertion in the promoter of the NAC transcription factor (TF) PpBL in blood-fleshed peaches, which enhances PpBL expression. Genome-wide association study identifies a significant association between PpBL and malate content. Silencing PpBL in peach fruit and ectopic overexpression of PpBL in tomatoes confirm that PpBL is a positive regulator of malate accumulation. Furthermore, we demonstrate that PpBL works synergistically with another NAC TF, PpNAC1, to activate the transcription of the aluminum-activated malate transporter PpALMT4, leading to increased malate content. Conclusions These findings, along with previous research showing that PpBL and PpNAC1 also regulate anthocyanin accumulation, explain the red coloration and sour taste in blood-fleshed peach fruits. |
| format | Article |
| id | doaj-art-9fd1c11cd7d047e5a36a7f4435491ee2 |
| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-9fd1c11cd7d047e5a36a7f4435491ee22025-01-12T12:26:00ZengBMCGenome Biology1474-760X2025-01-0126112010.1186/s13059-024-03470-wGraph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factorsWenbo Chen0Qi Xie1Jia Fu2Shaojia Li3Yanna Shi4Jiao Lu5Yuanyuan Zhang6Yingjie Zhao7Ruijuan Ma8Baijun Li9Bo Zhang10Donald Grierson11Mingliang Yu12Zhangjun Fei13Kunsong Chen14College of Agriculture & Biotechnology, Zhejiang UniversityCollege of Agriculture & Biotechnology, Zhejiang UniversityCollege of Agriculture & Biotechnology, Zhejiang UniversityCollege of Agriculture & Biotechnology, Zhejiang UniversityCollege of Agriculture & Biotechnology, Zhejiang UniversityCollege of Agriculture & Biotechnology, Zhejiang UniversityInstitute of Pomology, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural SciencesCollege of Agriculture & Biotechnology, Zhejiang UniversityInstitute of Pomology, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural SciencesCollege of Agriculture & Biotechnology, Zhejiang UniversityCollege of Agriculture & Biotechnology, Zhejiang UniversityThe State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang UniversityInstitute of Pomology, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural SciencesBoyce Thompson Institute, Cornell UniversityCollege of Agriculture & Biotechnology, Zhejiang UniversityAbstract Background Fruit acidity and color are important quality attributes in peaches. Although there are some exceptions, blood-fleshed peaches typically have a sour taste. However, little is known about the genetic variations linking organic acid and color regulation in peaches. Results Here, we report a peach graph-based pangenome constructed from sixteen individual genome assemblies, capturing abundant structural variations and 82.3 Mb of sequences absent in the reference genome. Pangenome analysis reveals a long terminal repeat retrotransposon insertion in the promoter of the NAC transcription factor (TF) PpBL in blood-fleshed peaches, which enhances PpBL expression. Genome-wide association study identifies a significant association between PpBL and malate content. Silencing PpBL in peach fruit and ectopic overexpression of PpBL in tomatoes confirm that PpBL is a positive regulator of malate accumulation. Furthermore, we demonstrate that PpBL works synergistically with another NAC TF, PpNAC1, to activate the transcription of the aluminum-activated malate transporter PpALMT4, leading to increased malate content. Conclusions These findings, along with previous research showing that PpBL and PpNAC1 also regulate anthocyanin accumulation, explain the red coloration and sour taste in blood-fleshed peach fruits.https://doi.org/10.1186/s13059-024-03470-wGraph pangenomePeachMalate contentBlood-fleshedNAC |
| spellingShingle | Wenbo Chen Qi Xie Jia Fu Shaojia Li Yanna Shi Jiao Lu Yuanyuan Zhang Yingjie Zhao Ruijuan Ma Baijun Li Bo Zhang Donald Grierson Mingliang Yu Zhangjun Fei Kunsong Chen Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors Genome Biology Graph pangenome Peach Malate content Blood-fleshed NAC |
| title | Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors |
| title_full | Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors |
| title_fullStr | Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors |
| title_full_unstemmed | Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors |
| title_short | Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors |
| title_sort | graph pangenome reveals the regulation of malate content in blood fleshed peach by nac transcription factors |
| topic | Graph pangenome Peach Malate content Blood-fleshed NAC |
| url | https://doi.org/10.1186/s13059-024-03470-w |
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