Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples
Low-acid apples are popular among consumers, but the mechanisms behind the complex differences in acidity among varieties that are caused by high altitude are not clear. In this study, we used the ‘Golden Delicious’ apple and its superior variant in the Western Sichuan Plateau of China to analyze or...
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MDPI AG
2025-05-01
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| Series: | Current Issues in Molecular Biology |
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| Online Access: | https://www.mdpi.com/1467-3045/47/5/341 |
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| author | Wenyuan Yang Hang Yu Lian Tao Hongjiang Xie |
| author_facet | Wenyuan Yang Hang Yu Lian Tao Hongjiang Xie |
| author_sort | Wenyuan Yang |
| collection | DOAJ |
| description | Low-acid apples are popular among consumers, but the mechanisms behind the complex differences in acidity among varieties that are caused by high altitude are not clear. In this study, we used the ‘Golden Delicious’ apple and its superior variant in the Western Sichuan Plateau of China to analyze organic acid composition, content, and the expression levels of related regulated genes during fruit development. We found that the organic acid content in the variant was significantly lower than that in the ‘Golden Delicious’ apple. In both apples, quinic and malic acids were the predominant organic acids, while citric and tartaric acids were present in lower amounts. In this multidimensional regulatory study, we used transcriptome sequencing, cluster analysis, and weighted gene co-expression network analysis (WGCNA) to reveal that differentially expressed genes are enriched in multiple pathways affecting fruit acidity during apple development; malate dehydrogenase (MDH) affects the malic acid content of fruits of different varieties; and H<sup>+</sup>-ATPase (VHA) mainly regulates the content of vacuolar organic acids, which affects fruit acidity. Additionally, we performed qRT-PCR experiments to validate our results. This study provides molecular insights into the mechanisms by which low-acidity traits form in apples and offers a theoretical basis for regulating the flavor of fleshy fruits. |
| format | Article |
| id | doaj-art-8b4f36867aa74fecb8d77942da3b8ac6 |
| institution | DOAJ |
| issn | 1467-3037 1467-3045 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Current Issues in Molecular Biology |
| spelling | doaj-art-8b4f36867aa74fecb8d77942da3b8ac62025-08-20T03:14:42ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452025-05-0147534110.3390/cimb47050341Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of ApplesWenyuan Yang0Hang Yu1Lian Tao2Hongjiang Xie3Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, ChinaHorticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, ChinaHorticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, ChinaHorticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, ChinaLow-acid apples are popular among consumers, but the mechanisms behind the complex differences in acidity among varieties that are caused by high altitude are not clear. In this study, we used the ‘Golden Delicious’ apple and its superior variant in the Western Sichuan Plateau of China to analyze organic acid composition, content, and the expression levels of related regulated genes during fruit development. We found that the organic acid content in the variant was significantly lower than that in the ‘Golden Delicious’ apple. In both apples, quinic and malic acids were the predominant organic acids, while citric and tartaric acids were present in lower amounts. In this multidimensional regulatory study, we used transcriptome sequencing, cluster analysis, and weighted gene co-expression network analysis (WGCNA) to reveal that differentially expressed genes are enriched in multiple pathways affecting fruit acidity during apple development; malate dehydrogenase (MDH) affects the malic acid content of fruits of different varieties; and H<sup>+</sup>-ATPase (VHA) mainly regulates the content of vacuolar organic acids, which affects fruit acidity. Additionally, we performed qRT-PCR experiments to validate our results. This study provides molecular insights into the mechanisms by which low-acidity traits form in apples and offers a theoretical basis for regulating the flavor of fleshy fruits.https://www.mdpi.com/1467-3045/47/5/341appleWestern Sichuan plateaumutant varietyfruit ripeningacidity |
| spellingShingle | Wenyuan Yang Hang Yu Lian Tao Hongjiang Xie Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples Current Issues in Molecular Biology apple Western Sichuan plateau mutant variety fruit ripening acidity |
| title | Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples |
| title_full | Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples |
| title_fullStr | Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples |
| title_full_unstemmed | Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples |
| title_short | Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples |
| title_sort | multidimensional transcriptomics reveals the key genes and pathways regulating the acidity of apples |
| topic | apple Western Sichuan plateau mutant variety fruit ripening acidity |
| url | https://www.mdpi.com/1467-3045/47/5/341 |
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