Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties
Fruit acidity is one of the main determinants of fruit flavor and a target trait in fruit breeding. However, the genomic mechanisms governing acidity variation among different pear varieties remain poorly understood. In this study, two pear varieties with contrasting organic acid levels, ‘Dangshansu...
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MDPI AG
2021-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/17/9622 |
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| author | Qionghou Li Xin Qiao Luting Jia Yuxin Zhang Shaoling Zhang |
| author_facet | Qionghou Li Xin Qiao Luting Jia Yuxin Zhang Shaoling Zhang |
| author_sort | Qionghou Li |
| collection | DOAJ |
| description | Fruit acidity is one of the main determinants of fruit flavor and a target trait in fruit breeding. However, the genomic mechanisms governing acidity variation among different pear varieties remain poorly understood. In this study, two pear varieties with contrasting organic acid levels, ‘Dangshansuli’ (low-acidity) and ‘Amute’ (high-acidity), were selected, and a combination of transcriptome and population genomics analyses were applied to characterize their patterns of gene expression and genetic variation. Based on RNA-seq data analysis, differentially expressed genes (DEGs) involved in organic acid metabolism and accumulation were identified. Weighted correlation network analysis (WGCNA) revealed that nine candidate TCA (tricarboxylic acid)-related DEGs and three acid transporter-related DEGs were located in three key modules. The regulatory networks of the above candidate genes were also predicted. By integrating pear resequencing data, two domestication-related genes were found to be upregulated in ‘Amute’, and this trend was further validated for other pear varieties with high levels of organic acid, suggesting distinct selective sweeps during pear dissemination and domestication. Collectively, this study provides insight into organic acid differences related to expression divergence and domestication in two pear varieties, pinpointing several candidate genes for the genetic manipulation of acidity in pears. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T08:10:04Z |
| publishDate | 2021-09-01 |
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| spelling | doaj.art-bdfd855aaee046d5b8c47e7d974d1a9d2023-11-22T10:46:24ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-09-012217962210.3390/ijms22179622Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear VarietiesQionghou Li0Xin Qiao1Luting Jia2Yuxin Zhang3Shaoling Zhang4State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, ChinaFruit acidity is one of the main determinants of fruit flavor and a target trait in fruit breeding. However, the genomic mechanisms governing acidity variation among different pear varieties remain poorly understood. In this study, two pear varieties with contrasting organic acid levels, ‘Dangshansuli’ (low-acidity) and ‘Amute’ (high-acidity), were selected, and a combination of transcriptome and population genomics analyses were applied to characterize their patterns of gene expression and genetic variation. Based on RNA-seq data analysis, differentially expressed genes (DEGs) involved in organic acid metabolism and accumulation were identified. Weighted correlation network analysis (WGCNA) revealed that nine candidate TCA (tricarboxylic acid)-related DEGs and three acid transporter-related DEGs were located in three key modules. The regulatory networks of the above candidate genes were also predicted. By integrating pear resequencing data, two domestication-related genes were found to be upregulated in ‘Amute’, and this trend was further validated for other pear varieties with high levels of organic acid, suggesting distinct selective sweeps during pear dissemination and domestication. Collectively, this study provides insight into organic acid differences related to expression divergence and domestication in two pear varieties, pinpointing several candidate genes for the genetic manipulation of acidity in pears.https://www.mdpi.com/1422-0067/22/17/9622organic acid metabolismWGCNAregulatory networkdomestication |
| spellingShingle | Qionghou Li Xin Qiao Luting Jia Yuxin Zhang Shaoling Zhang Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties International Journal of Molecular Sciences organic acid metabolism WGCNA regulatory network domestication |
| title | Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties |
| title_full | Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties |
| title_fullStr | Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties |
| title_full_unstemmed | Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties |
| title_short | Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties |
| title_sort | transcriptome and resequencing analyses provide insight into differences in organic acid accumulation in two pear varieties |
| topic | organic acid metabolism WGCNA regulatory network domestication |
| url | https://www.mdpi.com/1422-0067/22/17/9622 |
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