Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum
Abstract Background Heterosis breeding is one of the most important breeding methods for chrysanthemum. To date, the genetic mechanisms of heterosis for waterlogging tolerance in chrysanthemum are still unclear. This study aims to analyze the expression profiles and potential heterosis-related genes...
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| Format: | Article |
| Language: | English |
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BMC
2024-04-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-024-04954-4 |
| _version_ | 1797209443451011072 |
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| author | Jiangshuo Su Limin Zhao Yingnan Yang Yang Yang Xuefeng Zhang Zhiyong Guan Weimin Fang Fadi Chen Fei Zhang |
| author_facet | Jiangshuo Su Limin Zhao Yingnan Yang Yang Yang Xuefeng Zhang Zhiyong Guan Weimin Fang Fadi Chen Fei Zhang |
| author_sort | Jiangshuo Su |
| collection | DOAJ |
| description | Abstract Background Heterosis breeding is one of the most important breeding methods for chrysanthemum. To date, the genetic mechanisms of heterosis for waterlogging tolerance in chrysanthemum are still unclear. This study aims to analyze the expression profiles and potential heterosis-related genes of two hybrid lines and their parents with extreme differences in waterlogging tolerance under control and waterlogging stress conditions by RNA-seq. Results A population of 140 F1 progeny derived from Chrysanthemum indicum (Nanchang) (waterlogging-tolerant) and Chrysanthemum indicum (Nanjing) (waterlogging-sensitive) was used to characterize the extent of genetic variation in terms of seven waterlogging tolerance-related traits across two years. Lines 98 and 95, respectively displaying positive and negative overdominance heterosis for the waterlogging tolerance traits together with their parents under control and waterlogging stress conditions, were used for RNA-seq. In consequence, the maximal number of differentially expressed genes (DEGs) occurred in line 98. Gene ontology (GO) enrichment analysis revealed multiple stress-related biological processes for the common up-regulated genes. Line 98 had a significant increase in non-additive genes under waterlogging stress, with transgressive up-regulation and paternal-expression dominant patterns being the major gene expression profiles. Further, GO analysis identified 55 and 95 transgressive up-regulation genes that overlapped with the up-regulated genes shared by two parents in terms of responses to stress and stimulus, respectively. 6,640 genes in total displaying maternal-expression dominance patterns were observed in line 95. In addition, 16 key candidate genes, including SAP12, DOX1, and ERF017 which might be of significant importance for the formation of waterlogging tolerance heterosis in line 98, were highlighted. Conclusion The current study provides a comprehensive overview of the root transcriptomes among F1 hybrids and their parents under waterlogging stress. These findings lay the foundation for further studies on molecular mechanisms underlying chrysanthemum heterosis on waterlogging tolerance. |
| first_indexed | 2024-04-24T09:54:47Z |
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| id | doaj.art-d96010d0c6784f8c8e32b5d20061823e |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-24T09:54:47Z |
| publishDate | 2024-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-d96010d0c6784f8c8e32b5d20061823e2024-04-14T11:11:59ZengBMCBMC Plant Biology1471-22292024-04-0124111610.1186/s12870-024-04954-4Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicumJiangshuo Su0Limin Zhao1Yingnan Yang2Yang Yang3Xuefeng Zhang4Zhiyong Guan5Weimin Fang6Fadi Chen7Fei Zhang8State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural UniversityState Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural UniversityState Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural UniversityState Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural UniversityState Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural UniversityState Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural UniversityState Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural UniversityState Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural UniversityState Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural UniversityAbstract Background Heterosis breeding is one of the most important breeding methods for chrysanthemum. To date, the genetic mechanisms of heterosis for waterlogging tolerance in chrysanthemum are still unclear. This study aims to analyze the expression profiles and potential heterosis-related genes of two hybrid lines and their parents with extreme differences in waterlogging tolerance under control and waterlogging stress conditions by RNA-seq. Results A population of 140 F1 progeny derived from Chrysanthemum indicum (Nanchang) (waterlogging-tolerant) and Chrysanthemum indicum (Nanjing) (waterlogging-sensitive) was used to characterize the extent of genetic variation in terms of seven waterlogging tolerance-related traits across two years. Lines 98 and 95, respectively displaying positive and negative overdominance heterosis for the waterlogging tolerance traits together with their parents under control and waterlogging stress conditions, were used for RNA-seq. In consequence, the maximal number of differentially expressed genes (DEGs) occurred in line 98. Gene ontology (GO) enrichment analysis revealed multiple stress-related biological processes for the common up-regulated genes. Line 98 had a significant increase in non-additive genes under waterlogging stress, with transgressive up-regulation and paternal-expression dominant patterns being the major gene expression profiles. Further, GO analysis identified 55 and 95 transgressive up-regulation genes that overlapped with the up-regulated genes shared by two parents in terms of responses to stress and stimulus, respectively. 6,640 genes in total displaying maternal-expression dominance patterns were observed in line 95. In addition, 16 key candidate genes, including SAP12, DOX1, and ERF017 which might be of significant importance for the formation of waterlogging tolerance heterosis in line 98, were highlighted. Conclusion The current study provides a comprehensive overview of the root transcriptomes among F1 hybrids and their parents under waterlogging stress. These findings lay the foundation for further studies on molecular mechanisms underlying chrysanthemum heterosis on waterlogging tolerance.https://doi.org/10.1186/s12870-024-04954-4ChrysanthemumHeterosisWaterlogging toleranceRNA-seqOverdominant expression |
| spellingShingle | Jiangshuo Su Limin Zhao Yingnan Yang Yang Yang Xuefeng Zhang Zhiyong Guan Weimin Fang Fadi Chen Fei Zhang Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum BMC Plant Biology Chrysanthemum Heterosis Waterlogging tolerance RNA-seq Overdominant expression |
| title | Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum |
| title_full | Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum |
| title_fullStr | Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum |
| title_full_unstemmed | Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum |
| title_short | Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum |
| title_sort | comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in chrysanthemum indicum |
| topic | Chrysanthemum Heterosis Waterlogging tolerance RNA-seq Overdominant expression |
| url | https://doi.org/10.1186/s12870-024-04954-4 |
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