Comparative Transcriptome Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Barley
Waterlogging is becoming a global issue, affecting crop growth and yield in low-lying rainfed areas. A DH line, TamF169, showing superior waterlogging tolerance, and its waterlogging-sensitive parent, Franklin, were used to conduct transcriptome analyses. The results showed that 2209 and 2578 differ...
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2024-12-01
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| author | Juan Zhu Haoxin Yin Cong Cao Chengqun Sun Mengna Zhang Yi Hong Yuhang Zhang Chao Lv Baojian Guo Feifei Wang Rugen Xu |
| author_facet | Juan Zhu Haoxin Yin Cong Cao Chengqun Sun Mengna Zhang Yi Hong Yuhang Zhang Chao Lv Baojian Guo Feifei Wang Rugen Xu |
| author_sort | Juan Zhu |
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| description | Waterlogging is becoming a global issue, affecting crop growth and yield in low-lying rainfed areas. A DH line, TamF169, showing superior waterlogging tolerance, and its waterlogging-sensitive parent, Franklin, were used to conduct transcriptome analyses. The results showed that 2209 and 2578 differentially expressed genes (DEGs) in Franklin and 1997 and 1709 DEGs in TamF169 were detected by comparing gene expression levels under control and waterlogging after 4 and 8 days, respectively, with 392 and 257 DEGs being specific to TamF169 after 4 and 8 days under waterlogging, respectively. KEGG analysis showed that glycolysis/gluconeogenesis, the MAPK signaling pathway, plant hormone signaling, and galactose metabolism pathways were significantly enriched in the waterlogging-tolerant genotype TamF169 four days after waterlogging. The qPCR results were consistent with the transcriptome data, suggesting the reliability of the transcriptome sequencing. A total of 13 genes in the mapping region of a QTL for root cortical aerenchyma (RCA) showed different expression levels in Franklin or TamF169, and the potential candidate genes for <i>RCA−QTL</i> are discussed. This study offers valuable information on the mechanism of tolerance to waterlogging stress in the DH line TamF169 and provides the candidate genes for <i>RCA−QTL</i>. |
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| institution | Kabale University |
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| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
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| spelling | doaj-art-570d69f867e749149ed2bbad8d69c95b2025-01-10T13:19:32ZengMDPI AGPlants2223-77472024-12-011412810.3390/plants14010028Comparative Transcriptome Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in BarleyJuan Zhu0Haoxin Yin1Cong Cao2Chengqun Sun3Mengna Zhang4Yi Hong5Yuhang Zhang6Chao Lv7Baojian Guo8Feifei Wang9Rugen Xu10Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safetyof Ministry of Education of China, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safetyof Ministry of Education of China, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safetyof Ministry of Education of China, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safetyof Ministry of Education of China, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safetyof Ministry of Education of China, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safetyof Ministry of Education of China, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safetyof Ministry of Education of China, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safetyof Ministry of Education of China, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safetyof Ministry of Education of China, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safetyof Ministry of Education of China, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safetyof Ministry of Education of China, Yangzhou University, Yangzhou 225009, ChinaWaterlogging is becoming a global issue, affecting crop growth and yield in low-lying rainfed areas. A DH line, TamF169, showing superior waterlogging tolerance, and its waterlogging-sensitive parent, Franklin, were used to conduct transcriptome analyses. The results showed that 2209 and 2578 differentially expressed genes (DEGs) in Franklin and 1997 and 1709 DEGs in TamF169 were detected by comparing gene expression levels under control and waterlogging after 4 and 8 days, respectively, with 392 and 257 DEGs being specific to TamF169 after 4 and 8 days under waterlogging, respectively. KEGG analysis showed that glycolysis/gluconeogenesis, the MAPK signaling pathway, plant hormone signaling, and galactose metabolism pathways were significantly enriched in the waterlogging-tolerant genotype TamF169 four days after waterlogging. The qPCR results were consistent with the transcriptome data, suggesting the reliability of the transcriptome sequencing. A total of 13 genes in the mapping region of a QTL for root cortical aerenchyma (RCA) showed different expression levels in Franklin or TamF169, and the potential candidate genes for <i>RCA−QTL</i> are discussed. This study offers valuable information on the mechanism of tolerance to waterlogging stress in the DH line TamF169 and provides the candidate genes for <i>RCA−QTL</i>.https://www.mdpi.com/2223-7747/14/1/28waterlogging tolerancetranscriptome analysisdifferentially expressed genesKEGG analysiscandidate genes |
| spellingShingle | Juan Zhu Haoxin Yin Cong Cao Chengqun Sun Mengna Zhang Yi Hong Yuhang Zhang Chao Lv Baojian Guo Feifei Wang Rugen Xu Comparative Transcriptome Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Barley Plants waterlogging tolerance transcriptome analysis differentially expressed genes KEGG analysis candidate genes |
| title | Comparative Transcriptome Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Barley |
| title_full | Comparative Transcriptome Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Barley |
| title_fullStr | Comparative Transcriptome Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Barley |
| title_full_unstemmed | Comparative Transcriptome Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Barley |
| title_short | Comparative Transcriptome Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Barley |
| title_sort | comparative transcriptome analyses reveal the mechanisms underlying waterlogging tolerance in barley |
| topic | waterlogging tolerance transcriptome analysis differentially expressed genes KEGG analysis candidate genes |
| url | https://www.mdpi.com/2223-7747/14/1/28 |
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