Integrative Physiological and Transcriptomic Analysis Reveals Metabolic Adaptation and Cold-Tolerance Marker Development in Winter Rye Under Low-Temperature Stress
Rye (<i>Secale cereale</i>), a cereal crop with high cold tolerance, serves as an ideal model for investigating plant cold adaptation mechanisms. Despite recent progress in identifying numerous genes and metabolic changes associated with cold tolerance, the detailed regulatory networks a...
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MDPI AG
2025-05-01
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| author | Haonan Li Jiahuan Zhao Chenguang He Yang Guan Huimin Guan Ting He Dexu Meng Xiaoping Wang Yimiao Tang |
| author_facet | Haonan Li Jiahuan Zhao Chenguang He Yang Guan Huimin Guan Ting He Dexu Meng Xiaoping Wang Yimiao Tang |
| author_sort | Haonan Li |
| collection | DOAJ |
| description | Rye (<i>Secale cereale</i>), a cereal crop with high cold tolerance, serves as an ideal model for investigating plant cold adaptation mechanisms. Despite recent progress in identifying numerous genes and metabolic changes associated with cold tolerance, the detailed regulatory networks and coordinated interactions between metabolic pathways under low-temperature stress in rye remain unclear. In this study, we focused on the winter rye variety “Winter” and systematically explored its metabolic regulatory responses to cold stress through a combination of low-temperature treatments, phenotypic observations, antioxidant enzyme activity assays, and transcriptomic analysis. Four rye varieties (“Winter”, HZHM3, HZHM8, and “Victory”) were compared for cold tolerance, with the results indicating that “Winter” and HZHM3 exhibit superior cold tolerance. Physiological analysis revealed that after 12 h of exposure to −4 °C, the activities of catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) in “Winter” were significantly upregulated, displaying an initial increase followed by a decline over time. Transcriptomic sequencing identified 1643 differentially expressed genes (DEGs), and GO, KEGG, and GSEA enrichment analyses highlighted the critical roles of carbohydrate metabolism (ko00630) and amino acid metabolism (ko00250) pathways in the cold stress response. These pathways are interconnected through key metabolic intermediates such as L-glutamate, collectively regulating cold adaptation. Furthermore, based on the transcriptomic data, we identified and developed molecular markers associated with cold tolerance, detecting 10,846 EST-SSR and 250,116 EST-SNP markers. We successfully developed 13 EST-SSR primer pairs applicable to rye and 7 KASP markers. Notably, the KASP-665 marker effectively distinguishes between winter and spring rye, providing a reliable tool for marker-assisted selection in cold tolerance breeding. This study not only elucidates the metabolic regulatory mechanisms of rye under low-temperature stress but also provides a solid theoretical and technical foundation for future cold-tolerance breeding programs. |
| format | Article |
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| institution | OA Journals |
| issn | 2223-7747 |
| language | English |
| publishDate | 2025-05-01 |
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| series | Plants |
| spelling | doaj-art-e54e390fc2fe4efc9ebfdd47697af1bd2025-08-20T02:23:05ZengMDPI AGPlants2223-77472025-05-011411158810.3390/plants14111588Integrative Physiological and Transcriptomic Analysis Reveals Metabolic Adaptation and Cold-Tolerance Marker Development in Winter Rye Under Low-Temperature StressHaonan Li0Jiahuan Zhao1Chenguang He2Yang Guan3Huimin Guan4Ting He5Dexu Meng6Xiaoping Wang7Yimiao Tang8Key Laboratory of Molecular Cell Genetics and Genetic Breeding in Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, ChinaKey Laboratory of Molecular Cell Genetics and Genetic Breeding in Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, ChinaKey Laboratory of Molecular Cell Genetics and Genetic Breeding in Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, ChinaHeilongjiang Provincial Laboratory of Plant Physiology, College of Life Science and Technology, Harbin Normal University, Harbin 150025, ChinaKey Laboratory of Molecular Cell Genetics and Genetic Breeding in Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, ChinaKey Laboratory of Molecular Cell Genetics and Genetic Breeding in Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, ChinaKey Laboratory of Molecular Cell Genetics and Genetic Breeding in Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, ChinaKey Laboratory of Molecular Cell Genetics and Genetic Breeding in Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, ChinaBeijing Key Laboratory of Crop Molecular Design and Intelligent Breeding, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Institute of Hybrid Wheat Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, ChinaRye (<i>Secale cereale</i>), a cereal crop with high cold tolerance, serves as an ideal model for investigating plant cold adaptation mechanisms. Despite recent progress in identifying numerous genes and metabolic changes associated with cold tolerance, the detailed regulatory networks and coordinated interactions between metabolic pathways under low-temperature stress in rye remain unclear. In this study, we focused on the winter rye variety “Winter” and systematically explored its metabolic regulatory responses to cold stress through a combination of low-temperature treatments, phenotypic observations, antioxidant enzyme activity assays, and transcriptomic analysis. Four rye varieties (“Winter”, HZHM3, HZHM8, and “Victory”) were compared for cold tolerance, with the results indicating that “Winter” and HZHM3 exhibit superior cold tolerance. Physiological analysis revealed that after 12 h of exposure to −4 °C, the activities of catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) in “Winter” were significantly upregulated, displaying an initial increase followed by a decline over time. Transcriptomic sequencing identified 1643 differentially expressed genes (DEGs), and GO, KEGG, and GSEA enrichment analyses highlighted the critical roles of carbohydrate metabolism (ko00630) and amino acid metabolism (ko00250) pathways in the cold stress response. These pathways are interconnected through key metabolic intermediates such as L-glutamate, collectively regulating cold adaptation. Furthermore, based on the transcriptomic data, we identified and developed molecular markers associated with cold tolerance, detecting 10,846 EST-SSR and 250,116 EST-SNP markers. We successfully developed 13 EST-SSR primer pairs applicable to rye and 7 KASP markers. Notably, the KASP-665 marker effectively distinguishes between winter and spring rye, providing a reliable tool for marker-assisted selection in cold tolerance breeding. This study not only elucidates the metabolic regulatory mechanisms of rye under low-temperature stress but also provides a solid theoretical and technical foundation for future cold-tolerance breeding programs.https://www.mdpi.com/2223-7747/14/11/1588rye (<i>Secale cereale</i>)low-temperature stressmetabolismmolecular markers |
| spellingShingle | Haonan Li Jiahuan Zhao Chenguang He Yang Guan Huimin Guan Ting He Dexu Meng Xiaoping Wang Yimiao Tang Integrative Physiological and Transcriptomic Analysis Reveals Metabolic Adaptation and Cold-Tolerance Marker Development in Winter Rye Under Low-Temperature Stress Plants rye (<i>Secale cereale</i>) low-temperature stress metabolism molecular markers |
| title | Integrative Physiological and Transcriptomic Analysis Reveals Metabolic Adaptation and Cold-Tolerance Marker Development in Winter Rye Under Low-Temperature Stress |
| title_full | Integrative Physiological and Transcriptomic Analysis Reveals Metabolic Adaptation and Cold-Tolerance Marker Development in Winter Rye Under Low-Temperature Stress |
| title_fullStr | Integrative Physiological and Transcriptomic Analysis Reveals Metabolic Adaptation and Cold-Tolerance Marker Development in Winter Rye Under Low-Temperature Stress |
| title_full_unstemmed | Integrative Physiological and Transcriptomic Analysis Reveals Metabolic Adaptation and Cold-Tolerance Marker Development in Winter Rye Under Low-Temperature Stress |
| title_short | Integrative Physiological and Transcriptomic Analysis Reveals Metabolic Adaptation and Cold-Tolerance Marker Development in Winter Rye Under Low-Temperature Stress |
| title_sort | integrative physiological and transcriptomic analysis reveals metabolic adaptation and cold tolerance marker development in winter rye under low temperature stress |
| topic | rye (<i>Secale cereale</i>) low-temperature stress metabolism molecular markers |
| url | https://www.mdpi.com/2223-7747/14/11/1588 |
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