Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<)

Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related...
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Autor*in:	Yifei Yu [verfasserIn] YaJing Wu [verfasserIn] Wenfei Liu [verfasserIn] Jun Liu [verfasserIn] Ping Li [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	apple freeze-tolerance metabolome transcriptome metabolic pathway biomarker

Übergeordnetes Werk:	In: Metabolites - MDPI AG, 2012, 13(2023), 8, p 891
Übergeordnetes Werk:	volume:13 ; year:2023 ; number:8, p 891

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3390/metabo13080891

Katalog-ID:	DOAJ093581890

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allfields	10.3390/metabo13080891 doi (DE-627)DOAJ093581890 (DE-599)DOAJ1dceffe9d6c7481abc942d2547d6b309 DE-627 ger DE-627 rakwb eng QR1-502 Yifei Yu verfasserin aut Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<) 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related to its freeze-tolerance. In order to enhance our comprehension of freeze-tolerance metabolites and gene expression in dormant apple trees, we examined the metabolic and transcriptomic differences between ‘Ralls’ and ‘Fuji’, two apple varieties with varying degrees of resistance to freezing. The results of the freezing treatment showed that ‘Ralls’ had stronger freeze-tolerance than ‘Fuji’. We identified 302, 334, and 267 up-regulated differentially accumulated metabolites (DAMs) and 408, 387, and 497 down-regulated DAMs between ‘Ralls’ and ‘Fuji’ under −10, −15, and −20 °C treatment, respectively. A total of 359 shared metabolites were obtained in the upward trend modules, of which 62 metabolites were associated with 89 pathways. The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at −10, −15, and −20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4′-Dihydroxyflavone, and scolymoside. These discoveries advance our comprehension of the molecular mechanism underlying apple freeze-tolerance and provide genetic material for breeding apple cultivars with enhanced freeze-tolerance. apple freeze-tolerance metabolome transcriptome metabolic pathway biomarker Microbiology YaJing Wu verfasserin aut Wenfei Liu verfasserin aut Jun Liu verfasserin aut Ping Li verfasserin aut In Metabolites MDPI AG, 2012 13(2023), 8, p 891 (DE-627)718627164 (DE-600)2662251-8 22181989 nnns volume:13 year:2023 number:8, p 891 https://doi.org/10.3390/metabo13080891 kostenfrei https://doaj.org/article/1dceffe9d6c7481abc942d2547d6b309 kostenfrei https://www.mdpi.com/2218-1989/13/8/891 kostenfrei https://doaj.org/toc/2218-1989 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023 8, p 891
spelling	10.3390/metabo13080891 doi (DE-627)DOAJ093581890 (DE-599)DOAJ1dceffe9d6c7481abc942d2547d6b309 DE-627 ger DE-627 rakwb eng QR1-502 Yifei Yu verfasserin aut Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<) 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related to its freeze-tolerance. In order to enhance our comprehension of freeze-tolerance metabolites and gene expression in dormant apple trees, we examined the metabolic and transcriptomic differences between ‘Ralls’ and ‘Fuji’, two apple varieties with varying degrees of resistance to freezing. The results of the freezing treatment showed that ‘Ralls’ had stronger freeze-tolerance than ‘Fuji’. We identified 302, 334, and 267 up-regulated differentially accumulated metabolites (DAMs) and 408, 387, and 497 down-regulated DAMs between ‘Ralls’ and ‘Fuji’ under −10, −15, and −20 °C treatment, respectively. A total of 359 shared metabolites were obtained in the upward trend modules, of which 62 metabolites were associated with 89 pathways. The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at −10, −15, and −20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4′-Dihydroxyflavone, and scolymoside. These discoveries advance our comprehension of the molecular mechanism underlying apple freeze-tolerance and provide genetic material for breeding apple cultivars with enhanced freeze-tolerance. apple freeze-tolerance metabolome transcriptome metabolic pathway biomarker Microbiology YaJing Wu verfasserin aut Wenfei Liu verfasserin aut Jun Liu verfasserin aut Ping Li verfasserin aut In Metabolites MDPI AG, 2012 13(2023), 8, p 891 (DE-627)718627164 (DE-600)2662251-8 22181989 nnns volume:13 year:2023 number:8, p 891 https://doi.org/10.3390/metabo13080891 kostenfrei https://doaj.org/article/1dceffe9d6c7481abc942d2547d6b309 kostenfrei https://www.mdpi.com/2218-1989/13/8/891 kostenfrei https://doaj.org/toc/2218-1989 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023 8, p 891
allfields_unstemmed	10.3390/metabo13080891 doi (DE-627)DOAJ093581890 (DE-599)DOAJ1dceffe9d6c7481abc942d2547d6b309 DE-627 ger DE-627 rakwb eng QR1-502 Yifei Yu verfasserin aut Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<) 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related to its freeze-tolerance. In order to enhance our comprehension of freeze-tolerance metabolites and gene expression in dormant apple trees, we examined the metabolic and transcriptomic differences between ‘Ralls’ and ‘Fuji’, two apple varieties with varying degrees of resistance to freezing. The results of the freezing treatment showed that ‘Ralls’ had stronger freeze-tolerance than ‘Fuji’. We identified 302, 334, and 267 up-regulated differentially accumulated metabolites (DAMs) and 408, 387, and 497 down-regulated DAMs between ‘Ralls’ and ‘Fuji’ under −10, −15, and −20 °C treatment, respectively. A total of 359 shared metabolites were obtained in the upward trend modules, of which 62 metabolites were associated with 89 pathways. The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at −10, −15, and −20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4′-Dihydroxyflavone, and scolymoside. These discoveries advance our comprehension of the molecular mechanism underlying apple freeze-tolerance and provide genetic material for breeding apple cultivars with enhanced freeze-tolerance. apple freeze-tolerance metabolome transcriptome metabolic pathway biomarker Microbiology YaJing Wu verfasserin aut Wenfei Liu verfasserin aut Jun Liu verfasserin aut Ping Li verfasserin aut In Metabolites MDPI AG, 2012 13(2023), 8, p 891 (DE-627)718627164 (DE-600)2662251-8 22181989 nnns volume:13 year:2023 number:8, p 891 https://doi.org/10.3390/metabo13080891 kostenfrei https://doaj.org/article/1dceffe9d6c7481abc942d2547d6b309 kostenfrei https://www.mdpi.com/2218-1989/13/8/891 kostenfrei https://doaj.org/toc/2218-1989 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023 8, p 891
allfieldsGer	10.3390/metabo13080891 doi (DE-627)DOAJ093581890 (DE-599)DOAJ1dceffe9d6c7481abc942d2547d6b309 DE-627 ger DE-627 rakwb eng QR1-502 Yifei Yu verfasserin aut Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<) 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related to its freeze-tolerance. In order to enhance our comprehension of freeze-tolerance metabolites and gene expression in dormant apple trees, we examined the metabolic and transcriptomic differences between ‘Ralls’ and ‘Fuji’, two apple varieties with varying degrees of resistance to freezing. The results of the freezing treatment showed that ‘Ralls’ had stronger freeze-tolerance than ‘Fuji’. We identified 302, 334, and 267 up-regulated differentially accumulated metabolites (DAMs) and 408, 387, and 497 down-regulated DAMs between ‘Ralls’ and ‘Fuji’ under −10, −15, and −20 °C treatment, respectively. A total of 359 shared metabolites were obtained in the upward trend modules, of which 62 metabolites were associated with 89 pathways. The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at −10, −15, and −20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4′-Dihydroxyflavone, and scolymoside. These discoveries advance our comprehension of the molecular mechanism underlying apple freeze-tolerance and provide genetic material for breeding apple cultivars with enhanced freeze-tolerance. apple freeze-tolerance metabolome transcriptome metabolic pathway biomarker Microbiology YaJing Wu verfasserin aut Wenfei Liu verfasserin aut Jun Liu verfasserin aut Ping Li verfasserin aut In Metabolites MDPI AG, 2012 13(2023), 8, p 891 (DE-627)718627164 (DE-600)2662251-8 22181989 nnns volume:13 year:2023 number:8, p 891 https://doi.org/10.3390/metabo13080891 kostenfrei https://doaj.org/article/1dceffe9d6c7481abc942d2547d6b309 kostenfrei https://www.mdpi.com/2218-1989/13/8/891 kostenfrei https://doaj.org/toc/2218-1989 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023 8, p 891
allfieldsSound	10.3390/metabo13080891 doi (DE-627)DOAJ093581890 (DE-599)DOAJ1dceffe9d6c7481abc942d2547d6b309 DE-627 ger DE-627 rakwb eng QR1-502 Yifei Yu verfasserin aut Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<) 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related to its freeze-tolerance. In order to enhance our comprehension of freeze-tolerance metabolites and gene expression in dormant apple trees, we examined the metabolic and transcriptomic differences between ‘Ralls’ and ‘Fuji’, two apple varieties with varying degrees of resistance to freezing. The results of the freezing treatment showed that ‘Ralls’ had stronger freeze-tolerance than ‘Fuji’. We identified 302, 334, and 267 up-regulated differentially accumulated metabolites (DAMs) and 408, 387, and 497 down-regulated DAMs between ‘Ralls’ and ‘Fuji’ under −10, −15, and −20 °C treatment, respectively. A total of 359 shared metabolites were obtained in the upward trend modules, of which 62 metabolites were associated with 89 pathways. The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at −10, −15, and −20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4′-Dihydroxyflavone, and scolymoside. These discoveries advance our comprehension of the molecular mechanism underlying apple freeze-tolerance and provide genetic material for breeding apple cultivars with enhanced freeze-tolerance. apple freeze-tolerance metabolome transcriptome metabolic pathway biomarker Microbiology YaJing Wu verfasserin aut Wenfei Liu verfasserin aut Jun Liu verfasserin aut Ping Li verfasserin aut In Metabolites MDPI AG, 2012 13(2023), 8, p 891 (DE-627)718627164 (DE-600)2662251-8 22181989 nnns volume:13 year:2023 number:8, p 891 https://doi.org/10.3390/metabo13080891 kostenfrei https://doaj.org/article/1dceffe9d6c7481abc942d2547d6b309 kostenfrei https://www.mdpi.com/2218-1989/13/8/891 kostenfrei https://doaj.org/toc/2218-1989 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023 8, p 891
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source	In Metabolites 13(2023), 8, p 891 volume:13 year:2023 number:8, p 891
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callnumber-first	Q - Science
author	Yifei Yu
spellingShingle	Yifei Yu misc QR1-502 misc apple misc freeze-tolerance misc metabolome misc transcriptome misc metabolic pathway misc biomarker misc Microbiology Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<)
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topic_title	QR1-502 Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<) apple freeze-tolerance metabolome transcriptome metabolic pathway biomarker
topic	misc QR1-502 misc apple misc freeze-tolerance misc metabolome misc transcriptome misc metabolic pathway misc biomarker misc Microbiology
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title	Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<)
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title_full	Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<)
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title_sort	integration of metabolome and transcriptome reveals the major metabolic pathways and potential biomarkers in response to freeze-stress regulation in apple (<i<malus domestica</i<)
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title_auth	Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<)
abstract	Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related to its freeze-tolerance. In order to enhance our comprehension of freeze-tolerance metabolites and gene expression in dormant apple trees, we examined the metabolic and transcriptomic differences between ‘Ralls’ and ‘Fuji’, two apple varieties with varying degrees of resistance to freezing. The results of the freezing treatment showed that ‘Ralls’ had stronger freeze-tolerance than ‘Fuji’. We identified 302, 334, and 267 up-regulated differentially accumulated metabolites (DAMs) and 408, 387, and 497 down-regulated DAMs between ‘Ralls’ and ‘Fuji’ under −10, −15, and −20 °C treatment, respectively. A total of 359 shared metabolites were obtained in the upward trend modules, of which 62 metabolites were associated with 89 pathways. The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at −10, −15, and −20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4′-Dihydroxyflavone, and scolymoside. These discoveries advance our comprehension of the molecular mechanism underlying apple freeze-tolerance and provide genetic material for breeding apple cultivars with enhanced freeze-tolerance.
abstractGer	Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related to its freeze-tolerance. In order to enhance our comprehension of freeze-tolerance metabolites and gene expression in dormant apple trees, we examined the metabolic and transcriptomic differences between ‘Ralls’ and ‘Fuji’, two apple varieties with varying degrees of resistance to freezing. The results of the freezing treatment showed that ‘Ralls’ had stronger freeze-tolerance than ‘Fuji’. We identified 302, 334, and 267 up-regulated differentially accumulated metabolites (DAMs) and 408, 387, and 497 down-regulated DAMs between ‘Ralls’ and ‘Fuji’ under −10, −15, and −20 °C treatment, respectively. A total of 359 shared metabolites were obtained in the upward trend modules, of which 62 metabolites were associated with 89 pathways. The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at −10, −15, and −20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4′-Dihydroxyflavone, and scolymoside. These discoveries advance our comprehension of the molecular mechanism underlying apple freeze-tolerance and provide genetic material for breeding apple cultivars with enhanced freeze-tolerance.
abstract_unstemmed	Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related to its freeze-tolerance. In order to enhance our comprehension of freeze-tolerance metabolites and gene expression in dormant apple trees, we examined the metabolic and transcriptomic differences between ‘Ralls’ and ‘Fuji’, two apple varieties with varying degrees of resistance to freezing. The results of the freezing treatment showed that ‘Ralls’ had stronger freeze-tolerance than ‘Fuji’. We identified 302, 334, and 267 up-regulated differentially accumulated metabolites (DAMs) and 408, 387, and 497 down-regulated DAMs between ‘Ralls’ and ‘Fuji’ under −10, −15, and −20 °C treatment, respectively. A total of 359 shared metabolites were obtained in the upward trend modules, of which 62 metabolites were associated with 89 pathways. The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at −10, −15, and −20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4′-Dihydroxyflavone, and scolymoside. These discoveries advance our comprehension of the molecular mechanism underlying apple freeze-tolerance and provide genetic material for breeding apple cultivars with enhanced freeze-tolerance.
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container_issue	8, p 891
title_short	Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<)
url	https://doi.org/10.3390/metabo13080891 https://doaj.org/article/1dceffe9d6c7481abc942d2547d6b309 https://www.mdpi.com/2218-1989/13/8/891 https://doaj.org/toc/2218-1989
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The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at −10, −15, and −20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4′-Dihydroxyflavone, and scolymoside. 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Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (<i<Malus domestica</i<)

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