Pub Date : 2026-01-08DOI: 10.1016/j.fochms.2025.100352
Zihan Liu , Yongxin Li , Penta Pristijono , Cheng Liu
Sprouting of sweet potato during transportation and storage is a serious problem leads to weight loss and quality degradation. In this study, the effect of piperitone in inhibiting sprouting of ‘Yan 25’ sweet potato was analyzed through physiological and transcriptomic analyses. The results showed that untreated ‘Yan 25’ sweet potatoes sprouted after 14 d at 30 °C. While sweet potatoes treated with 150 μL/23 L piperitone did not grow any sprouts after 14 d. Furthermore, the investigation into the effect of piperitone on established sweet potato sprouts showed that the sprouts were damaged with the MDA content increased by 35 % after 18 h of piperitone fumigation, which then died after 48 h. The transcriptomic analyses showed that genes from the pathways of somatic embryogenesis, plant hormone metabolism or signal transduction, cell wall synthesis, cell wall loosening and DNA replication in the storage roots or sprout were altered by piperitone treatment. It is worth mentioning that, genes related to cell apoptosis are up-regulated in the sprout such as 1-amino-cyclopropane-1-carboxylate synthase (ACS), ACC oxidase (ACO), ethylene insensitive 3 family protein (EIN), senescence-associated gene (SAG) and so on, which was associated with the herbicidal effects of piperitone on sweet potato sprout. To facilitate the understanding of the results, two conceptual models elucidate the molecular mechanism of piperitone inhibited sweet potato sprouting were provided. This study provides new insights for inhibiting the sprouting of sweet potato during post-harvest storage.
{"title":"Transcriptomic analyses of piperitone inhibited sprouting of ‘Yan 25’ sweet potato storage roots","authors":"Zihan Liu , Yongxin Li , Penta Pristijono , Cheng Liu","doi":"10.1016/j.fochms.2025.100352","DOIUrl":"10.1016/j.fochms.2025.100352","url":null,"abstract":"<div><div>Sprouting of sweet potato during transportation and storage is a serious problem leads to weight loss and quality degradation. In this study, the effect of piperitone in inhibiting sprouting of ‘Yan 25’ sweet potato was analyzed through physiological and transcriptomic analyses. The results showed that untreated ‘Yan 25’ sweet potatoes sprouted after 14 d at 30 °C. While sweet potatoes treated with 150 μL/23 L piperitone did not grow any sprouts after 14 d. Furthermore, the investigation into the effect of piperitone on established sweet potato sprouts showed that the sprouts were damaged with the MDA content increased by 35 % after 18 h of piperitone fumigation, which then died after 48 h. The transcriptomic analyses showed that genes from the pathways of somatic embryogenesis, plant hormone metabolism or signal transduction, cell wall synthesis, cell wall loosening and DNA replication in the storage roots or sprout were altered by piperitone treatment. It is worth mentioning that, genes related to cell apoptosis are up-regulated in the sprout such as 1-amino-cyclopropane-1-carboxylate synthase (ACS), ACC oxidase (ACO), ethylene insensitive 3 family protein (EIN), senescence-associated gene (SAG) and so on, which was associated with the herbicidal effects of piperitone on sweet potato sprout. To facilitate the understanding of the results, two conceptual models elucidate the molecular mechanism of piperitone inhibited sweet potato sprouting were provided. This study provides new insights for inhibiting the sprouting of sweet potato during post-harvest storage.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100352"},"PeriodicalIF":4.7,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146037671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-02DOI: 10.1016/j.fochms.2025.100351
Malthe Fredsgaard , Andre Fussy , Gowri Købke Nybo , Jutta Papenbrock , Laura Sini Sofia Hulkko , Mina Dadjoo , Tanmay Chaturvedi , Mette Hedegaard Thomsen
Despite decades of polyphenol research, an integrated perspective on their biosynthesis, advanced extraction methods from food wastes, and potential as versatile inhibitors of pathogenic proteins and enzymes, particularly incorporating modified drug-likeness criteria, remains elusive. This integrative review compares and analyzes data on emerging polyphenol extraction and processing methods from various sources, including fruits, vegetables, berries, food production byproducts, and terrestrial sources of biomass. The drug-likeness of the reviewed polyphenols was assessed via a modified Lipinski's rule of five, and their interactions with proteins and enzymes in pathogenic pathways were investigated. The hypothesis is that polyphenols derived from food wastes exhibit high versatility as potential ligands with promising inhibitory effects that mitigate cascading disease effects in the human body. Therefore, the inhibition of proteins and enzymes involved in a wide range of diseases, including cancers, inflammatory diseases, diabetes and obesity, cardiovascular diseases, and mental and neurological disorders, was explored. Furthermore, the multifaceted nature of food and food waste-derived polyphenols was emphasized, highlighting their potential as extractable compounds with broad health-related applications. These novel insights enable targeted valorization of food wastes for personalized nutraceuticals, promote sustainable bioprocessing, and pave the way for clinical translation.
{"title":"Polyphenols in food and food wastes: Extraction, isolation, and health applications","authors":"Malthe Fredsgaard , Andre Fussy , Gowri Købke Nybo , Jutta Papenbrock , Laura Sini Sofia Hulkko , Mina Dadjoo , Tanmay Chaturvedi , Mette Hedegaard Thomsen","doi":"10.1016/j.fochms.2025.100351","DOIUrl":"10.1016/j.fochms.2025.100351","url":null,"abstract":"<div><div>Despite decades of polyphenol research, an integrated perspective on their biosynthesis, advanced extraction methods from food wastes, and potential as versatile inhibitors of pathogenic proteins and enzymes, particularly incorporating modified drug-likeness criteria, remains elusive. This integrative review compares and analyzes data on emerging polyphenol extraction and processing methods from various sources, including fruits, vegetables, berries, food production byproducts, and terrestrial sources of biomass. The drug-likeness of the reviewed polyphenols was assessed via a modified Lipinski's rule of five, and their interactions with proteins and enzymes in pathogenic pathways were investigated. The hypothesis is that polyphenols derived from food wastes exhibit high versatility as potential ligands with promising inhibitory effects that mitigate cascading disease effects in the human body. Therefore, the inhibition of proteins and enzymes involved in a wide range of diseases, including cancers, inflammatory diseases, diabetes and obesity, cardiovascular diseases, and mental and neurological disorders, was explored. Furthermore, the multifaceted nature of food and food waste-derived polyphenols was emphasized, highlighting their potential as extractable compounds with broad health-related applications. These novel insights enable targeted valorization of food wastes for personalized nutraceuticals, promote sustainable bioprocessing, and pave the way for clinical translation.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100351"},"PeriodicalIF":4.7,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145926708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-31DOI: 10.1016/j.fochms.2025.100345
Ting Cai , Jie Yao , Hongmei Jiang , Jie Zou , Ting Xia , Xinyue Mou , Shan Zhang , Xiao Tan , Jie Tang , Wenliang Xiang
Antibiotic residues in edible crops have become an increasing food safety concern, yet their impacts on crop nutritional quality and bioactive composition remain poorly understood. Here, we investigated the effects of tetracycline, a widely used antibiotic in soil–vegetable systems, on the growth and nutritional quality and bioactive composition of soybean sprouts. Results showed tetracycline exposure significantly inhibited sprout growth and nutrient accumulation in a dose-dependent manner, with high concentrations reducing vitamin C, total flavonoids, and coumestrol contents by approximately 50 %, 30 %, and 43 %, respectively. Transcriptomic analysis revealed that these related declines were associated with disruptions in carbon, amino acid, and lipid metabolism, as well as in flavonoid and coumestrol biosynthesis pathways. In parallel, rhizosphere microbiota analysis showed that tetracycline reshaped microbial community structure by reducing nitrogen-cycling-related taxa (Dokdonella, Acidibacter) and enriching resistant genera (Acinetobacter), which were significantly correlated with changes in sprout nutritional quality and bioactive composition. Together, these results demonstrate that tetracycline residues drive substantial losses of nutritional and bioactive composition in edible crops through coordinated metabolic and microbiome-mediated mechanisms, revealing an underappreciated pathway by which antibiotic contamination threatens crop nutritional value and food quality.
{"title":"Tetracycline residue alters the nutritional quality and bioactive composition of soybean sprouts: Evidence from transcriptomic and rhizosphere microbiota analyses","authors":"Ting Cai , Jie Yao , Hongmei Jiang , Jie Zou , Ting Xia , Xinyue Mou , Shan Zhang , Xiao Tan , Jie Tang , Wenliang Xiang","doi":"10.1016/j.fochms.2025.100345","DOIUrl":"10.1016/j.fochms.2025.100345","url":null,"abstract":"<div><div>Antibiotic residues in edible crops have become an increasing food safety concern, yet their impacts on crop nutritional quality and bioactive composition remain poorly understood. Here, we investigated the effects of tetracycline, a widely used antibiotic in soil–vegetable systems, on the growth and nutritional quality and bioactive composition of soybean sprouts. Results showed tetracycline exposure significantly inhibited sprout growth and nutrient accumulation in a dose-dependent manner, with high concentrations reducing vitamin C, total flavonoids, and coumestrol contents by approximately 50 %, 30 %, and 43 %, respectively. Transcriptomic analysis revealed that these related declines were associated with disruptions in carbon, amino acid, and lipid metabolism, as well as in flavonoid and coumestrol biosynthesis pathways. In parallel, rhizosphere microbiota analysis showed that tetracycline reshaped microbial community structure by reducing nitrogen-cycling-related taxa (<em>Dokdonella</em>, <em>Acidibacter</em>) and enriching resistant genera (<em>Acinetobacter)</em>, which were significantly correlated with changes in sprout nutritional quality and bioactive composition. Together, these results demonstrate that tetracycline residues drive substantial losses of nutritional and bioactive composition in edible crops through coordinated metabolic and microbiome-mediated mechanisms, revealing an underappreciated pathway by which antibiotic contamination threatens crop nutritional value and food quality.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100345"},"PeriodicalIF":4.7,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145926704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-31DOI: 10.1016/j.fochms.2025.100350
Qin He , Liang Xiong , Shuting Fang , Yan Chen , Jinge Ma , Zhangfeng Wang , Yanping Wu , Jiguo Xu , Xinwei Xiong
The local Chinese Kangle chicken breed has plump muscles, tender-tasting meat, and strong disease resistance. We aimed to identify muscle metabolites and associated regulatory genes that determine Kangle chicken muscle quality and flavor by elucidating the as yet unknown underlying molecular regulatory mechanism through omics-based analyses. Phenotype analysis and genome-wide association study (GWAS) showed that intramuscular fat (IMF) exhibited a high coefficient of variation and identified two SNPs that reached genome-wide significance levels (P < 1.23 × 10−6), with QTLs affecting IMF located on chromosomes 1, 2, 4, and 7. Transcriptome analysis screened 201 differential expression genes between chickens with high and low IMF content. Among these, the expression level of the FYVE-type zinc finger containing (PIKFYVE) gene located in the significant QTL region was significantly downregulated in the High-IMF group, which was validated by qRT-PCR. Metabolomics identified 17 intergroup differential metabolites, and the High-IMF group was significantly enriched in vitamin B6 metabolism and glycine, serine, and threonine metabolism. Differentially expressed gene and metabolite analyses in breast muscles and pathway enrichment and co-occurring network analyses showed that PIKFYVE impacted IMF. Its expression significantly and negatively correlated with most lipid metabolites. This study is the first to establish PIKFYVE as the primary regulatory gene of IMF in Kangle chickens. It provides crucial and valuable practical insights into genetically breeding high-quality meat chicken breeds.
{"title":"Integrated genomic, transcriptomic, and metabolomic profile analysis reveals molecular mechanism underlying meat quality traits in Chinese Kangle chickens","authors":"Qin He , Liang Xiong , Shuting Fang , Yan Chen , Jinge Ma , Zhangfeng Wang , Yanping Wu , Jiguo Xu , Xinwei Xiong","doi":"10.1016/j.fochms.2025.100350","DOIUrl":"10.1016/j.fochms.2025.100350","url":null,"abstract":"<div><div>The local Chinese Kangle chicken breed has plump muscles, tender-tasting meat, and strong disease resistance. We aimed to identify muscle metabolites and associated regulatory genes that determine Kangle chicken muscle quality and flavor by elucidating the as yet unknown underlying molecular regulatory mechanism through omics-based analyses. Phenotype analysis and genome-wide association study (GWAS) showed that intramuscular fat (IMF) exhibited a high coefficient of variation and identified two SNPs that reached genome-wide significance levels (<em>P</em> < 1.23 × 10<sup>−6</sup>), with QTLs affecting IMF located on chromosomes 1, 2, 4, and 7. Transcriptome analysis screened 201 differential expression genes between chickens with high and low IMF content. Among these, the expression level of the FYVE-type zinc finger containing (<em>PIKFYVE</em>) gene located in the significant QTL region was significantly downregulated in the High-IMF group, which was validated by qRT-PCR. Metabolomics identified 17 intergroup differential metabolites, and the High-IMF group was significantly enriched in vitamin B6 metabolism and glycine, serine, and threonine metabolism. Differentially expressed gene and metabolite analyses in breast muscles and pathway enrichment and co-occurring network analyses showed that <em>PIKFYVE</em> impacted IMF. Its expression significantly and negatively correlated with most lipid metabolites. This study is the first to establish <em>PIKFYVE</em> as the primary regulatory gene of IMF in Kangle chickens. It provides crucial and valuable practical insights into genetically breeding high-quality meat chicken breeds.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100350"},"PeriodicalIF":4.7,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145926702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Strawberry (Fragaria × ananassa Duch.) is an important economic crop all around the world. A new developed cultivar ‘Baozhu’ which has a similar fruit shape with ‘Hongyan’ is not yet proved to be a different genotype. The main purpose of the present study was to confirm the differences in genotypes and quality and volatile compounds of the two cultivars. The results showed that ‘Baozhu’ cultivar exhibited 39.6 % higher fruit weight, 35.1 % higher total soluble solids, 29.5 % higher firmness, 25.0 % higher total acidity, 45.0 % higher soluble sugars compared to ‘Hongyan’ cultivar (p < 0.05). A total of 51 volatile compounds were identified in the strawberries using headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS), and esters were the most abundant compounds, followed by aldehydes and alcohols. The results of chemometrics analysis reveal that ‘Baozhu’ and ‘Hongyan’ strawberries can be distinctly separated from each other. A panel of 28 volatiles with VIP > 1 and p < 0.05 were identified as discriminant factors for ‘Baozhu’ and ‘Hongyan’. Furthermore, ‘Baozhu’ cultivar had significantly more stomata than the ‘Hongyan’ cultivar. A clear and positive correlation was observed among quality, volatile and stomata number. The current findings contribute to the commercial value assessment of the ‘Baozhu’ cultivar at an industrial level, formulating a paradigm for improvement of daily eating pattern and driving the development of genetic tools for improvement of flavor.
{"title":"Cultivar-driven variations in physicochemical properties and volatile organic compound profiles of strawberry (Fragaria × ananassa Duch.)","authors":"Zhen-Peng Zhou, Li-Yuan Zhao, Jing-Yao Sun, Qing-Yun Li, Bing-Bing Cai, Xin-Xin Wang","doi":"10.1016/j.fochms.2025.100346","DOIUrl":"10.1016/j.fochms.2025.100346","url":null,"abstract":"<div><div>Strawberry (<em>Fragaria × ananassa</em> Duch<em>.</em>) is an important economic crop all around the world. A new developed cultivar ‘Baozhu’ which has a similar fruit shape with ‘Hongyan’ is not yet proved to be a different genotype. The main purpose of the present study was to confirm the differences in genotypes and quality and volatile compounds of the two cultivars. The results showed that ‘Baozhu’ cultivar exhibited 39.6 % higher fruit weight, 35.1 % higher total soluble solids, 29.5 % higher firmness, 25.0 % higher total acidity, 45.0 % higher soluble sugars compared to ‘Hongyan’ cultivar (<em>p</em> < 0.05). A total of 51 volatile compounds were identified in the strawberries using headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS), and esters were the most abundant compounds, followed by aldehydes and alcohols. The results of chemometrics analysis reveal that ‘Baozhu’ and ‘Hongyan’ strawberries can be distinctly separated from each other. A panel of 28 volatiles with VIP > 1 and <em>p</em> < 0.05 were identified as discriminant factors for ‘Baozhu’ and ‘Hongyan’. Furthermore, ‘Baozhu’ cultivar had significantly more stomata than the ‘Hongyan’ cultivar. A clear and positive correlation was observed among quality, volatile and stomata number. The current findings contribute to the commercial value assessment of the ‘Baozhu’ cultivar at an industrial level, formulating a paradigm for improvement of daily eating pattern and driving the development of genetic tools for improvement of flavor.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100346"},"PeriodicalIF":4.7,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145926703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-30DOI: 10.1016/j.fochms.2025.100347
Lina Wang , Qiaoling Liu , Chuan Chen , Rongfa Guan , Peilong Sun
Aroma is a critical determinant of fruit quality, largely synthesized through the lipoxygenase (LOX) pathway. We hypothesized that the dynamic regulation of the LOX pathway during jujube fruit ripening governs the distinct evolution of its key aroma compounds. This study used HS-SPME coupled with GC–MS to profile aroma compounds in jujube during ripening. Semi-quantitative analysis revealed hexanal (1160–1870 μg/kg) and (E)-2-hexenal (1470–3180 μg/kg) as the most abundant aldehydes, followed by benzaldehyde and (E)-2-pentenal. Odor activity value (OAV) analysis identified hexanal, (E)-2-hexenal, and (E)-2-nonenal as the key aroma compounds. LOX enzyme activity increased from 277 U/g to 711 U/g during ripening, while ADH and AAT activities showed fluctuating trends. Transcriptome analysis revealed 12 candidate transcripts involved in aroma synthesis, with multivariate statistical analysis demonstrating coordinated changes in gene expression associated with volatile accumulation. Our findings verify the hypothesis that LOX pathway regulation drives aroma evolution during jujube ripening and provide a genetic foundation for targeted quality improvement in jujube fruits.
{"title":"Transcriptomic and biochemical insights into LOX pathway aroma biosynthesis during ripening of Ziziphus jujuba Mill. cv. Li","authors":"Lina Wang , Qiaoling Liu , Chuan Chen , Rongfa Guan , Peilong Sun","doi":"10.1016/j.fochms.2025.100347","DOIUrl":"10.1016/j.fochms.2025.100347","url":null,"abstract":"<div><div>Aroma is a critical determinant of fruit quality, largely synthesized through the lipoxygenase (LOX) pathway. We hypothesized that the dynamic regulation of the LOX pathway during jujube fruit ripening governs the distinct evolution of its key aroma compounds. This study used HS-SPME coupled with GC–MS to profile aroma compounds in jujube during ripening. Semi-quantitative analysis revealed hexanal (1160–1870 μg/kg) and (E)-2-hexenal (1470–3180 μg/kg) as the most abundant aldehydes, followed by benzaldehyde and (E)-2-pentenal. Odor activity value (OAV) analysis identified hexanal, (<em>E</em>)-2-hexenal, and (<em>E</em>)-2-nonenal as the key aroma compounds. LOX enzyme activity increased from 277 U/g to 711 U/g during ripening, while ADH and AAT activities showed fluctuating trends. Transcriptome analysis revealed 12 candidate transcripts involved in aroma synthesis, with multivariate statistical analysis demonstrating coordinated changes in gene expression associated with volatile accumulation. Our findings verify the hypothesis that LOX pathway regulation drives aroma evolution during jujube ripening and provide a genetic foundation for targeted quality improvement in jujube fruits.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100347"},"PeriodicalIF":4.7,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145926706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-30DOI: 10.1016/j.fochms.2025.100348
Bahman Panahi , Rasmieh Hamid , Zahra Ghorbanzadeh , Saber Golkari , Mehmet Yildirim , Feba Jacob
Barley (Hordeum vulgare L.) is a cornerstone of the malting and brewing industry, yet the molecular regulation of its key quality traits remains incompletely understood. While the biochemical mechanisms governing starch metabolism, storage protein turnover, β-glucan remodeling, and hydrolytic enzyme activity are well characterized, the transcriptional networks orchestrating these processes during grain development and germination remain less defined. This review hypothesises that transcription factors (TFs) serve as central regulatory hubs, integrating hormonal signals with metabolic pathways to modulate malting quality. Advances in functional genomics, transcriptomics, and network biology increasingly support this model, highlighting the roles of MYB (e.g., GAMYB), DOF, bZIP, NAC, WRKY, and AP2/ERF TFs in regulating starch biosynthesis, endosperm protein dynamics, cell wall degradation, and enzyme induction, particularly under gibberellin–abscisic acid crosstalk. Multi-omics integration, weighted gene co-expression network analysis, and natural allelic variation have identified key regulatory modules associated with malt extract yield, fermentability, free amino nitrogen, and wort viscosity. These insights offer promising targets for genome editing, predictive breeding, and synthetic modulation of malting pathways. By linking TF biology to critical brewing performance traits, this review presents a mechanistic framework for leveraging these findings to develop climate-resilient barley cultivars with consistent and enhanced malting quality, paving the way for innovations in malting science.
{"title":"Transcriptional networks shaping malting quality in barley: From grain development to brewing performance","authors":"Bahman Panahi , Rasmieh Hamid , Zahra Ghorbanzadeh , Saber Golkari , Mehmet Yildirim , Feba Jacob","doi":"10.1016/j.fochms.2025.100348","DOIUrl":"10.1016/j.fochms.2025.100348","url":null,"abstract":"<div><div>Barley (<em>Hordeum vulgare</em> L.) is a cornerstone of the malting and brewing industry, yet the molecular regulation of its key quality traits remains incompletely understood. While the biochemical mechanisms governing starch metabolism, storage protein turnover, β-glucan remodeling, and hydrolytic enzyme activity are well characterized, the transcriptional networks orchestrating these processes during grain development and germination remain less defined. This review hypothesises that transcription factors (TFs) serve as central regulatory hubs, integrating hormonal signals with metabolic pathways to modulate malting quality. Advances in functional genomics, transcriptomics, and network biology increasingly support this model, highlighting the roles of MYB (e.g., GAMYB), DOF, bZIP, NAC, WRKY, and AP2/ERF TFs in regulating starch biosynthesis, endosperm protein dynamics, cell wall degradation, and enzyme induction, particularly under gibberellin–abscisic acid crosstalk. Multi-omics integration, weighted gene co-expression network analysis, and natural allelic variation have identified key regulatory modules associated with malt extract yield, fermentability, free amino nitrogen, and wort viscosity. These insights offer promising targets for genome editing, predictive breeding, and synthetic modulation of malting pathways. By linking TF biology to critical brewing performance traits, this review presents a mechanistic framework for leveraging these findings to develop climate-resilient barley cultivars with consistent and enhanced malting quality, paving the way for innovations in malting science.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100348"},"PeriodicalIF":4.7,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145926707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-18DOI: 10.1016/j.fochms.2025.100344
Gilberto Vinícius de Melo Pereira , Alexander da Silva Vale , Ana Isabel Ribeiro-Barros , Luiz Roberto Saldanha Rodrigues , Gisela Manuela de França Bettencourt Mirção , Bernadete Camilo , Inocência da Piedade Ernesto Tapaça , Vitoria de Mello Sampaio , Satinder kaur Brar , Carlos Ricardo Soccol
Post-harvest fermentation is a decisive stage in shaping the flavor complexity of Arabica coffee. In this study, we mapped for the first time the microbial-driven flavor metabolic network underlying the fermentation of high-quality African coffee, using a combined metabolomic, meta-barcoding, and metagenomic approach applied to samples from Chimanimani National Park, Mozambique. Over 72 h of spontaneous fermentation, chemical analyses revealed rapid sucrose hydrolysis, lactic acid accumulation, and the formation of 74 volatile compounds. These transformations were driven by a previously unreported core microbiome (Leuconostoc–Hanseniaspora–Galactomyces axis), whose functional repertoire (1791 genes) highlighted the Ehrlich pathway and ester biosynthesis as central flavor routes. Among the volatiles formed, linalool, phenylethyl alcohol, and ethyl acetate were most abundant, emerging as predictive drivers of the floral and fruity notes identified in the resulting high-quality coffee beverage (score 87.25 ± 0.25). This study underscores microbial terroir as a key factor adding value to emerging African origins.
{"title":"Integrated microbial–metabolomic analysis reveals how fermentation contributes to the unique flavor of African Arabica coffee","authors":"Gilberto Vinícius de Melo Pereira , Alexander da Silva Vale , Ana Isabel Ribeiro-Barros , Luiz Roberto Saldanha Rodrigues , Gisela Manuela de França Bettencourt Mirção , Bernadete Camilo , Inocência da Piedade Ernesto Tapaça , Vitoria de Mello Sampaio , Satinder kaur Brar , Carlos Ricardo Soccol","doi":"10.1016/j.fochms.2025.100344","DOIUrl":"10.1016/j.fochms.2025.100344","url":null,"abstract":"<div><div>Post-harvest fermentation is a decisive stage in shaping the flavor complexity of Arabica coffee. In this study, we mapped for the first time the microbial-driven flavor metabolic network underlying the fermentation of high-quality African coffee, using a combined metabolomic, meta-barcoding, and metagenomic approach applied to samples from Chimanimani National Park, Mozambique. Over 72 h of spontaneous fermentation, chemical analyses revealed rapid sucrose hydrolysis, lactic acid accumulation, and the formation of 74 volatile compounds. These transformations were driven by a previously unreported core microbiome (<em>Leuconostoc–Hanseniaspora–Galactomyces</em> axis), whose functional repertoire (1791 genes) highlighted the Ehrlich pathway and ester biosynthesis as central flavor routes. Among the volatiles formed, linalool, phenylethyl alcohol, and ethyl acetate were most abundant, emerging as predictive drivers of the floral and fruity notes identified in the resulting high-quality coffee beverage (score 87.25 ± 0.25). This study underscores microbial terroir as a key factor adding value to emerging African origins.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100344"},"PeriodicalIF":4.7,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146077454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-13DOI: 10.1016/j.fochms.2025.100342
Xiaoling Jiang , Qiang Li , Yanyan Geng , Jishun Zhao , Yang Li , Hongmin Li
Gluten protein quantity and quality, crucial factors determining the baking quality of wheat-based foods, are primary targets for wheat breeding. To elucidate their genetic basis, five key gluten traits were investigated utilizing a genome-wide association study (GWAS) approach: wet gluten content (WGC), residual gluten content (RGC), dry gluten content (DGC), water-holding capacity (WHC), and gluten index (GI). Using 48,057 SNPs across 200 wheat accessions, analyses employed one single-locus (SL) model and five multi-locus (ML) models. Genotype primarily influenced these gluten traits, with broad-sense heritability (H2) ranging from 0.85 (DGC) to 0.97 (GI). The SL-GWAS and ML-GWAS models identified 143 and 203 significant marker-trait associations (MTAs), respectively. Of these, 15 stable quantitative trait loci (QTL) were detected in at least three environments using multiple GWAS models. Most notably, qGI·1D for GI, which integrated from 138 significant MTAs, was identified in multi-environments and recognized by all five ML-GWAS models across all environments. This QTL was shown to be co-localized with qWGC·1D, qRGC·1D, and qWHC·1D. Furthermore, five candidate genes related to wheat gluten including TraesCS1A02G317500, TraesCS1A02G466400LC, TraesCS1A02G466500LC, TraesCS1B02G330000, and TraesCS1D02G317300 were indentified. Interestingly, TraesCS1B02G330000 has the PF13016 domain related to gliadins and has collinearity with two other genes, suggesting the genes in the first homologous group encoding gliadins may play an important role in GI. Additionally, four kompetitive allele-specific PCR (KASP) markers (K_AX-108,999,948, K_AX-110,940,435, K_AX-111,216,618 and K_AX-94,670,671) for GI were developed successfully and validated in the natural population. This work elucidates the genetic basis of wheat gluten traits and provides both valuable germplasm and robust molecular tools for breeding applications.
{"title":"Genetic dissection of gluten characteristics based on single- and multi-locus genome-wide association studies in wheat (Triticum aestivum L.)","authors":"Xiaoling Jiang , Qiang Li , Yanyan Geng , Jishun Zhao , Yang Li , Hongmin Li","doi":"10.1016/j.fochms.2025.100342","DOIUrl":"10.1016/j.fochms.2025.100342","url":null,"abstract":"<div><div>Gluten protein quantity and quality, crucial factors determining the baking quality of wheat-based foods, are primary targets for wheat breeding. To elucidate their genetic basis, five key gluten traits were investigated utilizing a genome-wide association study (GWAS) approach: wet gluten content (WGC), residual gluten content (RGC), dry gluten content (DGC), water-holding capacity (WHC), and gluten index (GI). Using 48,057 SNPs across 200 wheat accessions, analyses employed one single-locus (SL) model and five multi-locus (ML) models. Genotype primarily influenced these gluten traits, with broad-sense heritability (H<sup>2</sup>) ranging from 0.85 (DGC) to 0.97 (GI). The SL-GWAS and ML-GWAS models identified 143 and 203 significant marker-trait associations (MTAs), respectively. Of these, 15 stable quantitative trait loci (QTL) were detected in at least three environments using multiple GWAS models. Most notably, qGI·1D for GI, which integrated from 138 significant MTAs, was identified in multi-environments and recognized by all five ML-GWAS models across all environments. This QTL was shown to be co-localized with qWGC·1D, qRGC·1D, and qWHC·1D. Furthermore, five candidate genes related to wheat gluten including <em>TraesCS1A02G317500</em>, <em>TraesCS1A02G466400LC</em>, <em>TraesCS1A02G466500LC</em>, <em>TraesCS1B02G330000</em>, and <em>TraesCS1D02G317300</em> were indentified. Interestingly, <em>TraesCS1B02G330000</em> has the PF13016 domain related to gliadins and has collinearity with two other genes, suggesting the genes in the first homologous group encoding gliadins may play an important role in GI. Additionally, four kompetitive allele-specific PCR (KASP) markers (<em>K_AX-108</em>,<em>999</em>,<em>948</em>, <em>K_AX-110</em>,<em>940</em>,<em>435</em>, <em>K_AX-111</em>,<em>216</em>,<em>618</em> and <em>K_AX-94</em>,<em>670</em>,<em>671</em>) for GI were developed successfully and validated in the natural population. This work elucidates the genetic basis of wheat gluten traits and provides both valuable germplasm and robust molecular tools for breeding applications.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100342"},"PeriodicalIF":4.7,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145792045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-11DOI: 10.1016/j.fochms.2025.100343
Jianting Lin , Yanchao Du , Haoxuan Jiang , Huating Zhao , Bo Wang , Faqiang Feng
The solanesyl diphosphate synthase gene ZmSPS2 is known to modulate terpenoid metabolism and tocopherol biosynthesis in maize (Zea mays L.), though its system-wide metabolic effects remain poorly understood. In this study, a widely targeted metabolomic analysis revealed significant impacts of the Zmsps2 mutation on metabolic networks in both leaves and kernels at 20 days after pollination (DAP). A total of 2531 metabolites were detected, primarily comprising lipids, organoheterocyclic compounds, and benzenoids. Differential metabolite analysis identified 453 significantly altered metabolites in leaves and 334 in kernels. In leaves, differential metabolites were enriched in four metabolic pathways including zma00051 (Fructose and mannose metabolism), zma00520 (Amino sugar and nucleotide sugar metabolism), zma00941 (Flavonoid biosynthesis), and zma00052 (Galactose metabolism). Four significant pathways were enriched in kernels, including zma02010 (ABC transporters), zma00052 (Galactose metabolism), zma00591 (Linoleic acid metabolism), and zma01230 (Biosynthesis of amino acids). This study demonstrates that the Zmsps2 mutation triggers tissue-specific metabolic alterations: enhancing monosaccharide-driven energy supply in leaves, while promoting accumulation of protective sugars in kernels. These findings provide new insights into the regulation of metabolic profile by the Zmsps2 mutation.
{"title":"Comparative metabolomic analysis of leaves and kernels in wild type and Zmsps2 mutant","authors":"Jianting Lin , Yanchao Du , Haoxuan Jiang , Huating Zhao , Bo Wang , Faqiang Feng","doi":"10.1016/j.fochms.2025.100343","DOIUrl":"10.1016/j.fochms.2025.100343","url":null,"abstract":"<div><div>The solanesyl diphosphate synthase gene <em>ZmSPS2</em> is known to modulate terpenoid metabolism and tocopherol biosynthesis in maize (<em>Zea mays</em> L.), though its system-wide metabolic effects remain poorly understood. In this study, a widely targeted metabolomic analysis revealed significant impacts of the <em>Zmsps2</em> mutation on metabolic networks in both leaves and kernels at 20 days after pollination (DAP). A total of 2531 metabolites were detected, primarily comprising lipids, organoheterocyclic compounds, and benzenoids. Differential metabolite analysis identified 453 significantly altered metabolites in leaves and 334 in kernels. In leaves, differential metabolites were enriched in four metabolic pathways including zma00051 (Fructose and mannose metabolism), zma00520 (Amino sugar and nucleotide sugar metabolism), zma00941 (Flavonoid biosynthesis), and zma00052 (Galactose metabolism). Four significant pathways were enriched in kernels, including zma02010 (ABC transporters), zma00052 (Galactose metabolism), zma00591 (Linoleic acid metabolism), and zma01230 (Biosynthesis of amino acids). This study demonstrates that the <em>Zmsps2</em> mutation triggers tissue-specific metabolic alterations: enhancing monosaccharide-driven energy supply in leaves, while promoting accumulation of protective sugars in kernels. These findings provide new insights into the regulation of metabolic profile by the <em>Zmsps2</em> mutation.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100343"},"PeriodicalIF":4.7,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145791491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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