Search Results (1,824)

Background/Objectives: Direct-fed microbials (DFMs) are widely used in dairy calves to improve gut health and mitigate neonatal disorders, yet their systemic metabolic effects remain poorly defined. This study evaluated the impact of DFM supplementation on the plasma metabolome of pre-weaned dairy calves using untargeted liquid chromatography–mass spectrometry (LC–MS). Methods: Eighty-six Holstein bull calves (2 to 5 days old) were assigned to one of four treatments in a 2 × 2 factorial randomized complete block design: Lactobacillus plantarum in starter (CLP), a culture mix of Bifidobacterium animalis and Lactobacillus animalis in milk replacer (BBCM), and a combination of both (CMLP), or no supplementation (CON). Blood samples collected on days 0 and 56 were subjected to metabolomic profiling, and metabolites were annotated using Human Metabolome Database and Kyoto Encyclopedia of Genes and Genomes databases. Results: A total of 231 plasma metabolites were detected. Compared with CON, 24 metabolites were differentially abundant in DFM-treated calves (fold change ≥ 1.2 or ≤ 0.83; p ≤ 0.05). Supplemented calves exhibited increased abundances of ketone functional groups, aldehydes and amino acid-related metabolites. Metabolite set enrichment analysis identified 11 significantly enriched pathways. Branched-chain amino acid degradation pathways (valine, leucine, and isoleucine) were enriched in CLP and CMLP calves, whereas carbohydrate metabolism pathways, including pentose and glucuronate interconversions, were enriched in the CLP and BBCM groups. Conclusions: These findings demonstrate that DFM supplementation modulates systemic metabolism in dairy calves, particularly pathways involved in amino acid and carbohydrate utilization, suggesting enhanced metabolic efficiency during early life. Full article

Plant AT-rich sequence and zinc-binding proteins (PLATZs) act as critical modulators of plant growth, development, and responses to environmental stressors. Nevertheless, the PLATZ gene family (StPLATZs) has not yet been systematically characterized in potato, and this study seeks to identify members and prioritize genes associated with abiotic stress. A total of 13 StPLATZ genes were identified in the potato genome and classified into three distinct subfamilies based on phylogenetic analysis. Expression profiling and qRT-PCR analysis indicated that several StPLATZ genes responded to abiotic stress treatments. Yeast-based functional analysis suggested that Soltu06G018660 improved tolerance to PEG-induced osmotic stress, indicating its potential involvement in osmotic stress responses. These results provide candidate genes and hypotheses for future functional validation in potato. Further in-depth research on StPLATZs may contribute to potato stress-tolerance breeding. Full article

Background: Di19 (drought-induced 19)proteins belong to the C2H2-type zinc-finger family and play a crucial role in regulating plant growth, developmental processes, hormone signal transduction, and abiotic stress adaptation. However, research on the Di19 gene family in sweet potato and its diploid relatives remains relatively limited. Methods: At the whole-genome level, members of the Di19 gene family in sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30) were systematically identified, and multi-dimensional bioinformatics analyses were carried out. Results: Seven Di19 genes were identified per species, with the family’s overall evolutionary characteristics conserved. Some IbDi19s showed species-specific structural variations, mainly manifested as an increase in the number of exons, loss or substitution of conserved motifs. The expression patterns of Di19s of two diploid relatives are highly conserved. IbDi19s are mainly expressed in leaves and roots. Most members respond significantly to JA treatment, but hardly respond to IAA. The expression of IbDi19-1 was significantly up-regulated by 336-fold and 68-fold under GA3 and cold treatments, respectively. Based on bioinformatics and expression data, a hypothesis was proposed that IbDi19-1 may be involved in the regulation of low-temperature response and gibberellin signaling pathways. Conclusions: This study provides candidate genes and a theoretical basis for evolutionary analysis, stress-resistant molecular breeding of the Di19 gene family in sweet potato and its two diploid relatives. Full article

Citrus fruits are widely cultivated all over the world. Due to climatic conditions, citrus fruits are frequently exposed to periodic low temperatures, which poses a serious threat to their yield and quality. Cold not only restricts plant growth and deteriorates fruit quality but also leads to fruit abscission and tree mortality, posing severe constraints on large-scale citrus production. The TIFY family gene plays crucial roles in plant development and stress adaptation. However, the genome-wide identification and functional analysis of TIFY genes in cold stress adaptation of citrus plants remain largely unexplored. Here, we performed a systematic genome-wide analysis of the TIFY family in sweet orange (Citrus sinensis (L.) Osbeck) and identified 14 CsTIFY members. We conducted a comprehensive study on the protein characteristics, phylogenetic relationships, gene structure, chromosome distribution, promoter cis-acting elements, and subcellular localization of these genes. Phylogenetic analysis classified the CsTIFYs into ZML (ZML1–ZML4), JAZ (JAZ1–JAZ7), PPD (JAZ8, JAZ9), and TIFY (TIFY1) subfamilies, and they are distributed on seven chromosomes. Collinearity analysis revealed that segmental duplication is the primary driver for CsTIFY family expansion. Expression profiling under cold stress identified JAZ1, JAZ2, and JAZ3 as the most cold-inducible members. All three CsTIFY proteins are targeted to the nucleus, as confirmed by subcellular localization analysis. Overexpression of JAZ1, JAZ2, or JAZ3 in citrus calli significantly enhanced cold sensibility. Collectively, this study elucidates the gene function of CsTIFYs under cold stress and provides new insight for molecular breeding of cold-tolerant citrus varieties. Full article

Background: The NAC family constitutes one of the largest families of plant-specific transcription factors and plays crucial roles in fruit development, ripening, seed life, and stress responses. However, comprehensive characterization of NAC genes in Persea americana (avocado), an economically important horticultural crop, has been largely unexplored. Methods: We performed a genome-wide identification and systematic characterization of NAC transcription factor (TF) genes in P. americana using blastp analysis, phylogenetic reconstruction, expression profiling and weighted gene co-expression network analysis (WGCNA). Results: A total of 130 NAC genes (PaNACs) were identified and distributed across all 12 chromosomes. Phylogenetic analysis classified these PaNACs into eight distinct subfamilies. WGCNA identified 43 co-expression modules, with 68 PaNAC genes distributed across 24 modules associated with hormone signaling, cell wall modification, secondary metabolism, and fatty acid beta-oxidation. Among 48,785 developmental differentially expressed genes (DEGs), 70 PaNAC genes were differentially expressed, with PaNAC003 and PaNAC002 showing the strongest upregulation and PaNAC023 and PaNAC025 the strongest downregulation. Among 9488 ethylene-responsive DEGs, PaNAC041 was suppressed by ethylene and induced by 1-methylcyclopropene (1-MCP, a competitive inhibitor of ethylene perception), while PaNAC016, PaNAC085, and PaNAC086 showed the opposite pattern. Conclusions: These findings provide a genomic and transcriptional framework for future functional investigation of PaNAC genes and their potential relevance to avocado fruit development and postharvest ripening. Full article

Tomatoes are globally significant crops worldwide. Understanding the molecular mechanisms underlying their growth, development, and stress responses is crucial to enhance crop productivity and resilience. The WUSCHEL-related homeobox (WOX) gene family is implicated in developmental processes and stress responses, yet its regulatory complexity in tomato remains underexplored. This study presents an integrative genome-wide analysis approach to characterize the WOX family in tomato. Ten SlWOX genes were identified and phylogenetically classified into three clades, WUS, intermediate and ancient, underscoring their evolutionary relationships. Structural analysis revealed significant variability in gene structure even within the same clade, indicating potential diversity in functional roles. Conserved domains’ screening enables the detection of conserved motifs, including the homeodomain and WUS box. Cis-element analysis showed diverse regulatory elements across the SlWOXs, with a strong emphasis on elements involved in growth and development and stress response. Expression profiling across different organs and growth conditions including abiotic and biotic stresses revealed variability in SlWOXs’ expression patterns. Furthermore, several miRNAs were predicted to target the SlWOXs, emphasizing the existence of post-transcriptional regulation. Functional annotation and interactome analysis further revealed the key role of some SlWOXs, mainly SlWUS, SlWOX4 and SlWOX13, as central regulatory hubs. Collectively, these findings uncover the structural diversity, regulatory mechanisms and functional flexibility of the SlWOX gene family. It also highlights potential targets for improving tomato crop resilience and productivity, making it a significant contribution to plant biology and agriculture. Full article

Climate change is intensifying soil salinization, posing a major threat to crop establishment and productivity, particularly in arid and semi-arid regions. Barley (Hordeum vulgare L.), one of the most salt-tolerant cereals, offers valuable genetic resources for improving salinity resilience at early growth stages. This study exploited the genetic diversity of the Nested Association Mapping (NAM) population Halle Exotic Barley-25 (HEB-25) to dissect salinity tolerance during germination and seedling developmental stages. First, the HEB-25 parental lines (25 wild barley genotypes and cv. Barke) were evaluated under salinity treatment to identify contrasting responses. Based on this screening, four HEB families (01, 04, 09, and 22) were selected out of 25 HEB families for detailed phenotypic and genomic analysis. Seeds of the selected HEB families were subjected to 40% seawater salinity stress and control treatments to assess germination percentage and seedling traits, including shoot length, root length, fresh weight (FW), dry weight (DW), DW/FW ratio, root–shoot ratio, and salt tolerance index (STI). Substantial variation was observed among families for all measured traits under salinity stress. STI values enabled clear differentiation among families: Family 01 exhibited the most consistent overall tolerance profile, Family 22 showed the strongest sensitivity in biomass traits, and Family 04 displayed a trait-specific response with sensitivity at the family-mean level but exceptional within-family diversity, harboring some of the highest individual TI values across the population. A genome-wide association study was conducted using 32,995 SNP markers. A total of 27 significant SNPs were identified, corresponding to 20 quantitative trait loci (QTLs). Of these, 12 QTLs were detected under control conditions, 16 under seawater treatment, and 21 based on tolerance indices, indicating both constitutive and stress-responsive genetic effects. Gene annotation within these regions revealed approximately 23 candidate genes associated with abiotic stress tolerance, including genes involved in ion transport, osmotic adjustment, kinases and stress signaling pathways. HEB_22_003, HEB_04_087, and HEB_01_013 represent the most promising genotypes for salinity breeding. These findings highlight the effectiveness of combining precise phenotyping with high-resolution genomic analysis in the HEB-25 population to uncover the genetic architecture of salinity tolerance at early developmental stages. We identified 20 salinity-responsive QTLs, including five major-effect loci on chromosomes 2H, 4H, 5H, and 7H that consistently explained the largest share of phenotypic variation. These loci co-localized with candidate genes linked to ion homeostasis, Ca²⁺-mediated signaling, protein glycosylation, epigenetic regulation, and root system plasticity, revealing key mechanisms underlying early-stage salt adaptation in barley. The strong and contrasting responses of Family 01 and Family 04 provide an excellent genetic framework for functional validation of tolerance alleles. Collectively, these genomic resources establish a robust foundation for QTL pyramiding, marker-assisted breeding, and the development of climate-resilient barley cultivars for saline agroecosystems. Full article

Background: Anthocyanin biosynthesis is tightly controlled by MYB transcription factors, yet the role of repressors, particularly those in the DIVARICATA-like (DIV) subfamily, remains poorly characterized. Methods: A genome-wide identification of MYB family members was performed in the mulberry (Morus atropurpurea) genome using a hidden Markov model and BLAST-based searches. Putative MYB genes were phylogenetically classified, and their expression profiles were analyzed across three fruit developmental stages. A DIV-like R2R3-MYB candidate, MaDIV, was functionally characterized via subcellular localization, quantitative real-time PCR, and heterologous overexpression in tobacco. Results: A total of 145 MaMYB genes were identified and classified into 31 distinct subfamilies. MaDIV expression showed a progressive decline during fruit ripening, which significantly correlated with increasing anthocyanin accumulation. Heterologous overexpression of MaDIV in tobacco led to a 42% reduction in floral anthocyanin content compared with wild-type plants. Concomitantly, the expression of the key anthocyanin biosynthetic gene NtDFR was strongly suppressed, whereas the flavonol synthase gene NtFLS1 was significantly upregulated. Conclusions: These findings point to a possible involvement of MaDIV in the regulation of anthocyanin biosynthesis and provide preliminary evidence for the functional diversification of the DIV-like MYB subfamily in plants. The results contribute to a better understanding of the transcriptional control of fruit pigmentation in mulberry and related species. Full article

Auxin response factors (ARFs) are pivotal regulators mediating plant growth, development, and abiotic stress responses, especially during seed germination under stressful conditions. However, the ARF gene family has not been thoroughly studied or characterized in sesame. The identification and characterization of ARF family members in the sesame genome were analyzed by bioinformatics methods, and the expression patterns of sesame ARF genes were assessed by quantitative real-time PCR. In this study, a total of 23 ARF genes were identified in the sesame genome, distributed unevenly across 12 chromosomes. Additionally, 15 segmental duplication events were detected. Phylogenetic analysis classified the SiARF genes into four subfamilies, with members within each subgroup sharing conserved structural features and motif compositions. Promoter analysis revealed multiple cis-acting elements associated with plant growth, phytohormone responses, and stress responses. Expression profiling demonstrated distinct tissue-specific expression patterns among the SiARF genes. Notably, SiARF5 and SiARF15 showed predominant expression in seeds 5 days after pollination, whereas SiARF14 exhibited broad expression in roots, stems, leaves, and seeds germinated for 24 h. QRT-PCR analysis identified eight SiARF genes exhibiting biphasic expression patterns during seed germination under abiotic stresses, characterized by initial downregulation and subsequent upregulation. Among them, SiARF11 showed significant induction under all three stress conditions, while SiARF9 was specifically upregulated under salt stress, suggesting their critical roles in stress response regulation. These findings provide a foundation for further investigation into Auxin-mediated responses to abiotic stress during seed germination in sesame. Full article

JAZ (Jasmonate ZIM-Domain) proteins are key negative regulators of the jasmonic acid (JA) signaling pathway and are involved in various plant growth, development, and stress regulation. However, the functions of the JAZ gene family in Camellia nitidissima remain poorly understood. Here, ten CnJAZ genes were identified at the genome-wide level, encoding 134–398 amino acids and unevenly distributed across eight chromosomes. All CnJAZs were predicted to localize to the nucleus. Based on phylogenetic and structural analyses, the ten CnJAZs were classified into five subfamilies, with members of the same subfamily sharing similar exon–intron structures. Collinearity analysis with Arabidopsis thaliana and Malus domestica suggests that the JAZ gene family shares a common ancestor. Promoter analysis revealed cis-acting elements responsive to light, methyl jasmonate (MeJA), and anaerobic stress. Transcriptome profiling showed that most CnJAZs exhibit tissue- and development-specific expression, particularly during flower development and organ formation. RT-qPCR confirmed that MeJA and gibberellin (GA₃) significantly induced the expression of CnJAZ, whereas ethylene (ETH) treatment up-regulated CnJAZ3 and CnJAZ5 by 80-fold after three hours. These findings highlight their important roles in growth, development, and hormonal regulation in C. nitidissima, laying a foundation for functional studies. Full article

Background/Objectives: Banana (Musa spp.) production is severely threatened by Fusarium wilt caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), highlighting the need to identify genetic determinants of resistance. Methods: We performed a genome-wide analysis of NBS genes in Musa acuminata ssp. malaccensis, including phylogenetic, chromosomal, and microsynteny analyses. The genomic context and promoter regions of MamRGA2 were characterized, its response to defense-related phytohormones was evaluated by RT-qPCR, and its protein structure was predicted by homology modeling. Results: A total of 118 NBS genes were identified. Notably, we report for the first time in banana two NBS genes encoding proteins with integrated domains, corresponding to an ATP-binding cassette (ABC) transporter and a Nuclear Factor Y subunit A (NF-YA) transcription factor. Chromosomal mapping revealed a marked enrichment of NBS genes on chromosome 3, which harbors MamRGA2, an NBS gene associated with resistance to Foc TR4. RT-qPCR analyses showed that MamRGA2 is strongly induced by exogenous methyl jasmonate (MeJA) in the resistant wild genotype but not in a susceptible Cavendish cultivar, a pattern associated with divergence in promoter sequences between the two genotypes. Structural modeling suggested that the MamRGA2 protein possesses features consistent with a resistosome-like architecture. Conclusions: Overall, these findings expand current knowledge of NBS gene diversity in banana and provide a framework for future studies aimed at elucidating the molecular mechanisms underlying resistance to Foc TR4. Full article

Polygalacturonase (PG) is a key enzyme in cell wall metabolism and fruit ripening. Atemoya (Annona cherimola Mill. × A. squamosa L.) is a high-value tropical fruit that undergoes rapid postharvest softening at room temperature. However, the role of the atemoya PG gene family in this process remains unknown. This study determined that storing atemoya at 28 °C significantly reduced fruit firmness and the total pectin content but increased water-soluble pectin (WSP) and PG activity compared to storage at 15 °C. Genome-wide identification of the AaPG gene family in atemoya revealed that 40 AaPG genes were unevenly distributed across seven chromosomes. Nineteen genes were located within six tandem duplication clusters. AaPG proteins exhibited clade-specific differences: Clades B-E contained the polysaccharide lyase family 6 (PL-6) superfamily domain, while Clade A harbored the Aspergillus niger polygalacturonase 1 (Pgu1) domain and lacked several conserved motifs. Expression profiling and reverse transcription quantitative polymerase chain reaction (RT-qPCR) showed that AaPG19, AaPG21, AaPG23 and AaPG24 were specifically induced at 28 °C. Subcellular localization confirmed that these four proteins were located on the plasma membrane. These findings provide insights into the evolution and temperature-dependent regulation of the AaPG family, identifying candidate genes responsible for the rapid softening of atemoya fruit. Full article

Mulberry (Morus spp.) is valued for sericulture, medicine, and ecological restoration of degraded lands. Phospholipase A (PLA) enzymes hydrolyze membrane lipids and play critical roles in plant growth and stress responses, yet the PLA family in mulberry remains uncharacterized. Here, we performed genome-wide identification of Morus notabilis PLA genes in order to systematically analyze their phylogenetic relationships and gene structures, and profile their expression across tissues and under drought and salt stress, thereby providing candidate genes for future functional studies on stress tolerance. Fifty non-redundant PLA genes were identified and classified into three subfamilies: pPLA (22), PLA2 (nine), and PLA1 (19). Most predicted PLA proteins are small (100–500 aa) with predicted instability. Gene structures varied from 1 to 21 exons, and subfamily specific conserved domains (patatin/C2, PLATZ, lipase_3) were detected. Promoters contained stress- and hormone-responsive elements. Expression patterns across five tissues revealed distinct preferential patterns: 56% of genes showed highest expression in roots, with one-fifth in leaves. Under stress, 10 and 12 MnPLA genes were increased >2-fold (log₂FC > 1.0) by drought and salt, respectively. Notably, XP_010108435.1 and XP_024022961.1 exhibited leaf-specific high expression and were salt-induced (log₂FC > 1.0); XP_010090405.1 (leaf-specific low) was drought-induced (log₂FC > 1.0); and XP_024023462.1 (root-specific high) was induced by both stresses. These results provide a basis for functional studies and genetic improvement of stress tolerance in mulberry. Full article

Leptin (LEP) is an adipocyte-derived cytokine that integrates nutritional status, metabolism, and reproduction in cattle, with particular relevance for modern high-producing dairy cows. In ruminants, LEP and its receptors are widely expressed in metabolic and reproductive tissues, including adipose tissue, liver, hypothalamus, pituitary, ovary, uterus, and placenta, where LEP modulates energy homeostasis, neuroendocrine function, and local tissue responses. Changes in circulating LEP concentrations during the transition period reflect changes in body fat reserve, insulin and GH-IGF-1 dynamics, thyroid hormones, and inflammation and contribute to coordinated metabolic adaptations supporting the onset of lactation. At the reproductive level, LEP influences the hypothalamic–pituitary–gonadal axis, affects the pulsatility of luteinizing hormone (LH) under nutritional stress, and exerts direct effects on ovarian steroidogenesis, folliculogenesis, oocyte competence, embryo development, and uterine immune function. New evidence also links LEP profiles to major peripartum disorders, including subclinical ketosis, insulin resistance, postpartum ovarian inactivity, and uterine inflammatory diseases, and emphasises its potential as part of a panel evaluating the risk of metabolic and reproductive disorders. Furthermore, polymorphisms within the bovine LEP gene and its signalling network have been associated with milk production, feed efficiency, body condition, and fertility traits, suggesting opportunities to incorporate markers into genomic selection schemes aimed at improving robustness and reproductive performance. This review summarises current knowledge on LEP biology in cattle, with an emphasis on dairy cows, and discusses perspectives on translating this information into practical tools for nutritional management, health monitoring, and genetic improvement in bovine production systems. Full article

Pathogenesis-related 1 (PR1) proteins are important components of plant defense and stress responses and also serve as precursors of CAP-derived peptides (CAPE), a class of small bioactive peptides involved in immune and stress signaling. Despite their potential biological significance, CAPE-producing PR1 genes have not been systematically characterized in tobacco (Nicotiana tabacum). In this study, a genome-wide analysis identified 17 CAPE-producing PR1 genes, designated NtCAPE1 to NtCAPE17, in the tobacco genome. These genes encode proteins containing conserved CAP domains and N-terminal signal peptides, with predicted hydrophilic properties and mainly vacuolar localization, indicating conserved structural features within the family. Phylogenetic analysis, gene structure organization, conserved motif profiling, chromosomal distribution, and synteny analyses revealed both evolutionary conservation and duplication-driven diversification of the NtCAPE family. Promoter cis-element analysis showed enrichment of regulatory elements associated with phytohormone signaling, development, and stress responses. Public transcriptomic datasets revealed dynamic and gene-specific expression patterns under water-deficit and salinity stress, and qRT-PCR analysis further confirmed the stress-responsive expression of selected NtCAPE genes. Functional assays using synthetic mature peptides showed that NtCAPE9 and NtCAPE17 alleviated salinity stress- and osmotic stress-induced leaf yellowing, improved chlorophyll retention, suppressed senescence-associated responses, reduced H₂O₂ accumulation and POD activity, modulated stress-responsive gene expression, and promoted seed germination under salinity and osmotic stress, respectively. These results provide a comprehensive characterization of CAPE-producing PR1 genes in tobacco and identify NtCAPE9 and NtCAPE17 as candidate stress-associated peptides with exogenous activity under salinity and osmotic stress conditions. Full article