Search Results (39)

Phospholipase D (PLD) genes play key roles in plant abiotic stress responses, but the systematic identification of the maize (Zea mays) PLD family and its cold tolerance mechanism remain unclear. Using 26 maize genomes (pangenome), we identified 21 ZmPLD members via Hidden Markov Model (HMM) search (Pfam domain PF00614), including five private genes—avoiding gene omission from single reference genomes. Phylogenetic analysis showed ZmPLD conservation with Arabidopsis and rice PLDs; Ka/Ks analysis revealed most ZmPLDs under purifying selection, while three genes (including ZmPLD15) had positive selection signals, suggesting roles in maize adaptive domestication. For ZmPLD15, five shared structural variations (SVs) were found in its promoter; some contained ERF/bHLH binding sites, and SVs in Region1/5 significantly regulated ZmPLD15 expression. Protein structure prediction and molecular docking showed conserved ZmPLD15 structure and substrate (1,2-diacyl-sn-glycero-3-phosphocholine) binding energy across germplasms. Transgenic maize (B73 background) overexpressing ZmPLD15 was generated. Cold stress (8–10 °C, 6 h) and recovery (24 h) on three-leaf seedlings showed transgenic plants had better leaf cell integrity than wild type (WT). Transgenic plants retained 45.8% net photosynthetic rate (Pn), 47.9% stomatal conductance (Gs), and 55.8% transpiration rate (Tr) versus 7.6%, 21.3%, 13.8% in WT; intercellular CO₂ concentration (Ci) was maintained properly. This confirms ZmPLD15 enhances maize cold tolerance by protecting photosynthetic systems, providing a framework for ZmPLD research and a key gene for cold-tolerant maize breeding. Full article

Acyl-CoA-binding proteins (ACBPs) are essential lipid carrier proteins involved in plant lipid metabolism. However, the systematic identification and expression profiles of the ACBP gene family in citrus species remain poorly understood. Here, Citrus sinensis and Poncirus trifoliata were chosen as model species to examine the biological properties of citrus ACBPs. Using bioinformatics methods, five ACBP gene members were found in each species and named CsACBPs and PtrACBPs, respectively. All obtained ACBP members were divided into four subfamilies based on conserved domains and amino acid sequences. CsACBP and PtrACBP genes exhibited structural variation in motifs and exons. The predicted protein structures of CsACBPs and PtrACBPs exhibited conservation between the two species while displaying distinct variation within each species. Collinearity analysis showed one intraspecific pairing relationship in each of the two citrus species. Furthermore, there were more collinear couplings between citrus species and Arabidopsis thaliana but none between citrus species and Oryza sativa (rice). Notably, the analysis of cis-acting elements in ACBP gene promoters identified a number of motifs associated with light, abiotic stresses, and phytohormones. Expression profiling confirmed tissue-specific expression patterns of CsACBP1~5 and PtrACBP1~5. RT-qPCR analysis revealed that all CsACBP and PtrACBP genes responded to cold and salt stresses, though the magnitude of their responses varied significantly. Specially, although PtrACBP5 did not respond to low temperatures as rapidly as other members, its expression level increased significantly after 24 h of low-temperature treatment. Protein–protein interaction (PPI) network predictions indicated tight associations among four of the five CsACBPs, with CsACBP5 excluded from these interactions. Moreover, CsACBP1, CsACBP2, and CsACBP3 were predicted to be potential targets of csi-miR3952, csi-miR396a, and csi-miR477b, respectively. Overall, our research provides a solid foundation for further investigations into the biological functions and regulatory mechanisms of ACBP genes in citrus growth, development, and stress adaptation. Full article

Chronic cold stress is a severe test that animals in cold regions have to face during winter. However, the lack of precise dietary adjustments for animals in cold regions represents a significant gap in addressing their nutritional needs. Full-fat rice bran is one of the feed materials rich in protein, lipids, dietary fiber, and antioxidant-active substances. Glucose is the most common quick energy supply. We determined dietary full-fat rice bran and glucose can improve the growth and health of cold-exposed pigs. A total of 18 Yorkshire pigs were randomized to one of three treatment groups (basal diet, full-fat rice bran diet (20%), and glucose diet (10%)) for 22 d to evaluate the effects of full-fat rice bran and glucose on growth performance, antioxidants, microbiomes, and bile acid circulation in cold-exposed pigs. The results showed that dietary full-fat rice bran decreased the average daily feed intake (p < 0.05), increased superoxide dismutase (SOD) activity in plasma (p < 0.05), and decreased Rikenellaceae_RC9_gut_group and Campylobacter in the colon microbiota of cold-exposed pigs (p < 0.05). Dietary glucose improved the growth performance of cold-exposed pigs and decreased the abundance of Prevotellaceae_NK3B31_group (p < 0.05) in the colon microbiota of cold-exposed pigs. Dietary full-fat rice bran and glucose both downregulated the abundance of Alloprevotella, Bradymonadales, and Erysipelotrichaceae in colon microbiota (p < 0.05), promoted the production of SCFAs, and activated the FXR-CYP7A1 signaling pathway. Dietary full-fat rice bran or glucose promoted fecal excretion of bile acids. This study demonstrated that dietary supplementation with full-fat rice bran or glucose can improve the colonic microbiota structure and SCFA levels in cold-exposed pigs. When comparing the two dietary strategies, the glucose-supplemented diet is more beneficial to the growth performance of cold-exposed pigs, while the full-fat-rice-bran-supplemented diet is more conducive to enhancing the function of their antioxidant system. Additionally, dietary supplementation with full-fat rice bran or glucose can also regulate the bile acid circulation in pigs, thereby enhancing their cold adaptation ability. Full article

Group 1 LEA proteins are involved in embryo water dynamics during the maturation stage of seed development and contribute to desiccation stress protection in vegetative and embryonic tissues. Nevertheless, their roles in durum wheat remain largely unexplored. This study represents the first comprehensive survey of group 1 LEA proteins and their encoding genes in Triticum turgidum ssp. Durum (durum wheat). Eight group 1 LEA (TtEM1 to TtEM8) genes were identified in the durum wheat genome, which were named according to their chromosomal location. Analyses of the physiochemical characteristics and subcellular location revealed that all TtEM proteins exhibited a highly disordered structure (more than 90% of tendency of disorder) and were located in the nucleus. Evolutionary analysis between the durum wheat family and all other known group 1 LEA proteins from Arabidopsis thaliana, rice (Oryza sativa), barley (Hordeum vulgare), and barrel medic (Medicago truncatula) showed four phylogenetic groups; each group shares the same conserved motifs and gene structure. Interestingly, almost TtEM genes harbor cis-elements related to hormone regulation, stress response, and growth regulation, indicating their function in stress tolerance and developmental control. Subsequently, Expression analysis of two homoeologous genes, TtEM1 and TtEM4, demonstrated that the two genes exhibited distinct expression profiles across different tissues and in response to various stress treatments, suggesting that these genes may be involved in regulating growth, development, and stress adaptation in durum wheat. TtEM1 and TtEM4 purified proteins act as molecular chaperones and protect LDH activity against desiccation, cold, and heat treatments. Moreover, TtEM1 and TtEM4 genes were proved to enhance heat, cold, oxidative, and drought tolerance in yeast. These results clearly described the characteristics and the evolutionary dynamics of the EM gene family in wheat, and unveiled their role in wheat development and response to abiotic stress. Full article

Histone methylation plays important roles in plant development and adaptation to multiple stresses. SET domain group (SDG) proteins are identified as plant histone lysine methyltransferases in Arabidopsis and other crops. However, the SDG gene family and its functional roles in tomato remain unknown. In this research, 48 tomato SDG (SlSDG) gene family members were identified, and their chromosomal locations and conserved motifs were determined. According to phylogenetic analysis, the SlSDGs are divided into seven groups, which is consistent with Arabidopsis and rice. Promoter analysis indicated that the SlSDGs may be associated with biotic and abiotic stress responses. The expression pattern of SlSDGs illustrates that heat and cold stress significantly influence the transcript abundance of SDG14/19/21/23/48. The results of a VIGS assay showed that silencing SlSDG19 and SlSDG48 decreases tomato heat tolerance, while silencing SlSDG14 improves the heat tolerance of tomato plants. The analysis of downstream regulating genes indicated that heat shock proteins (HSPs), especially HSP70 and HSP90, act as critical effectors. Similarly, the experimental assay and expression analysis suggest that SDG21 and SDG23 positively and negatively regulate tomato cold tolerance through the CBF-COR pathway, respectively. These findings clarify the function of tomato SDG proteins and provide insight for the genetic improvement of tomato for temperature stress tolerance. Full article

Rice (Oryza sativa L.), a staple food for over half of the global population, plays a pivotal role in food security. Among its two primary groups, japonica and indica, temperate japonica varieties are particularly valued for their high-quality grain and culinary uses. Although some of these varieties are adapted to cooler climates, they often suffer from reduced productivity or increased disease susceptibility when cultivated in warmer productive environments. These limitations underscore the need for breeding programs to incorporate biotechnological tools that can enhance the adaptability and resilience of the plants. However, New Genomic Techniques (NGTs), including CRISPR-Cas9, require robust in vitro systems, which are still underdeveloped for temperate japonica genotypes. In this study, we developed a reproducible and adaptable protocol for protoplast isolation and regeneration from the temperate japonica cultivars ‘Ónix’ and ‘Platino’ using somatic embryos as the starting tissue. Protoplasts were isolated via enzymatic digestion (1.5% Cellulase Onozuka R-10 and 0.75% Macerozyme R-10) in 0.6 M AA medium over 18–20 h at 28 °C. Regeneration was achieved through encapsulation in alginate beads and coculture with feeder extracts in 2N6 medium, leading to embryogenic callus formation within 35 days. Seedlings were regenerated in N6R and N6F media and acclimatized under greenhouse conditions within three months. The isolated protoplast quality displayed viability rates of 70–99% within 48 h and supported transient PEG-mediated transfection with GFP. Additionally, the transient expression of a gene editing CRISPR-Cas9 construct targeting the DROUGHT AND SALT TOLERANCE (OsDST) gene confirmed genome editing capability. This protocol offers a scalable and genotype-adaptable system for protoplast-based regeneration and gene editing in temperate japonica rice, supporting the application of NGTs in the breeding of cold-adapted cultivars. Full article

Climate change poses significant challenges to temperate rice production, particularly affecting grain quality and market acceptance. This review synthesizes current knowledge of climate-induced quality changes, with a focus on the Australian rice industry as a case study with comparisons to other temperate regions. Environmental stressors such as extreme temperatures, variable rainfall, elevated CO₂, and salinity disrupt biochemical pathways during grain development, altering physicochemical, textural, and aromatic traits. Different rice classes exhibit distinct vulnerabilities: medium-grain japonica varieties show reduced amylose under heat stress, aromatic varieties experience disrupted aroma synthesis under drought, and long-grain types suffer kernel damage under combined stresses. Temperature is a key driver, with quality deterioration occurring above 35 °C and below 15 °C. Systems biology analyses reveal complex signalling networks underpinning these stress responses, although experimental validation remains limited. The Australian industry has responded by developing cold-tolerant cultivars, precision agriculture, and water-saving practices, yet projected climate variability demands more integrated strategies. Priorities include breeding for stress-resilient quality traits, refining water management, and deploying advanced phenotyping tools. Emerging technologies like hyperspectral imaging and machine learning offer promise for rapid quality assessment and adaptive management. Sustaining high-quality rice in temperate zones requires innovation linking physiology with practical adaptation. Full article

Background: Casein kinase I-like (CKL) protein is a member of the serine/threonine kinase CKI family and plays a pivotal regulatory role in various eukaryotic cellular processes, including stress responses. Objectives: This study aims to systematically identify the CKL gene family in the tomato genome and investigate its responsiveness to abiotic stress. Methods: Members of SlCKL were identified through genome-wide bioinformatics analysis, and their physicochemical properties, chromosomal localization, gene structure, conserved domains, phylogenetic relationships, cis-acting elements, cross-species collinearity, and tissue expression profiles were comprehensively analyzed. The expression patterns of SlCKL genes under abiotic stress were validated using real-time quantitative PCR. Results: A total of 16 SlCKL genes were identified and classified into three subfamilies (I–III), which are unevenly distributed across nine chromosomes, predominantly clustered at the ends. The gene structure, motifs, and functional domains exhibit high conservation. Collinearity analysis revealed stronger synteny between tomato and Arabidopsis thaliana or pepper compared to rice, maize, or tobacco, suggesting a common ancestral origin. The tissue expression profile indicates that SlCKLs are preferentially transcribed in roots. Promoter analysis and qRT-PCR validation demonstrated differential responses of SlCKLs to various abiotic stresses, such as drought, salt, heat, cold, and ABA treatment. Conclusions: This study represents the first systematic identification of the tomato SlCKL gene family, elucidating its evolutionary relationships, structural characteristics, tissue-specific expression patterns, and differential responsiveness to abiotic stress, thereby providing a critical foundation for further investigation into the molecular mechanisms underlying CKL-mediated abiotic stress adaptation in tomatoes. Full article

An exploration and understanding of cultivar adaptability to specific environmental conditions are critical in rice breeding. This study aimed to compare the agro-morphological data of 36 japonica rice cultivars (Oryza sativa L.) from Chinese rice accessions grown under two different environments (Fengyang and Hexian) and to identify important genes associated with key traits in the cultivars. Higher significant differences were observed between Fengyang and Hexian in traits like, grain width, grain length, yield per plot, plant height, and tiller number with cultivars grown in Hexian having the greatest values. This revealed that the environment in Hexian favored these traits, and most cultivars performed better in Hexian than in Fengyang. Correlation analysis also showed strong positive correlations between tiller number and yield per plot in both environments, indicating the influence of tiller number on rice yield potential. The PCR analysis showed the amplification of DEP1, Ghd7, Wx, Chalk5, COLD1, DST, Xa13, and Bph6 in most japonica cultivars, indicating presence of these genes in the cultivars. This study suggests that differences in agronomic performance between the cultivars grown in Fengyang and Hexian might be caused by differences in environmental conditions. This finding could be valuable for future breeding of high-yielding and climate-resilient cultivars. Full article

The Di19 (Drought-induced 19) gene family encodes Cys2/His2-type zinc finger proteins that are known to be involved in plant responses to various abiotic stresses, including drought, salinity, and temperature extremes. However, little is known about their roles in barley (Hordeum vulgare), particularly in cold stress adaptation. This study aimed to conduct a comprehensive genome-wide analysis of the barley genome to identify Di19 gene family members and examine their expression patterns under cold stress, providing theoretical support for stress-resistant barley breeding. By aligning Di19 gene sequences from Arabidopsis and rice and using BLASTp, seven HvDi19 genes were identified in barley. Bioinformatics analysis revealed that all members contain a conserved Cys2/His2-type zinc finger domain and nuclear localization signals. Phylogenetic analysis grouped the HvDi19 genes into four subfamilies, with three homologous gene pairs, and Ka/Ks analysis indicated strong purifying selection. Tissue-specific expression analysis showed significant variation in HvDi19 expression across barley organs. Under cold stress, different barley varieties exhibited distinct HvDi19 gene expression profiles: for instance, HvDi19-1 was downregulated in cold-tolerant varieties, whereas HvDi19-7 showed increased expression in a cold-tolerant mutant, suggesting their potential roles in modulating cold response. These findings reveal the evolutionary conservation and cold-responsive expression characteristics of the HvDi19 gene family, laying a foundation for future functional studies. The results also provide important molecular resources for the genetic improvement of cold tolerance in barley, contributing to the development of stress-resilient crop varieties under climate change. Full article

In this study, the LBD (Lateral Organ Boundaries Domain) gene family, a group of plant-specific transcription factors critical for plant growth and development as well as metabolic regulation, was comprehensively characterized in rice. We identified 36 LBD genes using multi-source genomic data and systematically classified them into Class I (31 genes) and Class II (5 genes). Analysis of their physicochemical properties revealed significant variations in amino acid length, molecular weight, isoelectric points, and hydropathicity. Motif analysis identified conserved LOB domains and other motifs potentially linked to functional diversity. Cis-acting element analysis indicated the involvement of these genes in various biological processes, including light response, hormone signaling, and stress response. Expression profiling demonstrated tissue-specific expression patterns, with several genes, such as XM_015770711.2, XM_015776632.2, and XM_015792766.2, showing relatively high expression in rice roots, implying their important role in root development. Transcriptome data further supported the involvement of specific genes in responses to phytohormones such as jasmonic acid (JA) and abscisic acid (ABA), as well as environmental stresses like cold and drought. Notably, XM_015770711.2, XM_015776632.2, and XM_015772758.2 may contribute to the regulation of rice environmental adaptability by mediating ABA and JA signaling pathways, respectively. In conclusion, this study identified members of the LBD gene family through the screening of two rice gene databases, and performed a comprehensive analysis of their physicochemical properties, evolutionary relationships, and expression profiles under various conditions. These findings provided valuable insights for further functional studies of LBD genes. Moreover, this study provides a foundation for targeting LBD genes to enhance stress resilience (e.g., drought/cold tolerance) and root architecture optimization. The LBD gene family possesses dual values in both stress resistance regulation and developmental optimization. The construction of its multidimensional functional map lays the theoretical and resource foundation for the precise design of high-yield and stress-resistant varieties. Full article

‘Dianheyou615’ (DHY615) is an elite Dian (D1)-type hybrid japonica rice variety, renowned for its high yield, exceptional grain quality, and unique adaptability to both irrigated and rainfed conditions in the Yungui Plateau of southwestern China. However, the genetic mechanisms underlying the agronomic performance of the D1-type hybrid japonica rice remain unclear. In this study, a comprehensive analysis of ‘DHY615’’s agronomic performance, genetic genealogy, and molecular genetic foundation was conducted to dissect its desirable traits for upland rainfed cultivation across diverse ecological environments. The main findings indicate that ‘DHY615’ possesses 6432 heterozygous SNPs, with 57.48% and 14.43% located in the promoter and coding regions, respectively, potentially affecting key phenotypic traits. High-impact SNPs variants and numerous well-known functional genes were identified, such as OsAAP6, GS3, Sd1, Rf1, BADH2, BPh14, Rymv1, OsFRO1, NRT1.1B, SKC1, OsNCED2, and qUVR-10, which are likely linked to traits including plant architecture, grain yield, grain quality, and resistance to various biotic and abiotic stresses (e.g., disease, cold, drought, salt, high iron, and high UV radiation). Notably, ‘Nan615’ harbors a greater number of functional allele variants compared to ‘H479A’, which potentially explaining its superior grain yield and remarkable adaptability. This study offers novel and valuable insights into the molecular genetic foundation of the plateau D1-type hybrid japonica rice, underscoring its potential for sustainable rice production across diverse ecological zones, especially with its unparalleled high-altitude adaptability to rainfed upland planting. Full article

Straw incorporation effectively improves soil fertility and crop yield, and its adaptation to single-season rice production in cold temperate regions is a current research focus. This study conducted a two-year continuous in situ field experiment with four treatments: no straw incorporation (CK), straw incorporation with autumn rotary tillage (SC), straw incorporation with autumn plowing (SH), and straw incorporation with spring rotary tillage (ST). This study investigated the effects of straw incorporation on rice growth and the soil environment to understand the soil-crop interactions and their impact on rice yield. The results indicate that in the single-season rice production system of Northeast China, straw incorporation reduces the number of tillers, dry matter accumulation, and leaf area index in the early rice growth stage but promotes dry matter accumulation in the later stages. Straw incorporation over two consecutive years increased the rice yield by 2.07%, with the SC treatments showing optimal performance. This increased yield could lead to higher economic returns for the farmers. Additionally, straw incorporation potentially increases the total nitrogen and soil organic matter (SOM) content in the topsoil, thus providing environmental benefits by reducing the need for synthetic fertilizers. Factor analysis reveals that the SC treatments enhances dry matter accumulation by influencing soil nutrient levels in the later rice growth stages, thereby improving rice yield and nitrogen recovery efficiency. By altering soil nutrient availability at different growth stages, different straw incorporation regimes regulate the material production strategy of rice and the ‘source-sink’ relationship. This research provides a theoretical basis for enhancing soil fertility and rice yield in cold temperate regions through improved straw management strategies. These findings support policy initiatives that promote large-scale straw incorporation in commercial rice production for its potential economic and environmental benefits. Full article

Background/Objectives: Cold stress poses a significant threat to Asian rice cultivation, disrupting important physiological processes crucial for seedling establishment and overall plant growth. It is, thus, crucial to elucidate genetic pathways involved in cold stress tolerance response mechanisms. Methods: We mapped OsUBC7, a Radiation-sensitive 6 (RAD6)-type homolog of rice, to a low-temperature seedling survivability (LTSS) QTL and used genomics, molecular genetics, and physiological assays to assess its role in plant resilience against low-temperature stress. Results: OsUBC7 is cold responsive and has higher expression levels in cold-tolerant japonica than cold-sensitive indica. Overexpression of OsUBC7 enhances LTSS of indica and freezing tolerance of Arabidopsis, increases levels of soluble sugars and chlorophyll A, boosts leaf development after cold exposure, and increases leaf cell numbers and plants size, but it does not affect membrane stability after cold stress exposure. Additionally, OsUBC7 has a positive role for germinability in the presence of salt and for flowering and yield-related traits. The OsUBC7 protein physically interacts with the developmental stage-specific and histone-modifying E3 ligases OsRFPH2-12 and OsHUB1/2, respectively, and potential target genes such as cell cycle dependent kinases were identified. Conclusions: OsUBC7 might contribute to cold resilience by regulating sugar metabolism to provide energy for promoting cellular homeostasis restoration after cold stress exposure via new cell growth, particularly in leaf cells crucial for photosynthesis and metabolic activity, possibly by interacting with cell cycle regulating proteins. Overall, the present study suggests that OsUBC7 may be involved in plant development, reproduction, and stress adaptation, and contributes to a deeper understanding of rice plant cold stress tolerance response mechanisms. OsUBC7 may be a promising candidate for improving crop productivity and resilience to stressful environments. Full article

Broadening the genetic base of an elite breeding gene pool is one important goal in a successful long-term plant breeding program. This goal is largely achieved through the search for and introgression of exotic germplasm with adaptive traits. However, little is known about the genetic backgrounds of acquired exotic germplasm, as germplasm selection is mainly based on trait information. Here, we expanded an average pairwise dissimilarity (APD) analysis to samples with SNP genotypes associated with genes for specific characters of breeding interest. Specifically, we explored a gene-associated APD analysis in a genomic characterization of 2643 rice lines based on their published FASTQ data. Published contigs for cloned genes conditioning heat tolerance, cold tolerance, fertility, and seed size were downloaded as gene reference sequences for SNP calling, along with those SNP calls based on the rice reference genome and published indels. Totally, eight SNP or indel data sets were formed for each of three sample groups (All2643, Indica1789, and Japonica854). APD estimation was made for each of the 24 data sets. For each sample group, four novel sets of the 25 most genetically distinct rice lines, each for an assayed character, were identified. Further analyses of APD estimates also revealed some interesting APD properties. Four contig-based SNP data sets for four specific characters displayed similar APD frequency distributions and positive high correlations of APD estimates. Contig-based APD estimates were negatively correlated with genome-based APD estimates and nearly uncorrelated with indel-based APD estimates. These findings are significant for plant germplasm characterization and germplasm utilization in plant breeding. Full article