Search Results (6,561)

Peanut (Arachis hypogaea L.) is a globally vital oilseed and cash crop. The LONELY GUY (LOG) gene family acts as a core regulator of cytokinin activation, governing plant meristem maintenance, growth, development, and stress responses. However, the genome-wide characteristics, evolutionary dynamics, and biological functions remain largely uncharacterized in peanut. In this study, 24 AhLOG genes were identified from the cultivated peanut Tifrunner. Phylogenetic analysis, gene structure characterization, and conserved motifs validated the high evolutionary conservation of the AhLOG gene family, and subcellular localization prediction indicated most AhLOG proteins were distributed in the cytoplasm. Promoter cis-element analysis revealed abundant hormone-responsive and stress-responsive cis-elements in the promoter regions of the AhLOG genes. Synteny analysis uncovered highly conserved collinear relationships between cultivated peanut and its diploid progenitors (A. duranensis, A. ipaensis) as well as the wild tetraploid relative (A. monticola), while numerous conserved orthologous syntenic pairs were detected between peanut and the model plant Arabidopsis thaliana. Tissue expression profiles revealed remarkable functional divergence among members: AhLOG3 and AhLOG16 were widely involved in both vegetative and reproductive development, while several other AhLOG genes exhibited strict tissue-specific expression. Furthermore, qRT-PCR analysis demonstrated that AhLOG genes were significantly induced by abscisic acid (ABA), gibberellin (GA), indole-3-acetic acid (IAA), methyl jasmonate (MeJA), drought and salt treatments, with distinct expression patterns under these abiotic stress conditions. Collectively, this work provides a systematic understanding of the AhLOG gene family and offers key candidate genes along with theoretical support for further functional investigation and molecular breeding of stress-resistant peanut. Full article

Background: Grain length is a key determinant of yield and quality in barley (Hordeum vulgare L.) and is typically governed by complex quantitative traits. Methods: In this study, a diverse natural population comprising 198 barley accessions was evaluated across two years to investigate the genetic basis of grain length. Results: Phenotypic analysis revealed continuous variation with near-normal distribution, indicating polygenic control. Genome-wide association study (GWAS) identified 84 stable single nucleotide polymorphism (SNP) loci significantly associated with grain length, predominantly enriched on chromosome 7. RNA sequencing (RNA-seq) was conducted using two contrasting genotypes at four developmental stages. Differentially expressed genes (DEGs) were mainly enriched in structural constituent of chromatin, protein heterodimerization activity, and the starch and sucrose metabolism. Integration of GWAS and RNA-seq identified 7 key candidate genes seven key candidate genes, including LOC123412467, LOC123408579, LOC123407599, LOC123410619, LOC123410954, LOC123411868, and LOC123426274. Sequence variation analysis further revealed functional polymorphisms, including non-synonymous mutations. The sequencing results show that LOC123412467 and LOC123410619 exhibited consistent allelic variation between long-grain and short-grain accessions, while LOC123426274 displayed stable differential expression across developmental stages, indicating their potential roles as key genes controlling grain length. Conclusions: Collectively, these findings suggest that chromosome 7 contains major regulatory loci controlling barley grain length and demonstrate that integrative multi-omics analysis is an effective strategy for identifying high-confidence candidate genes associated with complex agronomic traits. This study provides valuable insights into the genetic basis of grain length and offers key candidate genes for barley molecular breeding. Full article

The Northwest soybean production region (covering Shanxi, Shaanxi, Gansu, Ningxia, Xinjiang, central and western Inner Mongolia and northern parts of Hebei) possesses vast cultivated land resources and advantageous light–temperature conditions, endowing soybean with substantial yield potential. In this study, two natural soybean populations originating from this region were used to systematically investigate the phenotypic variation in two important agronomic traits, plant height (PH) and main stem node number (NN). The results showed abundant genetic variation for both traits. Through genome-wide association analysis (GWAS) and employing a joint detection across multi-environments (control false positives), 5 SNPs significantly associated with PH and 18 SNPs significantly associated with NN were identified, among which four SNPs were detected associated with both traits. Candidate genes were further screened within the ±100 kb intervals flanking lead SNPs at association peaks. By integrating gene expression levels of different soybean tissues and their correlations with the phenotypes, two candidate genes associated with both PH and NN were determined. These findings provide a theoretical basis for the identification and utilization of soybean germplasm resources in Northwest China, and lay a solid foundation for breeding high-yield and high-quality soybean varieties through molecular breeding. Full article

Background: Xyloglucan endotransglucosylase/hydrolase (XTH) acts as a key cell wall-modifying enzyme and contributes to plant stress resilience. This study aimed to identify the MeXTH gene family in cassava and characterize its potential functions in abiotic stress adaptation. Method: A full set of bioinformatic analyses was performed, including phylogeny, gene structure, conserved motifs, chromosomal localization, synteny, promoter cis-elements and subcellular localization. Expression patterns were examined by quantitative real-time PCR (qRT-PCR). Results: Forty-two MeXTH genes were identified and distributed on 14 chromosomes, encoding proteins with conserved Glyco_hydro_16 (Glycoside hydrolase family 16) and XET_C (Xyloglucan endotransglycosylase C-terminal domain) domains. Genes were clustered into four subfamilies with similar structures. Synteny was closer between cassava and dicots than monocots. Twenty-four stress-, hormone- and light-related cis-elements were detected. Ten MeXTH genes showed obvious differential expression under stress, and most proteins were located in the cell wall. Conclusions: The MeXTH gene family is structurally conserved and can serve as a readout of abiotic stress in cassava. These results provide a theoretical basis for molecular breeding aimed at enhancing stress resistance in cassava. Full article

The genus Cucurbita (pumpkin), encompassing C. maxima and C. moschata, is agriculturally and nutritionally significant globally. Herein, we re-sequenced 146 germplasm accessions (51 C. moschata and 95 C. maxima) to characterize genomic variations and identify loci associated with critical traits. Population structure analysis revealed four distinct subgroups: G1 (C. moschata), and G2–G4 (C. maxima), the latter classified by rind color (green, gray, and red, respectively). A genome-wide association study (GWAS) analysis identified 26 loci associated with eight fruit quality traits (e.g., rind color, pulp thickness, starch content) and leaf traits. Selective sweep analyses revealed 18 overlapping signals between the GWAS and selective regions, highlighting convergent evolution in starch content, pulp thickness, and water content driven by artificial and natural selection. We further validated these key fruit quality candidate genes, confirming that starch, cellulose, and pulp trait-related genes exhibited genotype-specific expression consistent with the quality divergence between CMO-X and CMO-E. Notably, C. moschata exhibited higher β-carotene and water content, while C. maxima showed higher starch content, reflecting divergent selection pressures. For leaf traits, 13 loci associated with leaf length were found, including LL9.2/LW9.1 with Cmax09G001045, which regulates leaf size. A novel haplotype in Cmax09G001045 explained the small-leaf phenotype of ‘Cuili 5’. This study provides a comprehensive genomic variation map of C. maxima and C. moschata, clarifies the genetic bases of key agronomic traits, and sheds light on their domestication and selection history, offering valuable resources for molecular breeding and crop improvement. Full article

Based on SLAF-seq technology, 174 white clover accessions were analyzed using population structure and genetic evolution to develop SNP markers of all accessions. We obtained 2329.4 Mb reads of sequenced data, and the reads of the samples ranged from 4,701,984 to 31,540,232. The sequencing quality value (Q30) uniformly changed from 90.61% to 96.82%, with an average of 93.11%. The GC content of the samples changed from 38.96% to 43.98%, averaging 40.96%, with a control of 34.21%. A total of 320,417 SLAF tags were developed, with an average sequencing depth of 16.42×. There were 202,625 polymorphic SLAF tags, accounting for 63.24% of the total number of SLAF tags. Finally, 2,999,555 polymorphic SNPs were found, and 102,025 high-quality SNPs were selected for downstream analyses after filtering with minor allele frequency (MAF) > 0.05 and completeness > 0.5. Population structure analysis supported K = 2, indicating two major ancestral genetic backgrounds among the accessions. Phylogenetic analysis and principal component analysis further divided the accessions into three genetic subclusters, suggesting finer-scale genetic differentiation. In addition, one-way ANOVA and chi-squared tests revealed a significant association between genetic groups and geographic origin (χ² = 25.78, df = 8, p = 0.0012; F = 3.489, p = 0.032), provided limited evidence for a possible association between genetic grouping and geographic origin. Compared with photosynthetic traits, agronomic traits showed a broader range of variations, with coefficient of variance values for agronomic traits ranging from 24.59% to 139.02% and for photosynthetic traits from 4.29% to 78.57%. This difference suggests that morphological traits were highly differentiated among the 174 accessions. The consistency between phenotypic clustering (based on agronomic traits) and molecular clustering (based on SNP data) suggests that our SNP dataset captures biologically meaningful genetic variation, providing a solid foundation for future genome-wide association studies (GWASs) and marker-assisted selection (MAS) in white clover. Full article

PP2C (protein phosphatases 2C) are key regulators of abscisic acid (ABA) signaling that play a crucial role in plant stress responses. Our analysis identified 71 DlPP2C genes in Dimocarpus longan, which were classified into distinct subgroups based on phylogenetic relationships with Arabidopsis thaliana and Oryza sativa. Structural analysis demonstrated conserved motif composition and gene organization within subgroups, while chromosomal distribution and synteny analysis revealed that segmental duplication events contributed to the expansion of this gene family. Promoter analysis uncovered several cis-acting elements related to hormone and stress responsiveness, especially abscisic acid-responsive elements (ABREs), suggesting that DlPP2C genes may play a role in ABA signaling pathways. Furthermore, we examined the ABA-responsive expression profiles of DlPP2C genes under exogenous ABA treatments. The expression patterns were dynamic and dose- and time-dependent, with several genes showing peak expression at 10 μM ABA after 16 h. The DlPP2C1 in particular displayed a strong transcriptional response, indicating its potential role in ABA regulation. While overexpression and GUS staining assays revealed enhanced activity under ABA treatment, further supporting the involvement of PP2C in ABA-responsive regulation, further mechanistic studies are needed for a full characterization. Finally, RNA sequencing analysis revealed a total of 1799 differentially expressed genes in response to ABA, with a prevalence of downregulated genes, showing extensive transcriptional reprogramming. Functional enrichment analysis demonstrated that these genes were largely associated with plant hormone signaling, stress response, and metabolic pathways. Weighted gene co-expression network analysis revealed a total of 32 key gene modules associated with ABA signaling. Collectively, our findings propose that DlPP2C genes, especially DlPP2C1, play a key role in ABA-mediated regulatory networks and provide valuable insights into stress adaptation mechanisms, especially during early somatic embryogenesis in longan. Full article

Although schistosome eggs are widely recognized as the principal drivers of hepatic granulomatous inflammation and fibrosis, the independent effects of adult worms may be masked by strong egg antigen-mediated responses. This study aimed to investigate whether adult Schistosoma japonicum worms alter the miRNA expression profile of hepatic stellate cells and to explore the potential relevance of these changes to liver fibrosis and hepatocellular carcinoma-related processes. A non-contact Transwell co-culture system was established using paired Schistosoma japonicum worms or male worms and hepatic stellate cells. Male worms were additionally included to further assess worm-derived effects independent of egg production–related influences. Untreated hepatic stellate cells served as controls. Total RNA was extracted for miRNA sequencing, and differentially expressed miRNAs were identified. Target gene prediction, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and validation using The Cancer Genome Atlas database were subsequently performed. Both paired worms and male worms significantly altered the miRNA expression profile of hepatic stellate cells. Several differentially expressed miRNAs were identified, among which hsa-miR-103a-3p showed relatively stable changes. Pathway enrichment analysis suggested that the potential target genes of hsa-miR-103a-3p were mainly enriched in AMP-activated protein kinase, mechanistic target of rapamycin, tumor necrosis factor, insulin signaling, and cellular senescence pathways. Further analysis using The Cancer Genome Atlas database showed that hsa-miR-103a-3p had diagnostic value in hepatocellular carcinoma and was associated with alpha-fetoprotein level, albumin level, Ishak fibrosis score, pathological stage, histological type, and tumor status. These findings suggest that adult S. japonicum worms may alter the miRNA expression profile of hepatic stellate cells, and that hsa-miR-103a-3p may be associated with fibrogenic responses and may have potential relevance to hepatocellular carcinoma-related processes. However, this inference is based on correlative TCGA data and does not imply a causal role in schistosomiasis-associated hepatocarcinogenesis. Full article

Objectives: The objective of this study was to evaluate the reproductive potential of crossbred heifers from dual-purpose systems using body conformation traits and to explore their genomic associations. Methods: A total of 522 heifers from the Colombian Caribbean region were phenotyped for structural and morphological traits, including body condition score, thoracic perimeter, height at withers, body length, ischium length, back level, hoof angle, stance width, hock angle, and rump level. Continuous variables were transformed into categorical classes and analyzed using multiple correspondence analysis (MCA) to build a reproductive potential index (RPI) that was used to perform a GWAS analysis to explore genomic regions. Results: The first two dimensions explained 11.6% and 8.2% of the total variation, respectively, and were used to construct an RPI. Heifers with higher RPI values exhibited greater thoracic perimeter, height, body length, and ischium length and were associated with wider chest and deeper body conformation, whereas lower RPI values were related to narrower and shallower body traits. However, some structurally desirable traits, such as centered stance, optimal hoof angle, and slightly sloped rump, were not clearly associated with high RPI. Genome-wide association analysis of the RPI did not reveal significant loci, although suggestive signals were identified on BTA3 and BTA19, near RSBN1, PHTF1, and WNT9B. Conclusions: These findings indicate that MCA-derived indices can summarize conformation-related variation in crossbred heifers, while the absence of strong associations suggests a polygenic architecture with small individual genetic effects. Full article

The fructose 1,6-bisphosphate aldolase (FBA) gene family plays crucial roles in plant energy metabolism, growth, development, and abiotic stress responses, as it modulates antioxidant synthesis and soluble sugar accumulation to enhance plant cadmium tolerance. Seashore paspalum (Paspalum vaginatum Sw.), a halophytic perennial C₄ turfgrass renowned for its exceptional cadmium tolerance, is ideal for phytoremediation of cadmium-contaminated soil. FBA family genes have been identified in several grass species, such as maize, rice, and wheat, but systematic investigations into FBA family genes and their functions in seashore paspalum remain scarce. In this study, seven class I FBAs (named as PvFBA1–PvFBA7) and one class II FBA (named as PvFBA8) in seashore paspalum were identified. The physicochemical properties, evolutionary relationships, gene structures, conserved domains, protein structures, cis-acting regulatory elements, chromosomal localizations, and collinearity relationships of eight PvFBAs were analyzed. These analyses suggested that PvFBA genes had highly conserved domains and belonged to ultra-conserved core genes. Expression pattern analysis indicated that the PvFBA gene family was dynamically responsive to cadmium stress. PvFBA6 and PvFBA7 were highly expressed in leaves, whereas PvFBA1 and PvFBA3 showed almost no expression. The RT-qPCR results suggested that the expression levels of PvFBA5 and PvFBA6 were highly consistent with the FPKM value trends analyzed in the transcriptomic data. Collectively, this study not only provides a theoretical foundation for the understanding of the evolution of the PvFBA gene family but also offers potential candidate genes for enhancing cadmium stress tolerance in plants. Full article

Cation/proton antiporters (CAXs) are key membrane transporters involved in plant development and stress adaptation. In this study, five CsCAX genes (CsCAX1–CsCAX5) were identified from the Citrus sinensis genome through comprehensive bioinformatic analysis. All CsCAX proteins are hydrophobic with 10–11 transmembrane domains, predominantly composed of α-helices and random coils, and are localized to either the plasma membrane or vacuole. Phylogenetic analysis classified them into two subfamilies (IA and IB). Promoter prediction identified stress- and hormone-responsive cis-elements (e.g., LTR, SA, and ABA), implying transcriptional regulation under environmental cues. Tissue-specific expression profiling revealed the highest CsCAX3 transcript abundance in stems and leaves. CsCAX3 was upregulated upon Xanthomonas citri subsp. citri (Xcc) infection but downregulated by Candidatus Liberibacter asiaticus (CLas). Subcellular localization confirmed CsCAX3 targeting to the plasma membrane. Functional verification showed that CsCAX3 overexpression increased susceptibility to Xcc, accompanied by a six-fold rise in bacterial load and substantial repression of antioxidant genes (CAT2, POD). Furthermore, transient overexpression of CsCAX3 in tobacco (Nicotiana benthamiana) will eliminate reactive oxygen species (ROS) accumulation. These results indicate that CsCAX3 negatively affects disease resistance by reducing sensitivity to ROS-mediated defense responses. Overall, this study elucidates the structural and functional characteristics of the CsCAX gene family and provides new insights into ROS-mediated immune regulation in citrus. Full article

Sophora tonkinensis Gagnep. is an important medicinal shrub native to the karst regions of southwestern China, where long-term overharvesting and habitat fragmentation have markedly reduced wild resources. Although recent phytochemical, transcriptomic, and chloroplast genomic studies have improved understanding of this species, its maternally inherited population structure has remained unclear. To address this gap, we developed nine novel chloroplast simple sequence repeat (cpSSR) markers and used them to genotype 274 individuals from eighteen wild populations. A total of 41 alleles were detected, with 2–10 alleles per locus, indicating moderate to high polymorphism at the species level. By combining the nine cpSSR loci, we further identified 25 chlorotypes, including 19 private chlorotypes. Within-population chloroplast diversity was generally low, and five populations were monomorphic, whereas HJSE and LYNG retained comparatively high chlorotype diversity. Genetic differentiation among populations was extremely strong (mean FST = 0.808), whereas historical gene flow was very limited (Nm = 0.112), and AMOVA showed that 85% of total chloroplast variation occurred among populations. Taken together, chlorotype network analysis, chlorotype geographic distribution, UPGMA, PCoA, and exploratory STRUCTURE analysis supported three geographically structured chloroplast groups, indicating long-term restriction of seed-mediated dispersal across the fragmented karst landscape. These newly developed cpSSR markers and the derived chlorotype framework provide a practical basis for tracing maternal lineages, prioritizing conservation units, guiding ex situ germplasm sampling, and informing future breeding of this nationally protected species. Overall, the present results describe chloroplast-based maternal structure rather than total genome-wide diversity in S. tonkinensis. Full article

M. micrantha is a highly destructive invasive weed causing severe ecological and economic damage in invaded regions. Conventional control methods remain insufficient, highlighting the need for targeted management strategies. NAC transcription factors, a plant-specific family, play key regulatory roles in growth, secondary metabolism, and stress responses. Here, we performed a genome-wide identification and characterization of the NAC gene family in M. micrantha using bioinformatic approaches based on Arabidopsis thaliana NAC sequences and the M. micrantha whole-genome assembly. A total of 76 MmNAC genes were identified from M. micrantha, and these members were classified into 13 subfamilies and one unclassified clade, with subdomains C and D being the most conserved. Five conserved motifs were identified; motifs 1 and 2 were present in over 94% of members. Chromosomal mapping showed 68 genes distributed unevenly across 18 of 19 chromosomes. Tissue expression analysis revealed that NAP and AtNAC3 subfamilies are highly expressed in seeds, while NAM and NAC2 subfamilies predominate in floral tissues, suggesting potential subfamily–tissue expression patterns. These findings provide a basis for understanding NAC functions in M. micrantha and identifying targets for its control. Full article

Maize (Zea mays L.) is one of the most important cereal crops worldwide, with yield being a complex quantitative trait controlled by multiple genetic factors. The aim of this study was to identify molecular markers associated with maize yield using next-generation sequencing (NGS), association mapping, and physical mapping approaches. A total of 122 maize hybrids were evaluated under field conditions in a randomized complete block design with three replications. Phenotypic data were collected for grain yield, while genotypic data were obtained using DArTseq technology, resulting in the identification of 60,436 SilicoDArT and 32,178 SNP markers. After quality filtering, 25,078 markers were used for further analyses. Analysis of variance revealed statistically significant differences among hybrids in terms of yield (p < 0.001), with values ranging from 12.67 to 18.52 kg/10 m². Genetic similarity among hybrids ranged from 0.434 to 0.957, indicating substantial genetic diversity. Cluster analyses based on phenotypic and genotypic data showed a lack of correspondence between yield performance and genetic similarity. Genome-wide association studies (GWAS) identified 2478 markers significantly associated with yield, including 47 highly significant markers (Logarithm of the Odds – LOD > 4.0). Individual markers explained between 2.4% and 18.7% of yield variation. Ten markers with the highest contribution to yield variability (13.30–18.70%) were selected as the most promising candidates for further breeding applications. These markers represent promising candidates for marker-assisted selection and genomic selection (GS) of high-yielding maize genotypes. These are some of the first positive results. The integration of phenotypic evaluation with high-throughput genotyping and association mapping provides valuable insights into the genetic architecture of yield and offers practical tools for the development of high-yielding maize cultivars. Full article

Background: Heat shock protein 100 (HSP100) is a key molecular chaperone that maintains intracellular proteostasis and enhances plant tolerance. However, the HSP100 gene family in soybean (Glycine max) has not been systematically characterized. Methods: In this study, we performed genome-wide identification and comprehensive analysis of the GmHSP100 gene family and analyzed their phylogeny, genomic distribution, synteny, protein structures, subcellular localization, promoter cis-elements, and expression patterns under heat and salt stresses via bioinformatics approaches and quantitative real-time PCR (qRT-PCR) validation. Results: Thirteen GmHSP100 members were identified, which were classified into CLPB, CLPC and CLPD subfamilies. Segmental and whole-genome duplications primarily drove the expansion of this gene family. All encoded proteins possessed conserved AAA+ ATPase domains, with distinct motifs across subfamilies. Most proteins localized to the cytoplasm, while CLPC and CLPD targeted chloroplasts and GmCLPB4 localized to mitochondria. Promoter analysis identified numerous elements associated with light, hormone and stress responses. Expression profiling showed strong tissue specificity and time-dependent stress-treatment induction. Heat stress triggered rapid and strong upregulation of the GmHSP100s, whereas salt stress salt stress induced their relatively delayed and sustained expression. Conclusion: These findings reveal the evolutionary conservation and diversification of the GmHSP100 gene family in soybean, providing a foundational framework for understanding the functions of GmHSP100 in stress adaptation. Full article