This study estimated the impact of main founders and ancestors on inbreeding subdivision in the Polish Simmental cattle population. Two reference populations were defined: subset A (20,827 cows born 1984-2009) and subset B (19,554 cows born 2010-2020). Ancestral inbreeding coefficients were calculated relative to the main founders and ancestors for all cows in both subsets. Significant changes in ancestor composition were observed in younger cows. The main founders with the highest genetic contribution numbered 10 in subset A and 7 in subset B, with 7 common to both. Main ancestors numbered 11 (all bulls) in subset A and 15 in subset B, with 6 shared between subsets. The frequency of occurrence of common founders in subset B ranged from 42% to 49%, while that of common ancestors ranged from 31% to 68%. Kalinowski's new inbreeding coefficient was six times higher in subset B than in subset A. Although overall inbreeding levels remained low, the proportion of cows with elevated inbreeding increased over time despite continuous importation of breeding animals. These findings suggest that breeders should scrutinize more carefully the pedigrees of imported animals to prevent further inbreeding accumulation.
As a key morphological trait of flag leaves, flag leaf thickness (FLT) directly modulates light energy capture efficiency and per-unit-area photosynthetic capacity, and is thus identified as a critical regulator of wheat grain yield formation. Dissecting the genetic basis underlying FLT is of great significance for accelerating the molecular breeding of high-yield wheat varieties. In this study, two recombinant inbred line (RIL) populations were employed to map quantitative trait locus (QTL) for FLT across five independent environments. A total of 19 QTLs controlling FLT were identified in the two RIL populations. Among them, QFLT.suas-2CN-4B.2, QFLT.suas-2CN-6A, QFLT.suas-2SY-3B.2, and QFLT.suas-2SY-6A exhibited stable expression across multiple environments, and comparative analysis with previously reported QTLs indicated that all four loci are likely novel. Notably, QFLT.suas-2CN-6A and QFLT.suas-2SY-6A were co-localized within the same physical interval, suggesting they are likely the same locus. Candidate gene analysis for the co-localized locus QFLT.suas-2CN-6A and QFLT.suas-2SY-6A identified seven putative candidate genes highly expressed in wheat leaves, all of which encode chlorophyll a-b binding proteins that may participate in the regulation of FLT development. Furthermore, significant positive correlations between FLT and spikelet number per spike (SNS) were detected in both RIL populations. The favorable alleles of QFLT.suas-2CN-6A and QFLT.suas-2SY-6A significantly increased SNS by 3.21% and 3.31%, respectively. Collectively, these results deepen our understanding of the genetic basis underlying wheat FLT, and provide stable, valuable QTL resources and candidate gene targets for molecular marker-assisted breeding of high-yield wheat.
Melatonin-mediated modulation of antioxidant enzyme activity is widely reported; however, the mechanism underlying this indirect free radical combating effect of melatonin remains unclear. In the present study, we explored the role of RORα and RORα dependent NF-κB activation in mediating the effects of melatonin on the activity of antioxidant enzymes. The daily variation in the expression of RORα and NF-κB along with the plasma melatonin level was assessed, and its possible association with the antioxidant enzyme activity in the lymphoid tissues of the Indian squirrel was evaluated during different reproductive seasons. Significant daily variation in the expression of RORα and NF-κB was observed, which was inversely related to circulatory melatonin levels and the activity of antioxidant enzymes. The expression of RORα and NF-κB was downregulated at the night when the plasma level of melatonin and activity of antioxidant enzymes namely superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) were at their peak. Tissue melatonin can further act as a complementary factor in counteracting oxidative stress; hence, we also checked the lymphoid melatonin content over 24 h. No temporal variations were noted in the tissue melatonin content over the day. Likewise, no significant daily variation was noted in the total antioxidant status (TAS) of the lymphoid tissues. The absence of daily variation in the TAS can be attributed to the direct free radical scavenging activity of tissue melatonin in the spleen and thymus. The daily rhythms in the activity of antioxidant enzymes can be considered an integral part of the adaptive strategy that is regulated by the endogenous melatonin rhythm. However, the melatonin-mediated regulation of the antioxidant enzyme activity is neither mediated by RORα nor NF-κB dependent pathway.
Cows with greater circulating pregnancy-associated glycoprotein (PAG) concentrations after artificial insemination (AI) are more likely to maintain pregnancy (i.e., less pregnancy loss). The objective was to evaluate the effect of cow genetic background and feeding level on circulating PAG during early pregnancy in seasonal-calving, pasture-based, lactating dairy cows. Three divergent genetic groups (GG) of dairy cows were enrolled: Elite Economic Breeding index (EBI) Holstein-Friesian cows (Elite), representative of the top 5% nationally; average EBI Holstein-Friesian cows (NA), representative of the national average in Ireland; and purebred Jersey (JE) cows, representative of Jersey genetics available in Ireland and used primarily for crossbreeding. The 3 GG were evaluated under 3 contrasting spring-calving pasture-based feeding treatments (FT): control (CTL), low grass allowance (LGA), and high concentrate (HC). A total of 108 cows (36 in each GG and each FT) were initially enrolled. Cows were artificially inseminated following detected estrus at the start of the seasonal breeding period, and if cows did not return to estrus, blood samples were collected on d 23, 25, and 28 after AI (n = 92 samples collected; 16 cows returned to estrus before d 23). Ultrasound examinations for pregnancy diagnosis were conducted on d 30 to 36 after AI (hereafter referred to as d 33); if pregnant, cows were re-examined on d 60 to 66 after AI (hereafter referred to as d 63). Plasma PAG concentrations were measured using an IDEXX kit, and pooled blood from Holstein-Friesian cows that were on d 35 ± 2.4 (mean ± SD) of gestation was used to create a standard curve. Blood PAG concentrations were expressed relative to the concentration in the pooled sample from pregnant cows (% PC). There was evidence of an effect of GG on the PAG profile observed during early gestation. Jersey (n = 21) cows had greater mean (95% CI) plasma PAG concentrations compared with Elite (n = 20) cows but not NA (n = 13) cows: 52.1% PC (39.5%, 66.8%), 32.0% PC (22.5%, 43.5%), and 36.3% PC (24.3%, 51.4%), respectively. There was no effect of FT on circulating PAG concentrations. Across all cows sampled, circulating PAG concentrations were greater in cows that subsequently maintained their pregnancy (n = 54) compared with cows that subsequently had pregnancy loss (n = 9), and concentrations were lowest in cows that had no evidence of pregnancy based on plasma PAG measurements in advance of ultrasound diagnosis on d 33 (n = 29). Overall, the study findings indicate that cow genetic background and feeding treatment had little effect on circulating PAG concentrations during early pregnancy in grazing dairy cows. Pregnancy-associated glycoprotein determination on d 23 to 28 after AI could aid identification of pregnancy status and future risk of pregnancy loss.
Understanding the genetic diversity and population structure of farm animals is key to developing effective breeding strategies and conserving genetic resources. The aim of this study was to assess the genetic diversity and population structure of the Auliekol cattle breed based on genotyping using the BovineSNP50 BeadChip. This study included 1440 animals from eight farms. Genetic diversity indices (observed and expected heterozygosity), the inbreeding coefficient (FIS), and allelic richness were calculated, and population structure was analyzed using PCA, ADMIXTURE, fineSTRUCTURE, and genomic relationship matrix (GRM) methods. The results showed comparable levels of observed and expected heterozygosity across populations (Ho = 0.3478-0.3537; He = 0.3445-0.3492) and negative FIS values ranging from -0.0211 to -0.0025, suggesting no strong population-level signal of inbreeding. Low FST (0.007-0.028) and GRM values indicate weak genetic differentiation between populations. PCA and fineSTRUCTURE analyses showed no clear clustering, while ADMIXTURE identified three main genetic components shared across all populations. TreeMix analysis further suggested genetic connectivity among farms, with the Moskalyevskoe population occupying a central position in the inferred network of genetic relationships and migration events. In general, the Auliekol breed is characterized by a high level of genetic coherence and preserved genetic diversity, which creates favorable conditions for its further selective improvement and the preservation of genetic resources.
This review highlights ND-FISH mechanisms, genomic integration, and workflows for karyotyping, rearrangement detection, and introgression, bridging cytogenetics and breeding for precision crop improvement. Fluorescence in situ hybridization (FISH) has been a pivotal technique for chromosome identification in plant species for over three decades. In particular, the non-denaturing FISH (ND-FISH) method, developed in 2009 and based on synthetic oligonucleotide probes derived from simple sequence repeats (SSRs), offers a highly efficient and labor-saving alternative to conventional FISH protocols. The ND-FISH method enables large-scale karyotyping at low cost, making it suitable for both large and small genomes, especially in polyploid plant species. In recent decades, improvements in chromosome preparation have facilitated high-throughput molecular cytogenetic identification for studying plant genetic variation and diversity. Notably, the rapid expansion of plant genomic resources and the development of bioinformatics-based computational tools have enabled the production of various types of diversified oligonucleotide probes. These advances support molecular cytogenetic mapping and precise chromosome engineering, as well as validation of genome assembly, which effectively bridges the gap between laboratory genomic research and practical field breeding applications. This review summarizes key technical advances and mechanistic insights into ND-FISH, highlights recent achievements, and discusses the prospects for its applications in the plant genomics era.
Crassostrea hongkongensis is an economically important mariculture species in southern China, and hybrid breeding has been applied to improve its growth traits. However, the molecular mechanisms underlying growth heterosis remain poorly understood. In this study, inter-population hybrid (HG) and intra-population (IG) groups of C. hongkongensis were compared using integrated transcriptomic and metabolomic analyses to investigate the regulatory basis of growth heterosis. Shell length and shell height were significantly greater in HG than in IG (p < 0.01). Transcriptomic analysis identified 474 false discovery rate (FDR)-supported significant differentially expressed genes (DEGs) (233 upregulated and 241 downregulated), which were treated as the primary statistically robust findings; a broader set of 3161 candidate DEGs, including genes associated with growth regulation and shell biomineralization, was retained for exploratory functional and multi-omics analyses. Metabolomic analysis detected 345 differential metabolites (DMs), which were mainly enriched in energy metabolism, nucleotide metabolism, and arachidonic acid metabolism. Exploratory pathway-level multi-omics integration revealed significant concordance between the transcriptomic and metabolomic profiles (M2 = 0.1962, p = 0.001) and highlighted the tricarboxylic acid cycle, oxidative phosphorylation, branched-chain amino acid degradation, nucleotide metabolism, and arachidonic acid metabolism. These findings suggest that growth heterosis in C. hongkongensis is associated with altered energy metabolism, biosynthetic processes, shell formation-related pathways, and potential changes in the growth-defense balance, providing molecular insights for genetic improvement and selective breeding.
Genetic improvement of growth traits is a key objective in aquaculture breeding. In this study, we performed whole-genome resequencing of 282 Japanese flounder individuals from a single farmed cohort and obtained approximately 6.67 million high-quality SNPs. Single-trait and multi-trait GWAS were conducted for 11 growth traits: body weight (BW), total length (TL), body length (BL), body depth (BD), trunk length (TUL), head length (HL), snout length (SnL), caudal peduncle depth (CPD), eye diameter (ED), postorbital head length (PoL), and interorbital width (IW). Heritability estimates ranged from 0.172 (IW) to 0.487 (HL). Head length showed the highest heritability, followed by PoL (0.328), ED (0.323), BD (0.300), and CPD (0.291). Genetic correlation analysis revealed that BW was strongly positively correlated with most body size traits (rg > 0.9), indicating that simultaneous improvement of these traits is feasible. Single-trait GWAS identified a total of 55 suggestive associated loci (top five SNPs per trait, combined across all 11 traits, at p < 1 × 10-5). Notably, we observed pronounced pleiotropic effects, where a single SNP or gene influences multiple growth traits. For example, multiple SNPs on chromosome 14 were associated with more than five traits (TL, BL, BD, TUL, BW), and the fras1 gene affected both head length and post-orbital head length, demonstrating a genetic basis of pleiotropy. Additionally, fras1 was associated with head length, and nkd1 with interorbital width. Multi-trait GWAS uncovered 12 novel loci not detected in single-trait analyses, with candidate gene annotation pointing to pathways such as ECM-receptor interaction (e.g., fras1, lamb4) and Wnt signaling (e.g., nkd1), suggesting that these biological processes may underlie the observed associations. These findings are preliminary and require validation in larger independent cohorts. KEGG enrichment analysis showed significant enrichment in ECM-receptor interaction and non-homologous end-joining pathways (corrected p < 0.05). Our results provide a genetic basis for growth trait improvement and candidate markers for breeding programs in Japanese flounder.
Precision livestock farming (PLF) relies on high-precision three-dimensional (3D) horse reconstruction and automatic body measurement to support refined breeding management and health surveillance. However, data collection is restricted by building environment noise and hardware layout constraints; complex equine body shapes and large individual variations induce local geometric distortions in reconstructed models, limiting field deployment. Drawing on generative 3D reconstruction, this study develops the first image-to-3D pipeline that leverages three consumer depth cameras to reconstruct high-fidelity 3D horse models, integrating reconstruction, non-rigid optimisation and automatic body measurement. The image-to-3D module accurately extracts core morphological traits such as torso outlines and limb ratios for initial reconstruction. To eliminate local geometric deformation and recover scene scale, coarse-to-fine non-rigid fitting optimisation with dynamic surface feature matching weights is proposed, strengthening alignment between reconstructed meshes and real horse anatomical structures. Comparative experiments on multiple equine datasets verify that our method surpasses existing algorithms in measurement precision and reconstruction integrity. Compared with baseline methods, the non-rigid registration reduces core body measurement errors and Chamfer Distance (CD) by over 50%, while increasing the F-Score by more than 20%. This work enables automatic horse body phenotyping and offers technical references for image-to-3D dimensional measurement of other livestock species in large-scale precise breeding.
Seasonal, pasture-based milk production imposes distinctive physiological demands on dairy cows: compact calving, prompt resumption of estrous cyclicity and completion of uterine involution, achieving peak milk production on a diet primarily composed of grazed grass with short-term variability in supply and quality, and re-establishing pregnancy during a short breeding period. Central to these adaptations is the somatotropic axis-growth hormone (GH), hepatic GH receptor (GHR), insulin-like growth factor-1 (IGF1), 6 IGF binding proteins (IGFBP1-IGFBP6), and the IGF binding protein acid labile subunit (IGFALS)-which orchestrates nutrient partitioning, lactation, and the return to cyclicity and potential to reestablish pregnancy. This review summarizes the insights from experiments conducted in Ireland and New Zealand comparing different cow genotypes managed under grazing systems (e.g., North American vs. New Zealand Holstein-Friesian cows; Holstein-Friesian cows with divergent fertility merit but similar milk merit) and integrates herd-scale postpartum phenotypes linked to reproduction. In seasonal-calving, pasture-based systems, breeding indexes to improve cow genetic merit (greater emphasis on fertility and milk solids) are associated with a more favorable somatotropic axis profile (greater serum IGF1 during lactation), more conservative nutrient partitioning (less BCS loss), and superior uterine health, estrous expression, luteal function, and conception, without compromising milk solids output per cow. The biology of the somatotropic axis in dairy cows has an important effect on nutrient partitioning and fertility under pasture-based systems of milk production.
The rapid expansion of aquaculture breeding has increased the need to identify wild genetic resources for germplasm management and sustainable breeding. However, distinguishing wild from domesticated populations remains challenging in species with recent domestication histories and low genetic differentiation. In this study, we used the large yellow croaker (Larimichthys crocea) as a case study species to develop specific insertion/deletion (InDels)-based identification methods for wild and domesticated populations based on whole-genome resequencing data. Four large-fragment InDels with significant allelic frequency differences between populations were selected as one marker panel. In addition, four coding-region InDels predicted to alter amino acid sequences were selected as another marker panel based on allele-frequency differences, coding-region annotation, and supporting SNP-based Fst or nucleotide-diversity signals. Principal component analysis (PCA) based on these selected InDel loci showed partial separation with some overlap between wild and domesticated samples. Therefore, multi-locus scoring models were established by assigning scores to wild-predominant alleles. Receiver operating characteristic (ROC) analysis showed strong discriminatory performance for both panels, with area under the ROC curve (AUC) values of 0.9608 and 0.9771 and classification agreement rates with known sample status of 90.0% and 91.7%, respectively. These results indicate that targeted InDel markers can provide a practical PCR-based approach for distinguishing wild and domesticated large yellow croaker populations with limited genetic differentiation. This workflow may provide a reference for marker development in other recently domesticated species, although further validation in independent populations and target species is needed.
Environmental temperature significantly influences the evolutionary adaptation of poultry, while abdominal fat deposition represents a crucial economic trait affecting feed conversion efficiency and carcass quality. However, reports on the genetic mechanisms governing their co-evolutionary trade-offs remain scarce. This study employed whole-genome resequencing data from 469 chickens across 31 varieties. Through comparative analyses of heat- versus cold-adapted groups and high- versus low-fat groups, structural variations (SVs) were utilized as genetic markers. Selection signatures were identified via the population differentiation index (FST) and nucleotide diversity ratio (π ratio). We identified 103 overlapping genes located within significantly differentiated SVs at the intersection of temperature adaptation and fat deposition. Pathway analysis revealed significant enrichment in the thyroid hormone signaling pathway, pinpointing MED17 as a key selection target. Further validation via PCR genotyping in the heat-tolerant Wenchang chicken revealed that individuals harboring the MED17 mutation exhibited significantly higher abdominal fat deposition than those without. These results suggest that MED17 is associated with fat deposition in heat-tolerant Wenchang chickens, serving as a potential candidate gene for this trait, providing robust molecular markers for breeding novel strains with both thermotolerance and superior carcass traits.
Abiotic stress limits cereal productivity, yet whether conserved stress-responsive genes retain similar transcriptional network organization and cellular deployment across cereal species remains unknown. Here, we developed a machine learning-guided comparative framework to integrate public leaf transcriptomes of rice (Oryza sativa) and wheat (Triticum aestivum) under major abiotic perturbations. Using harmonized compendia comprising 787 rice and 337 wheat samples, we found that rice samples resolved into more discrete stress-associated transcriptional states, whereas wheat samples formed a more continuous landscape with partial overlap among stress responses. Supervised learning prioritized compact sets of stress-predictive candidate genes, including heat-shock/chaperone-related, ABA-biosynthetic and membrane-associated features. Orthology-guided co-expression analysis further showed that homologous stress-predictive genes, particularly heat-associated candidates, can retain stress responsiveness while occupying divergent module neighborhoods in rice and wheat. Leaf single-cell projection resolved this divergence at cellular resolution: several rice predictors showed compartmentalized expression in parenchyma and vascular parenchyma, whereas their wheat counterparts were more broadly deployed across mesophyll, epidermal and vascular cell types. Our findings reveal context-dependent redeployment of homologous stress-associated genes in cereals and offer a scalable strategy for prioritizing candidates for functional validation and climate-resilience breeding.
Japanese encephalitis virus (JEV) is a zoonotic pathogen. Infection in breeding boars triggers severe testicular inflammatory storms, resulting in testicular swelling, asthenospermia, oligozoospermia and even irreversible loss of reproductive capacity. Magnolol, a natural extract, exhibits remarkable anti-inflammatory and antioxidant activities. This study utilized swine testicular (ST) cells as an in vitro model to explore magnolol's protective effects against JEV-mediated inflammation and its underlying mechanism. ST cells were infected with JEV at an MOI of 1 and treated with magnolol at 8, 12 and 16 μg/mL. We detected pro-inflammatory cytokine expression, performed 4D-FastDIA quantitative proteomics to screen differentially expressed proteins, verified key RIG-I and NF-κB cascade molecules at mRNA and protein levels, and tracked p65 nuclear translocation through immunofluorescence. The data showed that JEV significantly elevated TNF-α, IL-1β, IL-6, IL-8 and CCL5, while magnolol reduced these cytokines in a dose-dependent manner. JEV reshaped the proteome of innate immunity and inflammation, and excessively activated the RIG-I/NF-κB axis to increase IKKβ, TRAF2, TRAF6 transcription and p65 phosphorylation and nuclear import; 24 h treatment with 16 μg/mL magnolol greatly restrained this overactivation. In summary, magnolol alleviates JEV-triggered inflammatory injury by inhibiting the RIG-I/NF-κB pathway, offering experimental evidence for its use as a natural agent to mitigate JEV-induced cellular inflammatory response in boars.
Rana dybowskii is an economically important amphibian in Northeast China, valued for its medicinal oviduct (Oviductus Ranae). However, the low proportion of females in artificial culture severely restricts industrial productivity. To elucidate the molecular mechanisms of hormone-induced sex reversal, based on our previous research results, we exposed tadpoles to 17β-estradiol (E2) or testosterone propionate (TP). We then monitored gonadal histology, conducted multi-stage transcriptome sequencing, and validated key genes via qRT-PCR. The results show that induction treatment with 40 μg·L-1 E2 and 80 μg·L-1 TP resulted in 93.33% female and 100% male populations, respectively. Both hormones promoted germ cell proliferation at the undifferentiated stage and directed stable ovarian or testicular development without intersex abnormalities. Ovarian differentiation involved progressive multi-wave transcriptional reprogramming, whereas testicular differentiation exhibited a concentrated gene expression burst during gonadal maturation. Steroid hormone biosynthesis, Wnt, and PPAR pathways formed the core regulatory network. Three female-biased genes (3α-hsd, Adcy3, Rspo1) and three male-biased genes (Ptgs2, Sox9, Shbg) were identified, with their expression dynamics aligned with histological progression. This study defines the optimal parameters and molecular signatures of bidirectional sex reversal in R. dybowskii. It provides a practical foundation for sex-control breeding and offers amphibian-based evidence for the conservation and plasticity of vertebrate sex determination.
The advent of positive socioeconomic changes and rising incomes has precipitated a dramatic increase in demand for luxury seafood, including scallops. The nutritional quality of scallops has been reported for different species from various geographical regions, but this information is not well organized. In this context, the objective of this study was to conduct a systematic evaluation of the proximate composition, amino acid quality, and fatty acid quality of scallops on a global scale. The protein and lipid composition of scallops exhibited significant variability among studies. Scallops are a source of high-quality protein and lipids, with fatty acid profiles that are notably superior. While certain scallops are known to contain all essential amino acids in sufficient amounts, valine frequently emerges as the primary limiting essential amino acid in the majority of scallops. With respect to the composition of fatty acids, scallops exhibit a notable abundance of n-3 long-chain polyunsaturated fatty acids (LC-PUFA). The content of EPA + DHA in most scallops exceeds 20% of total fatty acids, and in some cases reaches as high as 50%. The lipid quality indices (n-3/n-6 and PUFA/SFA ratios) of scallops are generally higher than recommended values, with the exception of a few documented cases with unusually low PUFA/SFA ratios. The findings of this study offer consumers detailed nutritional information on scallops and serve as important guidance for developing aquaculture and selective breeding programs for scallops.
Dendrobium officinale, a perennial medicinal herb rich in flavonoids, exhibits multiple pharmacological properties including antioxidant and hypoglycemic effects. However, its medicinal quality is compromised by various abiotic stresses, such as heat, cold, and osmotic stresses. UDP-glycosyltransferases play critical roles in both flavonoid glycosylation and plant stress tolerance. Here, we report the identification of a heat-responsive glycosyltransferase gene, DoUGT71K2, from D. officinale transcriptomes, and a characterization of its stress-induced expression and transcriptional regulatory mechanisms. Quantitative real-time PCR (qRT-PCR) showed that DoUGT71K2 exhibits tissue-specific high expression in flowers, and its transcript abundance is strongly elevated in response to heat, cold, and abscisic acid (ABA) treatment. The direct promoter-binding and trans-activating function of DoMYB102 on DoUGT71K2 was confirmed via dual-luciferase reporter and yeast one-hybrid (Y1H) assays. These results establish a DoMYB102-DoUGT71K2 regulatory module that couples heat stress response with flavonoid biosynthesis, which provides a molecular basis for improving stress tolerance and medicinal quality in D. officinale through molecular breeding.
Shade stress severely constrains soybean yield in soybean-maize intercropping systems, yet the intensity threshold triggering shade avoidance responses and the underlying hormonal mechanisms remain elusive. Here, through two-year field experiments, we demonstrate that shading coverage rate exceeding 80% is the critical threshold initiating shade avoidance, increasing plant height by 16-61%. The seventh internode is the initial responsive site where epidermal cells elongate by 69.86% longitudinally, while radial growth is broadly suppressed (cell area reduced by approximately 41%). Furthermore, integrated hormonal profiling and gene expression analyses demonstrate that shade promotes active gibberellin (GA) accumulation via dual metabolic reprogramming: upregulating biosynthetic genes GmGA20ox1 and GmGA3ox1 and downregulating catabolic genes GmGA2ox-7a and GmGA2ox-7b, leading to a 56.87% increase in GA1 content. Notably, exogenous GA fully mimics the shade-induced phenotype, with genotype sensitivity ranking BX10 > BD2 > W82, indicating that GA plays a central role in mediating the shade response. Yield analysis shows that shade inhibits soybean biomass accumulation and grain yield and preferentially suppresses reproductive rather than vegetative growth, reducing effective pod number and seeds per plant by ~50% whereas 100-seed weight only decreases by 6.55%. Together, these findings reveal that shade modulates GA homeostasis via "enhanced biosynthesis and suppressed catabolism" to remodel internodes, providing a theoretical basis for shade-tolerant soybean breeding and optimizing intercropping systems.
Seed dormancy is a vital adaptive mechanism regulated by the DELAY OF GERMINATION (DOG) gene family. Here, we present the first systematic genome-wide identification and expression profiling of the DOG gene family (RsDOGs) in radish (Raphanus sativus). Comprehensive analysis of physicochemical properties, chromosomal distribution, and phylogeny revealed strong evolutionary conservation alongside functional divergence. Notably, several RsDOG proteins harbor natural fusions of the DOG1 domain with a bZIP domain, suggesting potential transcription factor activity and novel regulatory functions. Promoter analysis identified abundant ABA-responsive and abiotic stress-responsive cis-acting elements. Quantitative real-time PCR (qRT-PCR) profiling across contrasting cultivars-dormant variety Rs275 and non-dormant variety Rs100-at 4 h and 28 h post-imbibition revealed distinct differential expression patterns. In particular, TRs0x5c022182.1 exhibited high expression levels in dormant seeds, suggesting its potential involvement in seed dormancy regulation in radish. This study provides key insights into the structural evolution and expression dynamics of RsDOG genes, laying a solid foundation for molecular breeding aimed at optimizing seed germination traits.
Antheraxanthin (ANT) is an important xanthophyll carotenoid in maize, but its genetic basis in maize kernels remains poorly understood. Here, we investigated the genetic architecture of ANT content using a teosinte-maize BC2F5 population evaluated across multiple environments. ANT showed abundant phenotypic variation and high broad-sense heritability (H2 = 0.86), indicating strong genetic control. A total of 11 QTLs were identified on chromosomes 1, 4, 5, 7, and 8, among which the major-effect locus L4 on chromosome 7 was consistently detected across all environments and explained up to 37.46% of phenotypic variation. Fine mapping and candidate gene analysis identified DXS2, encoding 1-deoxy-D-xylulose 5-phosphate synthase 2, which is a key rate-limiting enzyme in the MEP pathway, as the strongest causal gene underlying L4. Functional validation using a MuDR insertion mutant demonstrated that loss of DXS2 function significantly reduced ANT accumulation in maize kernels. Transcriptomic analysis further revealed that DXS2 influences the MEP pathway, carotenoid biosynthesis, and downstream metabolic networks. These findings elucidate the genetic architecture of ANT accumulation, support DXS2 as a key regulator connecting the MEP pathway with downstream carotenoid and ANT metabolism, and provide valuable genetic resources and theoretical support for carotenoid biofortification in maize breeding.