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.
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.
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.
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.
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.
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.
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.
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.
GDSL esterase/lipases (GELPs) are important regulators of plant growth and development, lipid metabolism, and stress responses. However, their genomic characteristics and expression patterns have not been systematically characterized for Juglans mandshurica, a woody oil crop species of significant ecological and economic value. Here, we identified 61 JmGELP genes in J. mandshurica through genome-wide analysis. Phylogenetic analysis classified them into seven major clades, and variations in gene structure and conserved motifs suggested potential functional divergence. Promoter cis-acting element analysis revealed widespread enrichment of motifs responsive to light, phytohormones, and abiotic stresses. Transcriptomic sequencing and qRT-PCR validation revealed distinct tissue-specific and seed development stage-specific expression patterns of JmGELP members, as well as their differential responses to various stress and hormone treatments. Gene Ontology (GO) annotation and protein-protein interaction (PPI) network analyses further supported their involvement in lipid metabolism. In silico analyses of transcription factor binding sites, miRNA targets, and molecular docking predicted that JmGELP-3, -38, and -41 have distinct transcriptional and post-transcriptional regulatory networks and potentially divergent substrate preferences. This study provides the first comprehensive characterization of the GELP family in J. mandshurica, identifying candidate genes that may inform future germplasm improvement and stress-resistance breeding in Juglans species.
Salinity fluctuations pose a severe threat to the survival and physiological homeostasis of freshwater crustaceans. Here, an integrated transcriptomic and metabolomic approach was utilised to characterise the dynamic regulatory responses in the hepatopancreas of adult Macrobrachium rosenbergii subjected to acute high-salinity stress (20‱). The number of differentially expressed genes (DEGs) and metabolites (DMs) increased from 24 to 48 h, signalling a transition from an initial acute stress reaction to systemic homeostatic remodelling. At the molecular level, M. rosenbergii activated autophagy (Atg8a) and p53 (TP53INP) signalling, alongside the reprogramming of lipid and nucleotide metabolism. Pathway analysis identified "alanine, aspartate, and glutamate metabolism" as a central regulatory node. Notably, the downregulation of the glutamate dehydrogenase gene (Gdh) alongside the accumulation of L-glutamate suggests a potential transcriptional-metabolic decoupling phenomenon, wherein the organism appears to prioritise the conservation of critical osmoregulatory effectors over their oxidative degradation. These findings detail the systemic adaptive responses of M. rosenbergii to salinity fluctuations, providing candidate targets for the selective breeding of stress-resilient crustacean strains.
MicroRNAs (miRNAs) serve as pivotal post-transcriptional modulators of gene expression that govern animal growth and development processes. The present study aimed to investigate the relationship between a single-nucleotide polymorphism (SNP) located within the pre-miR-1453 precursor and growth traits, carcass traits, body size traits, and serum biochemical parameters in an F2 chicken resource population derived from Gushi and Anka crosses (n = 860). Genotyping of the rs16159272 polymorphism (+31 bp C > T) was performed using MALDI-TOF mass spectrometry, and population genetic parameters, secondary structure prediction, and association analyses were conducted. The results showed that the SNP was moderately polymorphic (PIC = 0.3174) and significantly associated with hatch weight (p < 0.01; CT > TT > CC), as well as body weight at 2 and 4 weeks of age (p < 0.05; TT > CT > CC), but not with carcass or body size traits (p > 0.05). For serum biochemical parameters, total protein, cholinesterase, and creatine phosphokinase showed extremely significant differences across genotypes (p < 0.01), whereas albumin, globulin, and lactate dehydrogenase showed significant differences (p < 0.05). Structural prediction revealed that the C > T mutation increased the minimum free energy by 3.8 kcal/mol, reducing the stability of the pre-miR-1453 stem-loop. Target gene prediction and enrichment analysis indicated that pre-miR-1453 may participate in the regulation of chicken growth and serum biochemical parameters through pathways related to neuron development, cytoskeletal dynamics, and energy metabolism. These findings suggest that the pre-miR-1453 rs16159272 polymorphism could act as a candidate genetic indicator for marker-aided breeding in poultry.
Understanding crop genetic diversity is essential for conservation and breeding, yet farmer-maintained germplasm remains largely underrepresented in genomic studies. Theobroma cacao L. has a complex domestication history, extensive global diversity, and is currently cultivated in Central America. Costa Rican cacao has been understudied compared to South American and Mexican cultivars despite cultural and historical importance. In this study, we investigate the genetic diversity of cacao from farmer-managed systems across Costa Rica to search for Criollo germplasm while identifying and characterizing unique local genetic groups. Ninety-four trees were sampled for whole genome resequencing from 17 farms across four regions of the country. Farmer materials were analyzed alongside 166 previously characterized reference accessions representing major cacao genetic groups. Population structure analyses, phylogenetic reconstruction, and network approaches revealed that Costa Rican cacao encompasses multiple known genetic groups, including Criollo-derived lineages while also harbouring locally distinct diversity not represented in current global reference collections. Analyses revealed close kinship between many accessions with no clear geographic patterns corresponding to the observed population differentiation, reflecting the influence of farmers in generating the dominant patterns of gene flow through seed-saving, clonal propagation, and sharing of genotypes among farms. Heterozygosity levels varied substantially among individuals, consistent with a mixture of highly inbred Criollo trees and more heterozygous, admixed genotypes. We find that farmer-managed cacao systems are reservoirs of genetic diversity that can include rare or historically important lineages, underscoring the value of these farming systems for effective conservation and management of genomic resources for cacao resilience and improvement.
Broiler production systems in Africa and the European Union (EU) differ substantially in terms of housing design, environmental control, welfare outcomes, and regulatory oversight. Understanding these differences is essential for identifying region-appropriate strategies for sustainable poultry production. This review aimed to compare broiler housing systems, welfare outcomes, environmental management, and regulatory frameworks in Africa and the EU. This review followed some aspects of the PRISMA 2020 guidelines. Searches were conducted in Scopus, Web of Science, PubMed, and CAB Abstracts from January 2023 to January 2025. The grey literature from the FAO, EU institutions, and NGOs was also screened. Eligible studies examined broiler housing systems, welfare indicators, environmental control, or regulatory frameworks in African or EU contexts. Two reviewers independently screened records, extracted data, and assessed risk of bias using the SYRCLE tool. No meta-analysis was performed due to heterogeneity; results were synthesized narratively. The search identified 86 records; 83 remained after duplicate removal. After screening, 45 studies met the inclusion criteria. EU systems were characterized by climate-controlled indoor housing, strict welfare regulations, and integrated supply chains. African systems ranged from intensive open-sided houses to semi-intensive and backyard systems, with major constraints including heat stress, limited access to veterinary care, and high feed costs. These systems also differ markedly across African regions, reflecting variation in infrastructure, market integration, and climatic conditions. Risk of bias was moderate across most studies. The certainty of the evidence was low to moderate due to heterogeneity in study designs and reporting. Heterogeneous study designs prevented quantitative synthesis. Reporting quality varied, and few African studies provided detailed welfare metrics. Broiler production systems in Africa and the EU reflect distinct climatic, economic, and institutional contexts. Sustainable improvements require region-specific strategies rather than universal housing models. In this review, region-specific strategies refer to climate-adaptive housing designs, modular environmental control technologies, and management approaches aligned with local infrastructure, market structures, and resource availability.
Advertisement calls convey individual information and play a vital role in amphibian reproduction. Body size is one of the key factors determining the diversity of frog advertisement calls. P. terentievi is distributed in mountainous areas across Tajikistan and Xinjiang, China. However, bioacoustic research on this species remains an unexplored field. In this study, the advertisement calls of 20 male frogs were recorded in the breeding season and six distinct call types were described based on spectrum morphology and auditory characteristics. The coefficient of variation analysis indicates some of their call types may serve as effective cues for individual recognition. Their advertisement calls exhibit a typical sentence structure and often conclude with a distinctive ending word. We also observed a distinct diel rhythm in their calls: advertisement calls begin before sunset, peak after sunset, and continue until noon. Furthermore, their acoustic parameters are significantly correlated with their head size, leg size and body weight. Males with larger heads and longer legs often make calls at higher frequencies, possibly to stand out in the louder chorus to enhance the efficiency of attracting females. This basic study can provide support for the behavioral and evolutionary biology research of Pelophylax species.
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.
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.
Rumen biohydrogenation is a microbial process that converts dietary unsaturated fatty acids into more saturated products and produces a range of intermediates that can affect animal products and rumen fermentation. This review summarizes current knowledge on the main biohydrogenation pathways, the microbial groups involved, and the nutritional and breeding strategies used to regulate this process. Particular attention is given to the transformation of C18 fatty acids, the formation of vaccenic acid and conjugated linoleic acid, the trans-10 shift, and the links between lipid metabolism, hydrogen use, and methane formation. Evidence indicates that diet composition, lipid source, plant secondary metabolites, rumen-protected fat technologies, microbial interventions, and host-related factors can all influence biohydrogenation outcomes. These strategies can improve the fatty acid profile of meat and milk, but their effects are context-dependent and vary with animal species, diet, and rumen microbial structure. Important gaps remain, including the identification of active microbial populations, the functions of many transient intermediates, and the extent to which changes in biohydrogenation directly contribute to methane mitigation. Clarifying these mechanisms is essential for improving the nutritional quality of ruminant products and the sustainability of production systems.