Background: The Tibetan pig, a highland breed with exceptional adaptability to harsh environments (cold, hypoxia, coarse feed) but poor growth/reproductive traits, was studied to uncover genetic mechanisms and support breeding improvements. Methods: We conducted de novo genome assembly of a male Tibetan pig using stLFR sequencing, supplemented with ONT data, and compared the assembly to the Duroc pig genome (v11.1). Results: The assembled genome (2.25 Gb, contig N50 = 136.5 Mb, GC content = 41.74%, 94.16× coverage) showed 96.9% BUSCO completeness. Structural variant (SV) analysis identified 22,008 insertions and 27,639 deletions, with an SV genotyping accuracy of 0.9735. Selective sweep analysis highlighted adaptive genes: XIRP2 (cardiac function), KSR2/CACNA1A (fat metabolism), COL11A1 (cartilage), and ADORA2A (vascular regulation). Tibetan pigs exhibited the fewest and shortest runs of homozygosity (ROHs) among four breeds, with ROH-linked SNPs implicating lipid catabolism genes (LIPE, PNPLA2, MGLL, DGAT1). An SNP-based GWAS revealed reproductive trait associations: immune gene IL2RB, energy metabolism genes PRKAG2, ADGRA1, and PTPRN2, and growth genes SLIT2 and BMP6. SV analysis identified additional candidates: energy metabolism genes HAO2 and NRG4, growth genes MTUS2 and FGF12, and immune genes SCGB1A1 and C8A. Conclusions: This study provides a chromosome-level genome assembly of a male Tibetan pig (generated from stLFR and ONT data), and, through whole-genome resequencing of 124 Tibetan sows, identifies key genetic factors underlying Tibetan pigs’ environmental adaptability and reproductive limitations, enabling genomic strategies to enhance breeding efficiency while preserving adaptive traits.

In vitro maturation (IVM) of oocytes is a critical initial step in mammalian in vitro production (IVP), and its quality directly influences the developmental competence of subsequent embryos. Oxidative stress is a major constraint on oocyte quality, which can be mitigated by exogenous antioxidants. In this study, porcine oocytes were matured in IVM medium supplemented with the antioxidant N-acetyl-L-cysteine (NAC; 0, 0.5, 1.5, and 4 mM) to evaluate its effects on maturation rate, antioxidant capacity, mitochondrial function, vitrification–warming survival rate, post-warming ROS levels, and early embryonic developmental rate. To elucidate the molecular mechanisms underlying the effects of NAC on porcine oocyte maturation, we conducted single-cell transcriptome sequencing. The results showed that, versus the control, 1.5 mM NAC substantially enhanced the IVM rate (p < 0.05), reduced ROS levels (p < 0.05), and increased mitochondrial activity, as assessed by MitoTracker, mitochondrial membrane potential (MMP), and ATP content (p < 0.05). These results suggest that 1.5 mM NAC relieves oxidative stress in oocytes and improves mitochondrial function. However, NAC addition showed no significant differences in vitrification–warming survival rate and post-warming ROS levels relative to the control group (p > 0.05). In addition, 1.5 mM NAC markedly improved the cleavage rate and blastocyst rate of porcine oocytes after in vitro fertilization (IVF, p < 0.05), and also enhanced the cleavage rate after parthenogenetic activation (PA, p < 0.05). Single-cell transcriptome sequencing revealed that, versus the control, differentially expressed genes (DEGs) identified after 1.5 mM NAC supplementation were mainly enriched in pathways related to oxidative phosphorylation (OXPHOS), spliceosome, and ubiquinone/terpenoid-quinone biosynthesis. Among these, the OXPHOS pathway showed the most significant enrichment, with upregulated expression of pathway-related genes such as COX6C, CYCS, and SDHD. The accuracy of the transcriptomic results was further validated by qPCR. In conclusion, supplementing with 1.5 mM NAC relieved oxidative stress, improved mitochondrial function, and thereby promoted oocyte maturation and improved oocyte quality, ultimately facilitating subsequent IVF early embryonic development.

As a crucial component of agriculture, livestock and poultry production supplies high-quality animal protein and is essential for the stability of food safety, ecological environment, human health, and global sustainability. However, frequent epidemics have emerged as a major constraint on industry development, with traditional vaccine and drug-based controls facing challenges such as rapid pathogen mutation, environmental pollution, and drug residue risks. Disease-resistant breeding thus offers a crucial strategy for sustainable livestock farming, yet its progress is hindered by the lack of effective molecular targets for major epizootics. Extensive studies on adaptive immune regulation have identified numerous regulatory genes and molecular targets associated with disease resistance, offering significant potential for breeding applications. Nevertheless, despite the well-established role of adaptive immunity in human medicine, its utilization in livestock breeding remains largely underdeveloped. This review outlines the significance and current status of disease-resistant breeding, focuses on adaptive immune mechanisms, and proposes innovative strategies.

During swine gestation, the placenta serves as the sole interface for nutrient, gas, and signaling molecule exchange between the dam and fetuses, and its function critically determines pregnancy outcomes. Branched-chain amino acids (BCAAs)—leucine, isoleucine, and valine—are substrates for protein synthesis, precursors for glutamate and glutathione, and signaling molecules that activate the mechanistic target of rapamycin (mTOR) pathway. This review synthesizes current evidence on BCAA transport, catabolism, and signaling in the porcine placenta, organized around four mechanistic axes: transporter-mediated transplacental transfer, local catabolism supporting energy production and antioxidant defense, mTORC1-dependent regulation of growth and differentiation, and modulation of endocrine and immune homeostasis. Both deficiency and excess of BCAAs compromise placental function, contributing to intrauterine growth restriction and metabolic programming abnormalities through a U-shaped dose–response relationship. Critical knowledge gaps remain, including the reliance on rodent and in vitro models, the absence of standardized supplementation protocols and dose–response data, unaddressed confounders (parity, litter size, environment), and the lack of formal power analyses or meta-analytic synthesis. We propose precision dietary strategies to optimize BCAA supplementation during gestation for improved reproductive performance in swine.

Porcine β-defensin 2 (pBD2) is an antimicrobial peptide with both antibacterial and immunomodulatory activities and plays an important role against pathogens. Our previous results suggested that pBD2 might exert its protective effects against E. coli by regulating cell apoptosis and proliferation through the Akt signaling pathway. However, the specific roles and underlying mechanisms of pBD2 in regulating these cellular processes remain unclear. In this study, porcine intestinal epithelial cells (IPEC-J2) were treated with pBD2 in the presence of Enterotoxigenic E. coli (ETEC) K88 challenge. pBD2 inhibited ETEC-induced apoptosis, decreased the levels of cleaved caspase-3 and caspase-9, and restored mitochondrial membrane potential, suggesting that pBD2 inhibited ETEC-induced apoptosis via the intrinsic apoptotic pathway. Moreover, pBD2 restored cell proliferation and attenuated ETEC-induced cell cycle arrest in the G0/G1 phase, and upregulated the expression of proliferation-related genes including CDC25A, CDC6, E2F2 and PCNA. In addition, the results further revealed that pBD2 attenuated cell apoptosis and restored cell proliferation in ETEC K88-infected IPEC-J2 cells by inhibiting the Akt signaling pathway. Our results provide further evidence for the protective effects of pBD2 on intestinal epithelial cells and extend its known biological roles. This study elucidates an anti-apoptotic and pro-proliferative mechanism of pBD2 against ETEC infection and provides insights into its potential application.

The quality of hatching eggs and their hatchability are key factors affecting the production efficiency of breeding flocks. The quality of hatching eggs is commonly graded directly based on the eggshell quality. Our study monitored the eggshell quality and hatchability in Hy-Line Brown laying hens aged 23 to 73 weeks, to determine core eigenvectors that influence hatchability from multiple eggshell quality indicators. Hatching performance indicators, including fertile egg rate, hatchability of fertile eggs and hatchability of eggs set, were found to exhibit a trend of low level in early laying stage, and increased to a peak at 39 weeks of age during mid-laying stage, followed by a continuous decline in late laying stage. Similar trend also observed in eggshell quality indicators, such as eggshell strength, eggshell thickness, eggshell weight, eggshell rate and eggshell microstructure. Canonical correlation analysis revealed egg weight, equatorial eggshell thickness and pointed end eggshell thickness showed strong correlation with the main indicators affecting hatchability of fertile eggs (r = 0.987, P = 0.013). Further, shell gland RNA sequencing was applied to explore candidate genes or pathways that might affect eggshell thickness. Short time series expression miner (STEM) analysis identified several key genes (ATP2C2, CA9, CDC20B, WNT4, WNT7A and CACNB3) that were enriched in pathways related to calcium signaling, bicarbonate metabolism, vesicle transport and Wnt signaling, thereby highlighting their potential critical roles in eggshell thickness regulation. Our findings preliminarily delineate the relationship between easily measurable eggshell quality and hatchability, which provides a theoretical basis and candidate gene targets for improving hatching performance.

Reproductive traits are critical for improving productivity and profitability in the pig industry, and genome-wide association studies (GWASs) are a powerful tool in detecting genetic markers related to target traits. Genome imputation provides an effective approach to obtain a greater number of genetic markers from low-density sequencing data. China's pig industry recently introduced an imputation panel and is now seeking to determine what types of data are required to meet breeding needs. In this study, we collected and analyzed two pig sequencing datasets, including Yorkshire pig (YY), Landrace pig (LL), and Duroc pig (DD), genotyped by either an SNP chip (n = 816) or genotyping-by-targeted sequencing (n = 314), and applied an imputation strategy before validation in a third dataset (n = 2401). The aim of this study was to identify SNPs associated with reproductive traits and compare imputation results of two different types of data to evaluate whether sample size or marker density more strongly impacts imputation-enabled GWAS performance. Through a GWAS, we identified 73 significant SNPs from imputed Chip data across seven reproductive traits, 94 SNPs from imputed GBTS data across three traits, and 34 SNPs from the combined dataset across seven traits. Seven of these SNPs passed validation and were associated with number born alive, number born healthy, and gestation length. Gestation length (GL) and number born alive (NBA) are the most noteworthy traits. LOXL2 and PTPRD are high-confidence candidate genes affecting GL and NBA, respectively. In addition to LOXL2, STC1, NKX2-6, HMGCLL1, MLIP, TINAG, FAM83B, GFRAL, HCRTR2, ENTPD4, MYH8, IER5L, and U5 are associated with GL. Moreover, in addition to PTPRD, KLHL32, U6, MMS22L, and FHL5 are associated with NBA. The results of this study indicate that sample size is of greater importance than marker density in imputation strategies and provide beneficial insights into genes affecting pigs' reproductive traits.

To evaluate the applicability and analytical performance of the Shennong 1 Chicken 40 K Liquid chip (Shennong chip) in commercial chicken populations, parental lines of Australorp (Arp) and Rhode Island Red (RIR) chickens were analyzed using both whole-genome resequencing (WGS) and Shennong chip genotyping. A total of 128 individuals were included. The performance of Shennong chip was evaluated by comparing its results with those of WGS through population genetics analyses, including assessment of population structure, genetic diversity and selection signatures. Across analyses, Shennong chip showed high concordance with WGS in population genetic inference. For example, the first two principal components derived from the two datasets showed nearly identical distributions, with Pearson correlation coefficients close to 0.99. Similar cluster pattern was observed between WGS and Shenong chip results in ancestry inference at K = 2 and K = 3. Genetic diversity estimates suggested moderate levels of variation (Shennong chip: He ≈ 0.34-0.40; WGS: pi ≈ 0.0027-0.0037) across all four parental lines, with relatively higher diversity(He ≈ 0.40; pi ≈ 0.0037) observed in the Rhode Island Red D line. The SNP chip reliably captured major population structure patterns, genetic diversity differences among parental lines, and biologically interpretable selection signals. Functional enrichment analyses based on SNP chip-derived candidate regions further revealed distinct selection orientations between parental lines. LSBL analysis identified Arp-specific selection signals, while joint F_ST and nucleotide diversity analyses revealed pronounced divergence between RIR C and D. Functional enrichment highlighted neural signaling-related genes in RIR C (e.g., GRIK1) and metabolic and immune-related genes in RIR D (e.g., AvBD genes) Overall, these results demonstrate that SNP chip provides a reliable, cost-effective, and scalable alternative to WGS for population genetic and breeding-oriented genomic analyses in commercial chicken populations.

High-throughput genome sequencing and genotyping have significantly accelerated genetic research. However, the high cost of whole-genome sequencing (WGS) remains a barrier to large-scale studies like genome-wide association studies (GWAS) and genomic prediction. Genotype imputation offers a cost-effective alternative by inferring unobserved variants from lower-density data using haplotype reference panels. In this study, we present the updated Pig Haplotype Reference Panel (PHARP) 4.0, comprising 6449 pig genomes from 154 breeds. PHARP 4.0 encompasses 50.3 million SNPs and 5.8 million indels, making it the largest and most diverse pig reference panel to date. PHARP 4.0 demonstrated superior imputation accuracy compared to existing panels (SWIM, AHC, AGIDB, and PGRP), achieving concordance rates (CR > 0.99) and correlation coefficients (R² > 0.98) in European breeds and improved accuracy in Chinese Jinhua pigs (CR = 0.936, R² = 0.924) when imputing from 80 K SNP chip data to whole-genome sequencing (WGS). We further optimized an RNA-seq-based imputation pipeline by incorporating multiple breeds and applying a 6× sequencing depth filter, achieving CR > 0.95 and R² > 0.90 in European breeds, and a CR of 0.93 with an R² = 0.92 in Chinese Jinhua pigs. Additionally, increasing the specific reference panel size to approximately 400 samples improved the imputation of rare variants. Utilizing PHARP 4.0, we successfully imputed low-density SNP chip data for two GWAS, identifying significant SNPs likely representing causal variants. Overall, PHARP 4.0 serves as a valuable resource for advancing pig genetic research and supporting breeding programs. PHARP 4.0 is an updated pig haplotype reference panel with 6449 genomes from 154 breeds. It demonstrates superior imputation accuracy from chip to WGS data, enables an optimized RNA-seq imputation pipeline, and successfully identifies novel causal variants in GWAS.

Yunong Black (YN) pigs and Yunong Black × Landrace (YL) hybrid pigs exhibit significant differences in meat quality characteristics. Studies have suggested that extrachromosomal circular DNA (eccDNA) may play a regulatory role in muscle development. In order to study the differences in eccDNA between two groups with different meat quality traits and their potential biological significance, this study used the Circle-seq method to detect eccDNA in the longest dorsal muscle (LDM) of Yunong Black pigs (YN) (n = 3) and Yunong Black × Landrace hybrid pigs (YL) (n = 3). EccDNA-related differentially expressed genes (eccDEGs) were then analyzed in combination with RNA-seq to explore the mechanisms by which eccDNA affects meat quality. The results showed that 1325 and 1304 differentially expressed eccDNAs were identified in the YN and YL groups, varying in size and distributed across multiple genomic functional regions. These eccDNAs were also annotated according to several protein-coding genes. Combined analysis with RNA-seq results revealed 19 and 27 eccDEGs in the YN and YL groups. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis enriched many lipid-related pathways, such as chemokine signals and ADP metabolic processes. By constructing a regulatory network, several potential regulatory networks that might be related to pork quality, for example, ecc_sus_8665/ssc-miR-212/ADAMTS16, were identified. In summary, we identified several potential eccDNAs that may regulate pig muscle, offering insights into the regulation of pig muscle traits for breeding.

Estradiol (E2), a pivotal mammalian reproductive hormone, is closely associated with estrogen-dependent diseases. 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1), a critical E2 synthesis enzyme, has been understudied for its post-translational regulation-despite its potential as a therapeutic target, no clinically approved inhibitors are currently available. In our investigation of porcine follicular atresia mechanisms, we identified five differentially phosphorylated residues in 17beta-HSD1. Using in vitro site-directed mutagenesis and transgenic mouse models carrying point mutations, we established that Ser30 and Ser274 are critical phosphorylation sites that robustly modulate 17beta-HSD1 enzymatic activity. We further demonstrated that activin A and insulin-like growth factor 1 (IGF-1) enhance 17beta-HSD1 activity by promoting its phosphorylation at these two sites. To target these regulatory residues, we designed and synthesized cell-penetrating peptides (CPPs) that specifically suppress 17beta-HSD1 phosphorylation. Functional assays conclusively demonstrated that these CPPs significantly suppressed 17beta-HSD1 activity in vitro. Notably, they also inhibited the proliferation, migration and invasion of MCF-7 cells, as well as tumor growth in a mouse model of breast cancer. Our study provides novel mechanistic insights into the regulation of 17beta-HSD1 and E2 synthesis, addressing a critical gap in steroid hormone biology. The identification of Ser30/Ser274 as functional phosphorylation sites and the development of CPP-based inhibitors offer both theoretical advances and translational potential, opening new avenues for the treatment of estrogen-dependent breast cancer. ### Competing Interest Statement The authors have declared no competing interest. National Natural Science Foundation of China, 32202671, 82400109 China Postdoctoral Science Foundation, 2023M730999 the Open project of State Key Laboratory of Animal Biotech Breeding, 2024SKLAB6-5 2024 Henan Province Science and Technology Research Project the 14th Five-Year National Key R&D Program, 2021YFD1301202 Pig Industry Technology System Innovation Team Project of Henan Province, HARS-22-12-G4 the Agricultural Breeds Research Project of Henan Province, 2022020101 the STI 2030-Major Projects, 2023ZD04046 the Science and Technology Program Project of Tibet Autonomous Region, XZ202501ZY0147

Animal stress is a complex physiological state characterized by a suite of non-specific responses (e.g., lethargy, anorexia, and impaired growth) to various internal or external threats, collectively known as stressors. It is the synthesis of non-specific responses produced by the body to various external or internal stimuli. Animals in livestock production are often stressed by breeding density, inappropriate temperature and humidity, harmful gases, noise and complicated immunization. Consequently, the nutritional requirements and underlying metabolic mechanisms in stressed animals are critical and growing research hotspots. Emerging evidence has shown that nutritional intervention can maintain animal health and performance under stresses. In addition, the regulation of metabolic pathways and targets under different stress states is also a potential way to alleviate the stress response of animals. With the rapid development of intensive farming and the aggravation of environmental changes, animals are facing increasing challenges such as heat stress, transportation stress, and pathogen infection. The resulting metabolic disorders and health problems seriously restrict the production efficiency of animals. This review aims to systematically analyze the variation in animal nutritional requirements under stress, clarify the molecular mechanism of metabolic imbalance, and summarize the regulatory targets and effects of nutritional intervention strategies, providing theoretical basis and technical support for solving stress-related problems in livestock production.

Sustaining egg production in late-laying chickens can extend their egg-laying cycle. Follicle selection is a pivotal process that determines the egg production rate, acting as the ultimate regulatory checkpoint to ensure only the most viable follicles progress to ovulation. This study aimed to identify and elucidate the role of a potential gene in follicle selection. Follicles measuring 6−8 mm were harvested from high egg-yielding (H) and low egg-yielding (L) Taihang chickens at 43 weeks of age for RNA sequencing to identify DEGs. The role of BMP15 in follicle selection was investigated by adding recombinant BMP15 protein to GCs. As a result, 99 DEGs were identified, and BMP15 was selected as the candidate gene for its role in follicle selection. The addition of recombinant BMP15 activated the SMAD1 signaling pathway, upregulated the expression of bone morphogenetic protein receptor type 1B (BMPR1B) and follicle-stimulating hormone receptor (FSHR), and increased cyclic adenosine monophosphate (cAMP) levels. However, BMP15 significantly repressed the expression of steroidogenic acute regulatory protein (STAR) and cytochrome P450 family 11 subfamily A member 1 (CYP11A1) and slightly decreased the progesterone (P4) levels. Furthermore, the co-administration of follicle-stimulating hormone (FSH) with recombinant BMP15 resulted in a significant decrease in BMPR1B expression and a marked increase in FSHR, STAR, and CYP11A1 expression, which led to a comparable change in P4 levels. These findings demonstrated that BMP15 is involved in follicle selection by enhancing FSHR expression and the cAMP level. BMP15 interacts with FSH to regulate follicle selection from the pre-hierarchical to hierarchical follicles.

To study the key genes that influence the body size of local pig breeds in China. Genome-wide SNP chip data from a total of 129 pigs from eight breeds, consisting of four large body size breeds (MZ, HT, ST, RC) and four small body size breeds (XI, BX, WZ, DN) were analyzed. Principal Component Analysis (PCA) was employed to assess the genetic clustering of the eight breeds. Fst and XP-CLR were used to detect selective signals between the large ans small body size breeds groups. The PCA results indicated a clear clustering of small breeds and a dispersion distribution among large breeds. Fst and XP-CLR identified 142 overlapping regions within a 500 kb up & down stream of significant loci. These regions encompassed 520 annotated genes, which were enriched in 34 biological pathways. Gene network analysis highlighted nine key genes, of which five (NPR3, TNFSF11, TBC1D7, FGF2, IGF1R) are known to be associated with bone growth and body size traits in animals. Additionally, four novel candidate genes (IKBKB, SFRP1, LRP6, SPRY1) were identified that might be related to pig body size. Our findings provide a theoretical basis for further revealing the genetic mechanism of pig body size traits.

17β-Hydroxysteroid dehydrogenase 1 (17β-HSD1) can catalyze the reduction of the less active estrone (E1) to the more active estradiol (E2). It has a significant impact on the reproduction of female animals, follicular development, the development of the breasts and reproductive organs in reproductive-age women, as well as the physical health, bones and cardiovascular system of postmenopausal women. This review summarizes the research progress on the expression, biological function, and regulatory mechanisms of 17β-HSD1 in estrogen-dependent diseases, including cancer. It also discusses the role of 17β-HSD1 in female reproduction processes, such as follicle development, and the regulation of its enzyme activity by activin A and insulin-like growth factor 1 (IGF-1). Furthermore, the review explores how phosphorylation at key sites influences its enzyme's activity, aiming to enhance the understanding of its regulatory mechanisms and improve the clarity of related research findings. This review systematically summarizes the research progress of 17β-HSD1 expression and enzyme activity regulation, which can provide theoretical reference for the development of animal breeding technology and the treatment of estrogen dependent diseases.

Objective: This study aims to investigate the selection history, genome regions, and candidate genes associated with different chicken body sizes, thereby providing insights into the genetic basis of complex economic traits such as chicken body size and growth.Methods: In this study, a total of 217 individuals from eight breeds were selected. According to body size, they were divided into two groups: large chickens and bantam chickens, with four breeds in each group. Firstly, we investigate population structure by principal component analysis (PCA), phylogenetic tree, and ancestry component analysis. Next, we recognize runs of homozygosity (ROH) islands through calculating ROH. Finally, we carry out selection signatures analysis utilizing population differentiation index and nucleic acid diversity.Results: The population structure analysis show that large and bantam chickens are clearly separated. Large chickens are clustered together, the bantam chickens are relatively dispersed. The results of ROH island analysis show that 48 and 56 ROH islands were identified in large and bantam chickens respectively. Among the interesting ROH islands, a total of eight candidate genes were identified. In selection signatures analysis, a total of 322 selected genes were annotated in large chickens, such as POU1F1, BMP10, enrichment in 16 gene ontology (GO) terms. In bantam chickens, a total of 447 selected genes were annotated, such as IGF1, GRB10, enrichment in 20 GO terms and 2 Kyoto encyclopedia of genes and genomes pathways. The haplotype analysis results show that GRB10 has differences in chickens of different body sizes.Conclusion: By population structure, ROH islands, and selection signatures analysis, we have identified multiple genes associated with chicken body size, growth, and development (such as BMP10, IGF1, GRB10, etc). This provides a theoretical reference for the subsequent development of molecular markers for chicken body size and the analysis of the genetic mechanism of chicken body size.

The "Yufen 1" D line (D) chicken is characterized by strong disease resistance and a high feed conversion rate as a newly bred line. There are few reports on D chicken. In order to investigate the genetic diversity, population structure and selection signals of the D chicken, this study analyzed the genome-wide data of 15 D line chickens and 11 publicly available Chinese indigenous chicken breeds, the red jungle fowls. The genetic diversity of the D chicken was significantly lower than that of the Chinese indigenous chicken breeds and the red jungle fowl, but the inbreeding coefficient (FROH) was lower. On the one hand, this may be due to the small size of the conserved population, and on the other hand, it suggests that the D line may have received artificial selection during the selection process. Population structure analysis revealed that the D chicken was separated from Chinese indigenous chicken breeds and red jungle fowl, and had a high degree of genetic differentiation from other non-D chicken populations, suggesting that the D chicken is a unique poultry genetic resource worthy of our subsequent enhanced protection and utilization. The selective sweep analysis revealed that the genes selected in the D chicken were mainly enriched in the Toll and Imd signaling pathway and the Gastric acid secretion signaling pathway, including REL, UBE2V1, KCNJ16, and SLC26A7, which might be related to the excellent traits of high disease resistance and high feed conversion ratio in D chicken. In addition, the constructed molecular identity card of D chickens can be used to identify the authenticity of D chickens. These results lay the foundation for further research, conservation, and breeding of "Yufen 1" D line chickens.

Litter size traits of sows are crucial for the economic benefits of the pig industry. Three phenotypic traits of 1,206 Large White pigs, the total number born (TNB), number born alive (NBA), and number of healthy piglets (NHP), were recorded. We evaluated a series of genomic best linear unbiased prediction models that sequentially added additive effects (model A), dominance effects (model A + D), and epistatic effects (model A + D + AA, model A + D + AA + AD, and model A + D + AA + AD + DD) using chip data and imputed whole-genome sequencing (WGS) data to estimate genetic parameters and predictive accuracy. The reproductive traits of sows showed low heritability in this study, with narrow heritability of the 3 traits ranging from 0.030 to 0.064, and broad heritability ranging from 0.125 to 0.145. The inclusion of nonadditive effects in the model improved the accuracy of genomic selection. In the chip data, compared with that of the A model, the A + D + AA + AD + DD model showed the greatest increase in accuracy for TNB, NBA, and NHP, with improvements of 1.78%, 1.67%, and 1.74%, respectively. Additionally, the accuracy of the imputed WGS data was greater compared to the chip data. For the TNB, NBA, and NHP traits, the predictive accuracy of the imputed WGS data improved by 3.26%, 7.72%, and 3.00%, respectively, compared with that of the chip data. In summary, these results suggest that nonadditive effects in genomic selection could improve prediction accuracy and should be considered in pig genomic evaluation procedures.

Circular RNA (circRNA) is ubiquitously expressed in highly differentiated eukaryotes, playing an extremely vital regulatory role in muscle growth and development. In this study, we identified circPICALM, a novel circRNA which consists of exons 5 to 9 of the PICALM gene, exhibiting differential expression in the longissimus dorsi muscle (LD) of adult (QA) and newborn (QN) Queshan Black pigs. CircPICALM is resistant to RNase R, mainly located in the cytoplasm with potential coding capacities. When circPICALM was over-expressed in porcine skeletal muscle satellite cells (PSMSCs), there was a significant decrease in the expression levels of PCNA, CDK4, CDK1 and CCND1, which consequently inhibited the proliferation of PSMSCs. Conversely, miR-132, a target molecule of circPICALM, was found to promote the proliferation of PSMSCs. In addition, circPICALM can up-regulate the expression of the target gene PHKB by competitively adsorbing miR-132. The circPICALM-ssc-miR-132-PHKB regulatory axis is regulated by METTL3, which increases the m6A level of both PSMSCs and circPICALM, thereby promoting the proliferation of PSMSCs. Overall, this study furnishes a fundamental reference for further in-depth exploration of the specific molecular mechanisms underlying m6A modification and circPICALM in muscle development and progression.