PGC-based cryobanking, regeneration through germline chimera mating, and CRISPR/Cas9-mediated TYRP1 modification in indigenous Chinese chickens.

Primordial germ cells (PGCs) are vital for producing sperm and eggs and are crucial for conserving chicken germplasm and creating genetically modified chickens. However, efforts to use PGCs for preserving native chicken germplasm and genetic modification via CRISPR/Cas9 are limited. Here we show that we established 289 PGC lines from eight Chinese chicken populations with an 81.6% success rate. We regenerated Piao chickens by repropagating cryopreserved PGCs and transplanting them into recipient chickens, achieving a 12.7% efficiency rate. These regenerated chickens carried mitochondrial DNA from female donor PGC and the rumplessness mutation from both male and female donors. Additionally, we created the TYRP1 (tyrosinase-related protein 1) knockout (KO) PGC lines via CRISPR/Cas9. Transplanting KO cells into male recipients and mating them with wild-type hens produced four TYRP1 KO chickens with brown plumage due to reduced eumelanin production. Our work demonstrates efficient PGC culture, cryopreservation, regeneration, and gene editing in chickens.

Integrative study of chicken lung transcriptome to understand the host immune response during Newcastle disease virus challenge.

Introduction: Newcastle disease is one of the significant issues in the poultry industry, having catastrophic effects worldwide. The lung is one of the essential organs which harbours Bronchus-associated lymphoid tissue and plays a vital role in the immune response. Leghorn and Fayoumi breeds are known to have differences in resistance to Newcastle disease. Along with genes and long non-coding RNAs (lncRNAs) are also known to regulate various biological pathways through gene regulation. Methods: This study analysed the lung transcriptome data and identified the role of genes and long non-coding RNAs in differential immune resistance. The computational pipeline, FHSpipe, as used in our previous studies on analysis of harderian gland and trachea transcriptome was used to identify genes and lncRNAs. This was followed by differential expression analysis, functional annotation of genes and lncRNAs, identification of transcription factors, microRNAs and finally validation using qRT-PCR. Results and discussion: A total of 8219 novel lncRNAs were identified. Of them, 1263 lncRNAs and 281 genes were differentially expressed. About 66 genes were annotated with either an immune-related GO term or pathway, and 12 were annotated with both. In challenge and breed-based analysis, most of these genes were upregulated in Fayoumi compared to Leghorn, and in timepoint-based analysis, Leghorn challenge chicken showed downregulation between time points. A similar trend was observed in the expression of lncRNAs. Co-expression analysis has revealed several lncRNAs co-expressing with immune genes with a positive correlation. Several genes annotated with non-immune pathways, including metabolism, signal transduction, transport of small molecules, extracellular matrix organization, developmental biology and cellular processes, were also impacted. With this, we can understand that Fayoumi chicken showed upregulated immune genes and positive cis-lncRNAs during both the non-challenged and NDV-challenge conditions, even without viral transcripts in the tissue. This finding shows that these immune-annotated genes and coexpressing cis-lncRNAs play a significant role in Fayoumi being comparatively resistant to NDV compared to Leghorn. Our study affirms and expands upon the outcomes of previous studies and highlights the crucial role of lncRNAs during the immune response to NDV. Conclusion: This analysis clearly shows the differences in the gene expression patterns and lncRNA co-expression with the genes between Leghorn and Fayoumi, indicating that the lncRNAs and co-expressing genes might potentially have a role in differentiating these breeds. We hypothesise that these genes and lncRNAs play a vital role in the higher resistance of Fayoumi to NDV than Leghorn. This study can pave the way for future studies to unravel the biological mechanism behind the regulation of immune-related genes.

Whole-genome resequencing reveals melanin deposition candidate genes of Luning chicken.

BACKGROUND: Melanin in the black-bone chicken's body is considered the material basis for its medicinal effects and is an economically important trait. Therefore, improving the melanin content is a crucial focus in the breeding process of black-bone chickens. Luning chickens are black-bone chickens, with black beaks, skin, and meat. To investigate the genetic diversity and molecular mechanisms of melanin deposition in Luning chickens, we conducted whole-genome resequencing to analyze their breeding history and identify candidate genes influencing their black phenotype, along with transcriptome sequencing of dorsal skin tissues of male Luning chickens. RESULTS: Population structure analysis revealed that Luning chickens tend to cluster independently and are closely related to Tibetan chickens. Runs of homozygosity analysis suggested potential inbreeding in the Luning chicken and Tibetan chicken population. By combining genetic differentiation index (Fst) and nucleotide diversity (θπ) ratios, we pinpointed selected regions associated with melanin deposition. Gene annotation identified 540 genes with the highest Fst value in LOC101750371 and LOC121108313, located on the 68.24-68.58 Mb interval of chromosome Z. Combining genomic and transcriptomic data, we identified ATP5E, EDN3, and LOC101750371 as candidate genes influencing skin color traits in black-bone chickens. CONCLUSIONS: This study characterized the evolutionary history of Luning chickens and preliminarily excavated candidate genes influencing the genetic mechanism of pigmentation in black-bone chickens, providing valuable insights for the study of animal melanin deposition.

Integrating Genomics and Transcriptomics to Identify Candidate Genes for Egg Production in Taihe Black-Bone Silky Fowls (Gallus gallus domesticus Brisson).

The Taihe Black-Bone Silky Fowl (Gallus gallus domesticus Brisson) possesses significant value in terms of consumption, medicinal applications, and ornamental appeal, representing a precious genetic resource and traditional Chinese medicinal material. However, considerable variation exists within populations regarding egg-laying performance. This study integrates a whole-genome selection signal analysis (SSA) with a transcriptome analysis to identify genes associated with egg-laying traits in Taihe Black-Bone Silky Fowls. We identified 31 candidate genes under selection from the high-yield chicken (HC) and low-yield chicken (LC) groups. Additionally, through RNA-seq analysis, 257 common differentially expressed genes (DEGs) were identified from four comparative groups. Two overlapping genes-LPL and SETBP1-were found in both the selected gene and DEG lists. These selected genes and DEGs were enriched in pathways related to ovarian development, including the lysosome pathway, the ECM-receptor interaction pathway, the TGF-beta signaling pathway, the Wnt signaling pathway, the PPAR signaling pathway, and the glycerolipid metabolism pathway. These research findings contribute to the breeding of Taihe Black-Bone Silky Fowls with high egg production traits and provide a theoretical foundation for exploring the regulatory mechanisms of avian reproduction.

Genome-wide re-sequencing reveals selection signatures for important economic traits in Taihang chickens.

Taihang chickens is precious genetic resource with excellent adaptability and disease resistance, as well as high-quality eggs and meat. However, the genetic mechanism underlying important economic traits remain largely unknown. To address this gap, we conducted whole-genome resequencing of 66 Taihang and 15 White Plymouth rock chicken (Baiyu). The population structure analysis revealed that Taihang chickens and Baiyu are 2 independent populations. The genomic regions with strong selection signals and some candidate genes related to economic and appearance traits were identified. Additionally, we found a continuously selected 1.2 Mb region on chromosome 2 that is closely related to disease resistance. Therefore, our findings were helpful in further understanding the genetic architecture of the Taihang chickens and provided a worthy theoretical basis and technological support to improve high-quality Taihang chickens.

Effect of heat stress on semen characteristics and genetics in Thai native grandparent roosters.

Grandparent roosters are crucial in poultry breeding programs and significantly influence future bird generations' genetic makeup and performance. However, these roosters face considerable challenges from heat stress, which can adversely affect their reproductive performance, semen quality, and overall health and welfare. Our study aimed to investigate the effects of heat stress on the genetics of semen characteristics, identify the appropriate temperature and humidity indices (THI), and determine the threshold point of heat stress to prevent thermal stress. We analyzed data from 3,895 records of 242 Thai native grandparent roosters in conjunction with the THI using 7 THI functions and the regression method. The threshold point of heat stress, genetic parameters, rate of decline of semen characteristics per level of THI, estimated breeding values and selection index values were analyzed using the multivariate test-day model in the AIREML and BLUPF90 programs. Based on the regression coefficient and statistical criteria of the lowest -2logL and AIC values, the results showed that a THI of 78 was considered the threshold point of heat stress. The estimated heritability values ranged from 0.023 to 0.032, 0.066 to 0.069, 0.047 to 0.057, and 0.022 to 0.024 for mass movement, semen volume, sperm concentration, and the semen index, respectively. The reduction rates of mass movement, semen volume, sperm concentration, and semen index at a THI of 78 were -0.009, -0.003, -0.170, and -0.083 per THI, respectively. The genetic correlations among the semen traits were moderately to strongly positive and ranged from 0.562 to 0.797. The genetic correlations between semen traits and heat stress were negative and ranged from -0.437 to -0.749. The permanent environmental correlations among the semen traits (0.648-0.929) were positive and greater than the genetic correlations. Permanent environmental correlations between semen traits and heat stress were negative and ranged from -0.539 to -0.773. The results of the selection indices showed that the higher the selection intensity was, the greater the degree to which the selection index corresponded to genetic progress. The recommendation for animal genetic selection is that the top 10% is appropriate because it seems most preferred. Therefore, using a multivariate test-day model and selection index for the high genetic potential of semen traits and heat tolerance in Thai native grandparent roosters makes it possible to achieve genetic assessment in a large population.

Direct in vitro propagation of avian germ cells from an embryonic gonad biorepository.

Direct introduction of cryopreserved embryonic gonadal germ cells (GGC) into a sterile chicken surrogate host to reconstitute a chicken breed has been demonstrated as a feasible approach for preserving and utilizing chicken genetic resources. This method is highly efficient using male gonads; however, a large number of frozen female embryonic gonads is needed to provide sufficient purified GGC for the generation of fertile surrogate female hosts. Applying this method to indigenous chicken breeds and other bird species is difficult due to small flock numbers and poor egg production in each egg laying cycle. Propagating germ cells from the frozen gonadal tissues may be a solution for the biobanking of these birds. Here, we describe a simplified method for culture of GGC from frozen embryonic 9.5 d gonads. At this developmental stage, the germ cells are autonomously shed into medium, yielding hundreds to thousands of mitosis-competent germ cells. The resulting cultures of GGC have over 90% purity, uniformly express SSEA-1 and DAZL antigens and can re-colonize recipient's gonads. The GGC recovery rate from frozen gonads are 42% to 100%, depending on length of cryopreservation and the breed or line of chickens. Entire chicken embryos can also be directly cryopreserved for later gonadal isolation and culture. This storage method is a supplementary approach to safeguard local indigenous chicken breeds bearing valuable genetic traits and should be applicable to the biobanking of many bird species.

Single-cell RNA sequencing reveals surface markers of primordial germ cells in chicken and zebra finch.

Primordial germ cells (PGCs) in avian species exhibit unique developmental features, including the ability to migrate through the bloodstream and colonize the gonads, allowing their isolation at various developmental stages. Several methods have been developed for the isolation of avian PGCs, including density gradient centrifugation, size-dependent separation, and magnetic-activated cell sorting (MACS) or fluorescence-activated cell sorting (FACS) using a stage-specific embryonic antigen-1 (SSEA-1) antibody. However, these methods present limitations in terms of efficiency and applicability across development stages. In particular, the specificity of SSEA-1 decreases in later developmental stages. Furthermore, surface markers that can be utilized for isolating or utilizing PGCs are lacking for wild birds, including zebra finches, and endangered avian species. To address this, we used single-cell RNA sequencing (scRNA-seq) to uncover novel PGC-specific surface markers in chicken and zebra finch. We screened for genes that were primarily expressed in the PGC population within the gonadal cells. Analyses of gene expression patterns and levels based on scRNA-seq, coupled with validation by RT-PCR, identified NEGR1 and SLC34A2 as novel PGC-specific surface markers in chickens and ESYT3 in zebra finches. Notably, these newly identified genes exhibited sustained expression not only during later developmental stages but also in reproductive tissues.

Candidate Genes Associated with Survival Following Highly Pathogenic Avian Influenza Infection in Chickens.

Highly pathogenic strains of avian influenza (HPAI) devastate poultry flocks and result in significant economic losses for farmers due to high mortality, reduced egg production, and mandated euthanization of infected flocks. Within recent years, HPAI outbreaks have affected egg production flocks across the world. The H5N2 outbreak in the US in 2015 resulted in over 99% mortality. Here, we analyze sequence data from chickens that survived (42 cases) along with uninfected controls (28 samples) to find genomic regions that differ between these two groups and that, therefore, may encompass prime candidates that are resistant to HPAI. Blood samples were obtained from survivors of the 2015 HPAI outbreak plus age and genetics-matched non-affected controls. A whole-genome sequence was obtained, and genetic variants were characterized and used in a genome-wide association study to identify regions showing significant association with survival. Regions associated with HPAI resistance were observed on chromosomes 1, 2, 5, 8, 10, 11, 15, 20, and 28, with a number of candidate genes identified. We did not detect a specific locus which could fully explain the difference between survivors and controls. Influenza virus replication depends on multiple components of the host cellular machinery, with many genes involved in the host response.

Molecular mechanisms of avian immunoglobulin gene diversification and prospect for industrial applications.

Poultry immunoglobulin genes undergo diversification through homologous recombination (HR) and somatic hypermutation (SHM). Most animals share a similar system in immunoglobulin diversification, with the rare exception that human and murine immunoglobulin genes diversify through V(D)J recombination. Poultry possesses only one functional variable gene for each immunoglobulin heavy (HC) and light chains (LC), with clusters of non-productive pseudogenes upstream. During the B cell development, the functional variable gene is overwritten by sequences from the pseudo-variable genes via a process known as gene conversion (GC), a kind of HR. Point mutations caused in the functional variable gene also contribute to immunoglobulin diversification. This review discusses the latest findings on the molecular mechanisms of antibody gene diversification in poultry, using chickens as a model. Additionally, it will outline how these basic research findings have recently been applied especially in the medical field.

HSF1 is required for cellular adaptation to daily temperature fluctuations.

The heat shock response (HSR) is a universal mechanism of cellular adaptation to elevated temperatures and is regulated by heat shock transcription factor 1 (HSF1) or HSF3 in vertebrate endotherms, such as humans, mice, and chickens. We here showed that HSF1 and HSF3 from egg-laying mammals (monotremes), with a low homeothermic capacity, equally possess a potential to maximally induce the HSR, whereas either HSF1 or HSF3 from birds have this potential. Therefore, we focused on cellular adaptation to daily temperature fluctuations and found that HSF1 was required for the proliferation and survival of human cells under daily temperature fluctuations. The ectopic expression of vertebrate HSF1 proteins, but not HSF3 proteins, restored the resistance in HSF1-null cells, regardless of the induction of heat shock proteins. This function was associated with the up-regulation of specific HSF1-target genes. These results indicate the distinct role of HSF1 in adaptation to thermally fluctuating environments and suggest association of homeothermic capacity with functional diversification of vertebrate HSF genes.

Single nucleus/cell RNA-seq of the chicken hypothalamic-pituitary-ovarian axis offers new insights into the molecular regulatory mechanisms of ovarian development.

The hypothalamic-pituitary-ovarian (HPO) axis represents a central neuroendocrine network essential for reproductive function. Despite its critical role, the intrinsic heterogeneity within the HPO axis across vertebrates and the complex intercellular interactions remain poorly defined. This study provides the first comprehensive, unbiased, cell type-specific molecular profiling of all three components of the HPO axis in adult Lohmann layers and Liangshan Yanying chickens. Within the hypothalamus, pituitary, and ovary, seven, 12, and 13 distinct cell types were identified, respectively. Results indicated that the pituitary adenylate cyclase activating polypeptide (PACAP), follicle-stimulating hormone (FSH), and prolactin (PRL) signaling pathways may modulate the synthesis and secretion of gonadotropin-releasing hormone (GnRH), FSH, and luteinizing hormone (LH) within the hypothalamus and pituitary. In the ovary, interactions between granulosa cells and oocytes involved the KIT, CD99, LIFR, FN1, and ANGPTL signaling pathways, which collectively regulate follicular maturation. The SEMA4 signaling pathway emerged as a critical mediator across all three tissues of the HPO axis. Additionally, gene expression analysis revealed that relaxin 3 (RLN3), gastrin-releasing peptide (GRP), and cocaine- and amphetamine regulated transcripts (CART, also known as CARTPT) may function as novel endocrine hormones, influencing the HPO axis through autocrine, paracrine, and endocrine pathways. Comparative analyses between Lohmann layers and Liangshan Yanying chickens demonstrated higher expression levels of GRP, RLN3, CARTPT, LHCGR, FSHR, and GRPR in the ovaries of Lohmann layers, potentially contributing to their superior reproductive performance. In conclusion, this study provides a detailed molecular characterization of the HPO axis, offering novel insights into the regulatory mechanisms underlying reproductive biology.

Purposive breeding strategies drive genetic differentiation in Thai fighting cock breeds.

BACKGROUND: Fighting cock breeds have considerable historical and cultural place in Thailand. Breeds such as Lueng Hang Khao (LHK) and Pradu Hang Dam (PDH) are known for their impressive plumage and unique meat quality, suggesting selection for fighting and other purposes. However, information regarding the genetic diversity and clustering in indigenous and local Thai chickens used for cockfighting is unclear. OBJECTIVE: To investigates the genetic diversity and differentiation in Thai fighting cock breeds, including populations for cockfighting, ornamental aspects, and consumption. METHODS: Thai fighting cook breeds, including LHK and PDH chickens were analyzed using genotyping with 28 microsatellite loci. Data were compared to a gene pool library from "The Siam Chicken Bioresource Project" to understand the impact of human selection on genetic differentiation. Fighting cock strains from different breeds may cluster owing to shared breeding goals. RESULT: The analysis of several chicken breeds showed subpopulation differentiation driven by artificial selection and genetic drift, affecting the genetic landscape and causing genetic hitchhiking. Eleven of 28 microsatellite loci showed hitchhiking selection, indicating directional selection in fighting cocks. Additionally, analyses revealed admixture with domestic chicken breeds and minimal influence of red junglefowl in the gene pool of Thai fighting chickens. These findings inform breed improvement, selection strategies, genetic resource management, and maintaining genetic diversity in fighting cocks. CONCLUSION: Analysis of Thai Fighting chicken breeds revealed a correlation between utilization and subpopulation differentiation. Specifically, selection for cockfighting and ornamental traits appears to explain the observed genetic structure within these breeds.

Hemoglobin polymorphism and its association with morphometric and egg production traits in Ethiopian indigenous and Sasso chicken breeds.

The present study investigated the biochemical polymorphism of hemoglobin (Hb) and its relationship with performance traits of Ethiopian indigenous and Sasso chicken breeds. A total of 284 chickens reared in three agro-ecologies were examined for genetic diversity and associations with productive traits at Hb locus using agarose gel electrophoresis. The results showed that the HbA allele was dominant in both breeds, and a higher proportion of male chickens were HbAA genotypes, while females were predominantly HbBB types. In the highland agro-ecology, chickens with the HbAA genotype were the most dominant, whereas in mid- and low-land agro-ecologies, chickens with HbBB and HbAB genotypes were found to be more frequent. A moderate level of expected heterozygosity was obtained with 0.47 and 0.445 for indigenous and Sasso chickens, respectively, with an average effective number of alleles per locus of 1.89 and 1.80. Moreover, chickens with HbAA genotypes showed significantly (p ≤ 0.05) higher body weight and linear body measurements than those of HbAB and HbBB genotypes. However, for appendage body structures (comb and wattle dimensions), chickens with the HbAB and HbBB genotypes had higher mean values. Additionally, clutch size (14.2 ± 0.4), clutch length (21.8 ± 0.7), and eight-month egg production (84.1 ± 1.2) were significantly (p ≤ 0.05) higher for hens with HbBB genotypes, followed by those with HbAB-types. Therefore, the considerable hemoglobin variability and significant associations of Hb variants with the performance traits can be sought as guiding information for further genetic improvement interventions in the chicken breeds under investigation. Further microsatellite marker-based genotyping is recommended to validate the higher morphometric values for HbAA genotypes and the better egg production for HbBB and HbAB genotypes.

Effect of genotype and outdoor enrichment on productive performance and meat quality of slow growing chickens.

The optimization of animal welfare, meat quality, environmental impact, and economic sustainability in alternative poultry farming can be achieved by modulating several productive factors and improving the synergy between the chicken genotype and the outdoor environment. The objective of the study was to characterize 4 slow-growing chicken genotypes reared in free range conditions. Eight hundred chickens (SGs; 25 chickens/replicates/genotype/enrichment) belonging to the following genotypes, Red JA57 (RJ), Naked Neck (NN), Lohmann Dual meat-type (LD), and an Italian crossbreed (Robusta Maculata x Sasso, CB). were utilised and slaughtered at 81 d: The grazing areas were alternatively provided with enrichment constituted by strips of sorghum plants (ENR) or only grass (NO ENR). Productive performance (daily weight gain, daily feed intake, feed conversion ratio, live weight) were recorded weekly. Behaviour observations (walking and grass pecking), carcass and meat quality of breast and drumstick were also assessed in 15 chickens/replicate/genotypes/enrichment. Results demonstrated that both LD and CB showed the highest walking activity, but the different strains were differently capable of using the foraging resources (eating grass). The better productive performance was recorded in RJ followed by NN, CB and LD. In LD and CB, the different walking activities also affected the physico-chemical profiles (lower pHu, WHC, and lipids) of the breast and drumstick. The oxidative status was worse in CB than in the other groups (lower tocols, higher carbonyls), in both meat cuts. Fatty acid profile was also related to the genetic strain: a higher amount of n-3 polyunsaturated fatty acids was recorded both in the breast and drumstick of RJ and NN. The Healthy Fatty Index resulted excellent in all the chicken genotypes. In conclusion, the environment/animal interaction resulted as an important factor affecting the adaptability of genotypes to an extensive rearing system. All four genotypes, to different extents, showed good adaptability and production performance, with the exception of LD and CB, which were too light for the commercial supply chain requirements.

Whole-genome resequencing identifies candidate genes associated with heat adaptation in chickens.

The wide distribution and diverse varieties of chickens make them important models for studying genetic adaptation. The aim of this study was to identify genes that alter heat adaptation in commercial chicken breeds by comparing genetic differences between tropical and cold-resistant chickens. We analyzed whole-genome resequencing data of 186 chickens across various regions in Asia, including the following breeds: Bian chickens (B), Dagu chickens (DG), Beijing-You chickens (BY), and Gallus gallus jabouillei from China; Gallus gallus murghi from India; Vietnam native chickens (VN); Thailand native chickens (TN) and Gallus gallus spadiceus from Thailand; and Indonesia native chickens (IN), Gallus gallus gallus, and Gallus gallus bankiva from Indonesia. In total, 5,454,765 SNPs were identified for further analyses. Population genetic structure analysis revealed that each local chicken breed had undergone independent evolution. Additionally, when K = 5, B, BY, and DG chickens shared a common ancestor and exhibited high levels of inbreeding, suggesting that northern cold-resistant chickens are likely the result of artificial selection. In contrast, the runs of homozygosity (ROH) and the ROH-based genomic inbreeding coefficient (FROH) results for IN, TN, and VN chickens showed low levels of inbreeding. Low population differentiation index values indicated low differentiation levels, suggesting low genetic diversity in tropical chickens, implying increased vulnerability to environmental changes, decreased adaptability, and disease resistance. Whole-genome selection sweep analysis revealed 69 candidate genes, including LGR4, G6PC, and NBR1, between tropical and cold-resistant chickens. The genes were further subjected to GO and KEGG enrichment analyses, revealing that most of the genes were primarily enriched in biological synthesis processes, metabolic processes, central nervous system development, ion transmembrane transport, and the Wnt signaling pathway. Our study identified heat adaptation genes and their functions in chickens that primarily affect chickens in high-temperature environments through metabolic pathways. These heat-resistance genes provide a theoretical basis for improving the heat-adaptation capacity of commercial chicken breeds.

Linking gastrointestinal tract structure, function, and gene expression signatures to growth variability in broilers: a novel interpretation for flock uniformity.

Variation in body weight (BW) within broiler flocks is a significant challenge in poultry production. Investigating differences in gut-related parameters between low (LBW) and high BW (HBW) chicks may provide insights into the underlying causes of BW heterogeneity. 908 day-old male broiler chicks were reared until d 7 and then ranked into LBW and HBW groups. Thereafter, performance parameters were compared between BW groups periodically. On d 7, 14, and 38, visceral organ characteristics, intestinal permeability, and duodenal and ileal histomorphology were examined. Expression profiles were analyzed for 79 ileal genes related to gut barrier function, immune function, nutrient transport, gut hormones, nutrient receptors, metabolism, and oxidation using high-throughput qPCR. Student's t-tests were performed to compare measurements. Multivariate statistics, including partial least square regression (PLSR) analysis, were applied to identify combinations of key genes discriminating BW groups, offering predictive capability for phenotypic variations. The HBW group remained heavier at each timepoint, which could be explained by higher feed intake. The HBW group had shorter relative small intestine length but higher villus height and villi height/crypt depth ratios. The LBW group demonstrated increased intestinal permeability on d 38. The LBW group showed upregulation of immune response genes including TNF-α on d 7 and CYP450 on d 38, while the HBW group showed higher AHSA1 and HSPA4 expressions on d 7. The LBW group had upregulation of the metabolism genes mTOR and EIF4EBP1 on d 7 and the satiety-induced hormone cholecystokinin on d 14, while the HBW group tended to increase expression of the hunger hormone ghrelin on d 38. Genes related to gut barrier function, nutrient transport, and oxidation categories were consistently upregulated in the HBW group. PLSR models revealed 4, 12, and 11 sets of key genes highly predictive of BW phenotypes on d 7, 14, and 38, respectively. These findings suggest that growth rates are linked to the intestinal size, structure, and function of broiler chickens, offering insights into the underlying mechanisms regulating BW.

Effects of heat stress on the feeding preference of yellow-feathered broilers and its possible mechanism.

Heat stress is the most critical factor affecting animal feeding in summer. This experiment was conducted to investigate the effects of heat stress on the feeding preference of yellow-feathered broilers and its possible mechanism. As a result, the preference of yellow-feathered broilers for Tenebrio molitor was significantly decreased, and the fear response and serum corticosterone of broilers were significantly increased when the ambient temperatures are 35 °C (P < 0.05). In the central nervous system, consistent with the change in feeding preference, decreased dopamine in the nucleus accumbens (NAc) and increased mRNA levels of MAO-B in the ventral tegmental area (VTA) and NAc were found in yellow-feathered broilers (P < 0.05). In addition, we found significantly increased mRNA levels of corticotropin-releasing hormone receptor 1, corticotropin-releasing hormone receptor 2 and glucocorticoid receptor in the VTA and NAc of female broilers (P < 0.05). However, no similar change was found in male broilers. On the other hand, the serum levels of insulin and glucagon-like peptide-1 were increased only in male broilers (P < 0.05). Accordingly, the mRNA levels of insulin receptor and glucagon-like peptide-1 receptor in the VTA and the phosphorylation of mTOR and PI3K were increased only in male broilers (P < 0.05). In summary, the preference of yellow-feathered broilers for Tenebrio molitor feed decreased under heat stress conditions, and hedonic feeding behavior was significantly inhibited. However, the mechanism by which heat stress affects hedonic feeding behavior may contain gender differences. The insulin signaling pathway may participate in the regulation of heat stress on the male broiler reward system, while stress hormone-related receptors in the midbrain may play an important role in the effect of heat stress on the reward system of female broilers.

Integrative analysis of RNA-seq and Ribo-seq reveals that lncRNA-GRN regulates chicken follicular atresia through miR-103-3p/FBXW7 axis and encoding peptide.

Follicular atresia in chickens seriously reduced the egg production and economic benefits of chickens. LncRNA plays a key role in the process of follicular atresia. In this study, RNA-seq and Ribo-seq were performed on normal and atretic follicles of Dahen broilers to screen out lncRNAs that may regulate follicle atresia, and to study the molecular mechanisms of their regulation. GRN granulin precursor (lncGRN, ID: 101748909) was highly expressed in atretic follicles with translational ability. A molecular regulatory network of lncGRN/miR-103-3p/FBXW7 was constructed through bioinformatics analysis and dual luciferase reporting. LncGRN promoted the expression of FBXW7 by adsorption of miR-103-3p, thereby inhibiting the proliferation of chicken granulosa cells (GCs), promoting apoptosis of chicken GCs and inhibiting steroid hormone synthesis thus induced follicular atresia. Meanwhile, we also found a micropeptide named GRN-122aa derived by lncGRN which can promote follicular atresia. In conclusion, our study found that lncGRN promoted follicular atresia through the lncGRN/miR-103-3p/FBXW7 axis and the translation micropeptide GRN-122aa. This study provided new insight into the post-transcriptional regulation mechanism of lncGRN suggesting that lncGRN may act as a potential to regulate chicken follicle development, and provided a theoretical argument for further improving the egg production of chickens through molecular breeding.

Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches.

Local village chicken, or "Ayam kampung" as it's known in Malaysia, is considered a premium chicken breed with a higher price than other chicken breeds. As a result of their comparable appearances and sizes, colored broiler chickens are often sold as village chickens, which is a form of food fraud that can result in a 3- to 4-fold rise in profit. Therefore, developing a breed-specific authentication method is crucial for preventing food fraud in the poultry industry. This study aims to investigate the genetic diversity of village chickens from other commercial chicken breed populations available in the market (broiler [Cobb], colored broiler [Hubbard], and layer [DeKalb]) to identify breed-specific DNA fragments as biomarkers for village chicken authentication. The Whole-genome sequencing and mutation calling of 12 chickens (3 chickens/breed) led to the identification of a total of 73,454,654 single nucleotide polymorphisms (SNP) and 8,762,338 insertion and deletions (InDel) variants, with more variants detected in the village chicken population (6,346,704 SNPs; 752,408 InDels) compared to commercial breeds. Therefore, this study revealed that village chickens were more genetically variable compared to other breeds in Malaysia. Furthermore, the breed-specific genomic region located on chromosome 1 (1:84,405,652) harboring SNP (C-T) with high discrimination power was discovered and validated which can be considered as a novel breed-specific biomarker to develop a method for accurate authentication of village chickens in Malaysia. This authentication method offers potentialw applications in the chicken industry and food safety.