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Background In Tibet, the two most important breeds are Tibetan chicken and Lhasa white chicken, and the duo exhibit specific adaptations to the high altitude thereby supplying proteins for humans living in the plateau. These breeds are partly included in the conservation plans because they represent important chicken genetic resources. However, the genetic diversity of these chickens is rarely investigated. Based on whole-genome sequencing data of 113 chickens from 4 populations of Tibetan chicken including Shigatse (SH), Nyemo (NM), Dagze (DZ) and Nyingchi (LZ), as well as Lhasa white (LW) chicken breed, we investigated the genetic diversity of these chicken breeds by genetic differentiation, run of homozygosity (ROH), genomic inbreeding and selection signature analyses. Results Our results revealed high genetic diversity across the five chicken populations. The linkage disequilibrium decay was highest in LZ, while subtle genetic differentiation was found between LZ and other populations (Fst ranging from 0.05 to 0.10). Furthermore, the highest ROH-based inbreeding estimate (FROH) of 0.11 was observed in LZ. In other populations, the FROH ranged from 0.04 to 0.06. In total, 74, 111, 62, 42 and 54 ROH islands containing SNPs ranked top 1% for concurrency were identified in SH, NM, DZ, LZ and LW, respectively. Genes common to the ROH islands in the five populations included BDNF, CCDC34, LGR4, LIN7C, GLS, LOC101747789, MYO1B, STAT1 and STAT4. This suggested their essential roles in adaptation of the chickens. We also identified a common candidate genomic region harboring AMY2A, NTNG1 and VAV3 genes in all populations. These genes had been implicated in digestion, neurite growth and high-altitude adaptation. Conclusions High genetic diversity is observed in Tibetan native chickens. Inbreeding is more intense in the Nyingchi population which is also genetically distant from other chicken populations. Candidate genes in ROH islands are likely to be the drivers of adaptation to high altitude exhibited by the five Tibetan native chicken populations. Our findings contribute to the understanding of genetic diversity offer valuable insights for the genetic mechanism of adaptation, and provide veritable tools that can help in the design and implementation of breeding and conservation strategies for Tibetan native chickens.

Sexual maturation is fundamental to the reproduction and production performance, heterosis of which has been widely used in animal crossbreeding. However, the underlying mechanism have long remained elusive, despite its profound biological and agricultural significance. In the current study, the reciprocal crossing between White Leghorns and Beijing You chickens were performed to measure the sexual maturation heterosis, and the ovary lncRNAs and mRNAs of purebreds and crossbreeds were profiled to illustrate molecular mechanism of heterosis. Heterosis larger than 20% was found for pubic space and oviduct length, whereas age at first egg showed negative heterosis in both crossbreeds. We identified 1170 known lncRNAs and 1994 putative lncRNAs in chicken ovary using a stringent pipeline. Gene expression pattern showed that nonadditivity was predominant, and the proportion of nonadditive lncRNAs and genes was similar between two crossbreeds, ranging from 44.24% to 49.15%. A total of 200 lncRNAs and 682 genes were shared by two crossbreeds, respectively. GO and KEGG analysis showed that the common genes were significantly enriched in the cell cycle, animal organ development, gonad development, ECM-receptor interaction, calcium signaling pathway and GnRH signaling pathway. Weighted gene co-expression network analysis (WGCNA) identified that 7 out of 20 co-expressed lncRNA-mRNA modules significantly correlated with oviduct length and pubic space. Interestingly, genes harbored in seven modules were also enriched in the similar biological process and pathways, in which nonadditive lncRNAs, such as MSTRG.17017.1 and MSTRG.6475.20, were strongly associated with nonadditive genes, such as CACNA1C and TGFB1 to affect gonad development and GnRH signaling pathway, respectively. Moreover, the results of real-time quantitative PCR (RT-qPCR) correlated well with the transcriptome data. Integrated with positive heterosis of serum GnRH and melatonin content detected in crossbreeds, we speculated that nonadditive genes involved in the GnRH signaling pathway elevated the gonad development, leading to the sexual maturation heterosis. We characterized a systematic landscape of ovary lncRNAs and mRNAs related to sexual maturation heterosis in chicken. The quantitative exploration of hybrid transcriptome changes lays foundation for genetic improvement of sexual maturation traits and provides insights into endocrine control of sexual maturation.

This study aimed to investigate the effects of feed systems in parent pigeons on the growth performance, carcass characteristics, organ index, and serum biochemical parameters of squabs. A total of 60 pairs of parent pigeons were selected and divided into 2 groups randomly. The parent pigeons were fed with two feed systems that were whole grains plus granulated feed (WGG) and complete-formula granulated feed (CFG) for 21 d. The results showed that CFG diet could increase carcass yield, heart index, content of trypsin, and growth hormone of squabs (P0.05), but decrease feed intake, gizzard index, b* value, malondialdehyde concentration, and uric acid concentration significantly (P0.05) comparing with WGG diet. There were no significant differences among the 2 groups in feed intake from d 1 to d 21, abdominal fat yield and body weight changes of squabs and parent pigeons (P0.05). It can be concluded from these observations that CFG was beneficial to squab which could improve digestive enzyme and antioxidant ability in the serum, so the CFG should be suggested in practice.

Heterosis has been widely utilized in chicken breeding to improve economically important traits. However, few studies focused on revealing the factors contributing to egg production heterosis. In this study, White Leghorn and Beijing-You chickens were used as parental breeds to generate purebreds (WW, YY) and reciprocal crossbreeds (WY, YW) to characterize heterosis for egg production traits including age at first egg (AFE), clutch traits, oviposition pattern, and egg quality traits. Results showed that egg number until 35 wk of age (EN35) was higher in crossbreeds than the average of purebreds (P0.05) and exhibited positive heterosis of 4.03% and 2.84%) in WY and YW respectively. Crossbreeds commenced laying earlier than the average of purebreds (P0.05) with negative heterosis of -1.24% and -0.92% for WY and YW respectively. Moreover, EN35 had negative correlation with AFE (r = -0.85) and positive correlation with average clutch length (ACL) (r = 0.48) and maximum clutch length (MCL) (r = 0.66). However, negative heterosis for ACL (-19.62%, -16.51%) and MCL (-22.88%, -18.97%) were obtained in WY and YW, respectively. This may be due to the positive heterosis for number of pauses, which was highly correlated with ACL (r = -0.68) and MCL (r = -0.74). The crossbreeding improved the oviposition pattern. Percent egg laying that occurs between 7:00 and 14:00 was 91.50% (WW), 68.28% (YY), 76.87% (WY), and 79.68% (YW) in the experimental populations. On the other hand, oviposition interval (OI) had negative heterosis in crossbreeds and was negatively correlated with EN35 (r = -0.60). Positive heterosis for egg weight of 2.63% and 3.94% and yolk weight of 4.74% and 6.07% were observed in WY and YW, respectively. Taken together, egg production related traits did not contribute equally to EN heterosis. The AFE and OI exhibited significant correlation with EN indicating that they would be important drivers for EN heterosis.

Crossbreeding advantage in hybrids compared with their parents, termed heterosis, has been exhaustively exploited in chicken breeding over the last century. Reports for crossbreeding of elite laying chickens covering rearing and laying period remain infrequent. In this study, resource populations of Rhode Island Red (RIR) and White Leghorn (WL) pure-bred chickens were reciprocally crossed to generate 4 distinct groups that were evaluated for prelaying growth, egg production, and egg quality. Birds monitored for prelaying growth consists of 105 (RIR), 131 (WL), 207 (RIR × WL) and 229 (WL × RIR), and 30 pullets from each group were evaluated. Egg laying records were collected from 102, 89, 147, and 191 hens in the 4 populations, respectively. In addition, expression of 5 candidate genes for egg production in the ovarian follicles was measured by RT-qPCR. Results showed that BW of hatched chicks in the WL line was higher than the other populations. However, the 2 crossbreds grew faster than WL purebred throughout the prelaying period. Low to medium heterosis was observed for BW and body length before the onset of lay. White Leghorn and the hybrids commenced laying earlier than RIR pullets and egg production traits were favorable in the crossbreds compared with purebreds. Heterosis for egg number and clutch size was moderate in WL × RIR but low in RIR × WL hens. Expression of antimullerian hormone gene was high in WL and RIR × WL hybrids, suggesting WL parent-specific enhancing dominant expression. Shell weight was higher in the crossbreds than purebreds at 52 wk of age, but RIR hens laid eggs with higher shell ratio than the other populations (P

The prevalence of crossed beaks ranging from 0.2 to 7.4% was documented in at least 12 chicken strains. Previous studies focused largely on candidate molecules, whereas the morphological observation was missing. This study reported a detailed phenotype and prevalence of crossed beaks based on morphological observation in nine thousand nine hundred 1-day-old female Beijing-You chicks. Affected chicks were classified into 2 categories based on the direction of the mandibular deformation: left and right. Each category was selected to sacrifice for the measurement of length, width, and thickness of the bilateral mandibular ramus (MR). The normal chicks were used as controls. Paraffin section was made for the bilateral MR of a crossed beak and a normal control for histology analysis. A total of 97 out of 9,900 chickens showed beak deformity including 71 crossed beaks (0.72%) and 26 side beaks (0.26%) for which the upper and lower beak were both bent in the same direction. There was no difference in the direction of the bend of the lower beak in crossed beaks (P > 0.05). The incidence of crossed beaks increased quickly from 0 to 56 d and no new incidence after 56 d. The angle of the crossed beaks was below 5° in the first week and had grown more severe with age until 56 d. The mandible structure showed that condyle served as a growth center for the MR extension. The short-side MR of crossed beaks was thicker than normal ones (P

The objective of this study was to investigate the effects of replacing antibiotics with a combination of plant essential oils on the growth performances and gastrointestinal health of broilers. A total of 720 1-day-old male AA broilers were randomly divided into 3 treatments: the control treatment (CON), the Aureomycin supplementation treatment (AGP), and the combined plant oils supplementation treatment (POC), with a 42-D period feeding procedure. Growth performances, carcass performances, intestinal sections, and cecal microbiota were investigated. Results indicated that POC supplementation decreased the feed conversion ratio compared with CON and AGP treatments, though not significantly. No significant differences were found for feed intake, BW gain, and culling rate among the 3 treatments (P > 0.05). In addition, no significant differences were seen on carcass performance. For the aspects of intestinal section, POC supplementation did not make significant effects on intestinal wall thickness, villus heights, crypt depths, and the ratio of villus heights/crypt depths compared with CON and AGP treatments. Cecal microbiota results demonstrated that bacterial diversity and some representative probiotic bacteria were significantly increased in numbers (P < 0.05) after POC supplementation. In conclusion, the combination of essential oils promoted intestinal health through improving gut bacterial diversity and probiotic bacteria, as well as improving feed conversion ratio of broilers. These results indicated that the combination of essential oils may benefit the gastrointestinal health and be applied as an antibiotic alternative.

Providing green light during incubation has been shown to accelerate the embryo development and shorten the hatching time in broilers. Few studies have concentrated on the exact effects on layer breeders in the aspects of hatching and posthatch performance. In this study, 4 strains of layer breeder eggs, namely White Leghorn, Rhode Island Red, Columbia Rock, and Barred Rock were used to assess the effects of monochromatic green light during embryogenesis on hatching performance, chick quality, and pubertal growth. Each strain of 600 eggs was incubated under photoperiods of either 12 h of light and 12 h of darkness (12L:12D, light group) or 0 h of light and 24 h of darkness (0L:24D, dark group) for 18 D, with 2 replicates for each treatment. The results showed hatch time, time reaching 90% hatch, and average hatch time were significantly shorter among the 4 strains in the light group (P 0.05). There was no significant difference in hatchability of fertile eggs, chick weight/egg weight, or chick quality among the 4-strain eggs between the light group and dark group (P > 0.05). There was no difference (P > 0.05) in posthatch BW between different light treatments of the 3 strains (White Leghorn, Columbia Rock, and Barred Rock), whereas the BW of Rhode Island Red was higher in light group than that of the dark group at 8 to 12 wk of age (P

Background Marek’s disease (MD) is a highly neoplastic disease primarily affecting chickens, and remains as a chronic infectious disease that threatens the poultry industry. Copy number variation (CNV) has been examined in many species and is recognized as a major source of genetic variation that directly contributes to phenotypic variation such as resistance to infectious diseases. Two highly inbred chicken lines, 63 (MD-resistant) and 72 (MD-susceptible), as well as their F1 generation and six recombinant congenic strains (RCSs) with varied susceptibility to MD, are considered as ideal models to identify the complex mechanisms of genetic and molecular resistance to MD. Results In the present study, to unravel the potential genetic mechanisms underlying resistance to MD, we performed a genome-wide CNV detection using next generation sequencing on the inbred chicken lines with the assistance of CNVnator. As a result, a total of 1649 CNV regions (CNVRs) were successfully identified after merging all the nine datasets, of which 90 CNVRs were overlapped across all the chicken lines. Within these shared regions, 1360 harbored genes were identified. In addition, 55 and 44 CNVRs with 62 and 57 harbored genes were specifically identified in line 63 and 72, respectively. Bioinformatics analysis showed that the nearby genes were significantly enriched in 36 GO terms and 6 KEGG pathways including JAK/STAT signaling pathway. Ten CNVRs (nine deletions and one duplication) involved in 10 disease-related genes were selected for validation by using quantitative real-time PCR (qPCR), all of which were successfully confirmed. Finally, qPCR was also used to validate two deletion events in line 72 that were definitely normal in line 63. One high-confidence gene, IRF2 was identified as the most promising candidate gene underlying resistance and susceptibility to MD in view of its function and overlaps with data from previous study. Conclusions Our findings provide valuable insights for understanding the genetic mechanism of resistance to MD and the identified gene and pathway could be considered as the subject of further functional characterization.

Molecular mechanisms underlying sperm motility have not been fully explained, particularly in chickens. The objective was to identify seminal plasma proteins associated with chicken sperm motility by comparing the seminal plasma proteomic profile of roosters with low sperm motility (LSM, n = 4) and high sperm motility (HSM, n = 4). Using a label-free MS-based method, a total of 522 seminal plasma proteins were identified, including 386 (∼74%) previously reported and 136 novel ones. A total of 70 differentially abundant proteins were defined, including 48 more-abundant, 15 less-abundant, and seven proteins unique to the LSM group (specific proteins). Key secretory proteins like less-abundant adhesion G-protein coupled receptor G2 (ADGRG2) and more-abundant serine peptidase inhibitor Kazal-type 2 (SPINK2) in the LSM suggested that the corresponding secretory tissues played a crucial role in maintaining sperm motility. Majority (80%) of the more-abundant and five specific proteins were annotated to the cytoplasmic domain which might be a result of higher plasma membrane damage and acrosome dysfunction in LSM. Additionally, more-abundant mitochondrial proteins were detected in LSM seminal plasma associated with lower spermatozoa mitochondrial membrane potential (ΔΨm) and ATP concentrations. Further studies showed that the spermatozoa might be suffering from oxidative stress, as the amount of spermatozoa reactive oxygen species (ROS) were largely enhanced, seminal malondialdehyde (MDA) concentrations were increased, and the seminal plasma total antioxidant capacity (T-AOC) were decreased. Our study provides an additional catalogue of chicken seminal plasma proteome and supports the idea that seminal plasma could be as an indicator of spermatozoa physiology. More-abundant of acrosome, mitochondria and sperm cytoskeleton proteins in the seminal plasma could be a marker of sperm dysfunction and loss of motility. The degeneration of spermatozoa caused by the reduced seminal T-AOC and enhanced oxidative stress might be potential determinants of low sperm motility. These results could extend our understanding of sperm motility and sperm physiology regulation.

Egg fertilization is a dynamic process, including varieties of biochemical changes. To better understand the molecular mechanisms during the egg embryo development, the objective of this study was to quantify protein expression changes between fertilized and unfertilized Beijing-You chicken eggs using label-free liquid chromatography-tandem mass spectrometry method. The results showed that a total of 1241 proteins were identified from fertilized and unfertilized eggs, 229 proteins were observed difference in fertilized eggs (p

The objective of this study was to determine the effect of age at photostimulation on sexual maturity and performance of layer breeders. A total of 192 fourteen-wk-old White Leghorn (WL) breeder hens were randomly allocated to 4 treatments of 48 birds each, with 2 replicates per treatment. The birds were photostimulated at 16 (PS16), 18 (PS18), 20 (PS20), and 22 (PS22) wk of age. Four birds per treatment were randomly selected to evaluate sexual organ development at 1 D before photostimulation and 2, 4, and 6 wk after photostimulation. The ovary weight, large yellow follicles number (LYF), oviduct weight, and oviduct length of PS18 increased sharply after photostimulation. Conversely, the increase in PS16 was not observed until 2 wk after photostimulation. There was no difference in age at sexual maturity between treatments (P > 0.05). The PS16 had the longest interval (28 D) from photostimulation to 5% egg production, while PS22 reached 5% egg production 7 D before photostimulation. The PS22 had lower peak production (P = 0.02) and less egg production (P = 0.02) than other treatments. The PS16 had more broken and abnormal eggs (P = 0.01) and lower hatchability (P = 0.04) than other treatments. In conclusion, photostimulation at 16 and 22 wk of age decreases hatchability and egg production, respectively, and photostimulation at 18 wk is appreciated for the WL breeder hens.

In poultry industry, around 5 to 12% roosters were eliminated from the breeding program because of low sperm motility. Relatively few studies have been directed toward understanding and explaining the genetics mechanisms involved in sperm motility regulation in chickens. In the present study, digital gene expression (DGE) profiling and bioinformation analysis were used to explore the globally differentially expressed genes (DEG) in the testis of low sperm motility and high sperm motility roosters. Further validation study of key candidate genes was also performed. The DGE identified 652 DEGs, including 473 up-regulated and 179 down-regulated genes in the low sperm motility testis. Those DEGs were enriched on 21 terms of biological process category, 10 terms of cellular component category, including motile cilium, and 13 terms of molecular function category including microtubule motor activity and ATP binding. The kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis indicated that these DEGs were involved in the FoxO signaling pathway and insulin resistance pathway. Quantitative real time PCR (qRT-PCR) studies of 8 DEGs were used to validate the DGE results. A key candidate gene Cyclin F (CCNF) was extremely low expressed in the low sperm motility testis (log2 ratio (low sperm motility/high sperm motility) = -5.23). The CCNF gene silencing in the chicken DF-1 cell line induced the reduced cell activity and proliferation. In summary, the present study provides insight into the potential genetic regulation of sperm motility and highlighted the underlying pathways (Insulin resistance and FoxO signaling pathways) and important candidate genes such as CCNF.

This work studied the effect of age at photostimulation on reproductive performance of Beijing-You Chicken (BYC) breeders. A total of 384 fourteen-week-old BYC breeder hens were randomly allocated to 4 treatments of 96 birds each, with 2 replicates per treatment. The treatments represent photostimulation at 16, 18, 20, and 22 wk of age, respectively (PS16, PS18, PS20, and PS22) by incrementally increasing day length from 8L:16D to 14L:10D and by increasing lighting intensity from 10 to 80 lx. Egg production was recorded for each replicate until 51 wk. Four birds randomly selected from each treatment were sacrificed to characterize sexual organ development at 4 time points: 1 D before photostimulation and 2, 4, and 6 wk after photostimulation. Eggshell quality at peak laying was measured. The results showed that the changes in ovary and oviduct weight in PS22 were 8.68- and 4.27-fold higher than in PS16 at 6 wk after photostimulation. PS16 had an earlier age at 5% egg production than PS20 and PS22 (P = 0.003). The interval from photostimulation to age at 5% egg production in PS20 and PS22 was shorter than in other treatments (P = 0.005). Later peak egg production was seen in PS20 (211.0 D) and PS22 (218.0 D) than in PS16 (183.0 D) and PS18 (190.0 D, P = 0.020), but the laying rate of PS20 decreased slowly after peak laying. PS20 and PS22 had higher egg weights than PS16 and PS18 at peak laying (P = 0.018). Age at photostimulation had no effect on egg number, defective egg number, or hatchability (P > 0.05). In summary, the onset of lay can be advanced by photostimulation at early ages, but there is no difference on egg production until 51 wk. Photostimulation at 20 wk improves peak of laying and laying uniformity.

Marek's Disease (MD) is a neoplastic disease of chickens and remains as a chronic infectious disease that threatens the poultry industry. Improving genetic resistance to MD in poultry is an important long-term goal, which would significantly augment the current control measures against MD and eventually reduce the annual economic loss. In this study, survival patterns of F2 birds from 2 reciprocal crosses were compared to examine possible difference in survival between the reciprocal crosses in response to MD virus (MDV) challenge. A total of 246 and 224 F2 chicks derived from reciprocal crosses of lines 63 × 72 and lines 72 × 63, respectively, were sampled from an MDV challenge trial and survival days were recorded from the MDV-inoculation date to the end of experiment. Statistical analyses, including Principal Component Analysis (PCA) followed by a cox-regression model, showed there was no significant difference in survival days between reciprocal crosses (P > 0.05). To the best of our knowledge, this is the first MD survival study on reciprocal crosses of 2 genetically diversified lines of chickens differing in MD resistance. This report documented the experimental evidence that the genetic lineage of grandparental (maternal or paternal) effect on survival days was minimal, if present at all.

The long-term semen cryopreservation is increasingly crucial for conservation of endangered livestock and poultry species. Glycerol is the most widely used cryoprotectant for freezing chicken semen. Continuous improvement in details with glycerol may help increase the fertility of post-thawed semen. Two experiments were performed in the present study to investigate the effects of glycerol concentration, removal method, and straw type on the quality of post-thawed sperm. In experiment 1, glycerol concentration (3%, 5%, 7%, 9%, 11%, and 13%) and glycerol removal method (final dilution ratio 1:1, 1:2, 1:4, 1:8, 1:16, and 1:20) combination groups were investigated for post-thawed sperm quality, residual glycerol concentration, and fertility to find the best combinations. Experiment 2 was performed to evaluate the effects of straw type (0.25 and 0.5 mL) and glycerol concentration (3%, 5%, 7%, 9%, 11%, and 13%) on the post-thawed sperm quality. Results showed that post-thawed sperm motility of 6 glycerol concentration groups were different (P0.01). Sperm motility of 5%, 7%, 9%, 11% and 13% was higher than that of 3% (P0.01). There was no difference among different concentrations of glycerol in VSL, VCL, VAP, ALH, WOB, BCF, LIN, or STR (P0.05). As for the glycerol removal method, sperm motility of 1:8 dilution was the highest, followed by 1:1 and 1:2, while the difference among groups was not statistically significant (P = 0.11). Glycerol concentration and removal method had no interaction effect on sperm motion parameters (P0.05). The highest fertility (48.70%) was found for the 5% and 1:2 combination. There was no difference for sperm motility between 0.25 and 0.5 mL straws (P0.05). Glycerol concentration and straw type had no interaction effect on the sperm motion parameters (P0.05). It can be concluded from these observations that the combination of 5% glycerol and 1:2 dilution rendered higher fertility should be suggested in practice, and that both 0.25 and 0.50 mL straws fit the present procedure.

Preclinical and clinical data show a close relationship between high infiltration of tumor-associated macrophages (TAMs) and a poor prognosis in most types of tumors, thus targeting TAMs stands out as promising anticancer immunotherapies. Recent studies have demonstrated the anti-tumor effects of artemisinin via enhancing anti-tumor immunity within tumor microenvironment, but the underlying mechanism is still not clear. In the present study we uncovered an important role of dihydroartemisinin (DHA) in regulating intratumoral TAM polarization and anti-tumor immune responses in mouse Lewis Lung carcinoma model. We found that DHA inhibited Lewis Lung carcinoma progress, moderately decreased the frequencies of TAMs within tumor stroma, and significantly increased CD86 expression while decreased CD206 expression on TAMs which indicates the role of DHA in polarizing TAMs into a M1-like phenotype. Then, our in vitro data confirmed that DHA dose-dependently promoted macrophage M1 phenotype transition by increasing M1 phenotype-related molecules, meanwhile decreasing the expression of M2 phenotype-related molecules. In addition, DHA increased proinflammatory cytokine production, enhanced the phagocytic capacity while decreased anti-inflammatory cytokine production. Finally, in order to prove that AKT/mTOR signaling potentially mediated DHA-induced macrophage differentiation, we used rapamycin to specifically block the activity of mTOR and stimulated macrophages under M1 stimuli. Our data clearly showed that rapamycin significantly decreased DHA-induced M1-related phenotypes and proinflammatory cytokine expression. In summary, our study highlighted DHA as one of future potential therapeutic options for the development of novel anticancer immunotherapies in lung cancer.

The beak is the dominant avian facial feature, and beak deformity occurs in 0.5 to 2.5% of some indigenous chicken breeds, resulting in difficulties when eating, drinking, and performing natural behaviors. Previous studies on beak deformity focused largely on candidate molecules associated with skeletogenic development, providing insight into the molecular and genetic underpinnings of beak deformity. The present study was performed to identify candidate proteins related to this malformation in chickens. Three 12-day-old Beijing-You roosters with deformed beaks (D1, D2, and D3) and 3 with normal beaks (N1, N2, and N3) were used, and total beak proteins were isolated and subjected to standard iTRAQ labeling, strong cation-exchange chromatography, and liquid chromatography-tandem mass spectrometry. Mascot 2.3.02 was used to identify and quantitatively analyze proteins. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were used to identify functions and metabolic pathways of differentially expressed proteins, and key proteins were further validated using western blot. A total of 2,370, 2,401, and 2,378 proteins were reliably quantified in 3 biological replicates, among which, 2,345 were common to all, and 92 were differentially expressed between the 2 groups. These included 37 upregulated and 55 downregulated proteins in deformed beaks. Pentraxin-related protein 3, hemopexin, lipoprotein lipase, retinoid-binding protein 7, and biliverdin reductase A were downregulated in all 3 sets, while parvalbumin, peptidyl-prolyl cis-trans isomerase, and ubiquitin-fold modifier 1 were upregulated. Pathway analysis returned no enriched pathways, and western blot validated the iTRAQ results. Parvalbumin and lipoprotein lipase could be firstly selected as key proteins in view of their known functions in regulating the buffering of intracellular free Ca2+ in both cartilage and bone cells and bone mass, respectively. Their potential roles in beak deformity, however, deserve further studies. In summary, the onset of beak deformity could be very complex, and this study will be helpful for future investigation of mechanistic explanation for beak deformity.

Sperm motility is one of the most important indicators for evaluating roosters' fecundity. However, molecular regulation underlying chickens' sperm motility remains to be understood. MicroRNA (miRNA) plays an epigenetic role in reproduction. In this study, we compared the testicular miRNAs of Beijing-you roosters with high (HS) and low (LS) sperm motility using Illumina sequencing to try to understand the associated molecular regulation. Length distribution analysis showed that the dominant size of small RNAs detected in the testes of the chicken samples was 24-28 nt. In total, 518 known and 106 novel miRNAs were identified. A total of 23 miRNAs were found differentially expressed (P 0.05, |log

The 2 × 4 factorial experiment was designed to determine the effect of strain and photostimulation age on sexual maturity and reproductive performance of rooster breeders. A total of 96 White Leghorn (WL) and 120 Beijing You Chicken (BYC) roosters were randomly allocated to 4 treatments at 14 wk of age. The treatments represent photostimulation at 16, 18, 20, and 22 wk of age, respectively (PS16, PS18, PS20, and PS22), in both strains. Photostimulation was achieved by increasing the day length from 8L:16D to 14L:10D and by increasing lighting intensity from 10 lx to 80 lx. Three birds from each interaction were sacrificed to characterize the comb and testis weights at 4 time points: 1 d before photostimulation and 2, 4, and 6 wk after photostimulation. Semen quality and hatching performance with the semen of the experimental roosters were measured at 30 and 45 wk of age, respectively. Results showed that the testis weight of PS20 and PS22 in WL and BYC was 6.4- and 2.9-fold higher than that of PS18 before photostimulation, while testis weight of PS18 in both strains increased sharply after photostimulation. The diameter of seminiferous tubules increased in the photostimulated roosters as compared with the nonphotostimulated ones, and mature spermatozoa were produced 4 wk after photostimulation and at 20 wk of age for PS16. The WL had lower semen volume and total sperm count than BYC (P 0.05). In addition, semen quality traits were not affected by age at photostimulation (P > 0.05) in both strains. The fertility and hatching performance were not affected by strain or photostimulation age (P > 0.05). In summary, the sexual maturation of rooster breeders can be advanced by photostimulation at an early age, which does not lead to a difference in semen quality or hatching performance at adult stage.

Poultries including chickens, ducks, geese, and pigeons are widely used in the biological and medical research in many aspects. The genetic quality of experimental poultries directly affects the results of the research. In this study, following electrophoresis analysis and short tandem repeat (STR) scanning, we screened out the microsatellite loci for determining the genetic characteristics of Chinese experimental chickens, ducks, geese, and pigeons. The panels of loci selected in our research provide a good choice for genetic monitoring of the population genetic diversity of Chinese native experimental chickens, ducks, geese, and ducks.

Pigeons have the ability to produce milk and feed their squabs. The genetic mechanisms underlying milk production in the crops of &rsquo, lactating&rsquo, pigeons are not fully understood. In this study, RNA sequencing was employed to profile the transcriptome of lncRNA and mRNA in lactating and non-&lsquo, pigeon crops. We identified 7066 known and 17,085 novel lncRNAs. Of these lncRNAs, 6166 were differentially expressed. Among the 15,138 mRNAs detected, 6483 were differentially expressed, including many predominant genes with known functions in the milk production of mammals. A GO annotation analysis revealed that these genes were significantly enriched in 55, 65, and 30 pathways of biological processes, cellular components, and molecular functions, respectively. A KEGG pathway enrichment analysis revealed that 12 pathways (involving 544 genes), including the biosynthesis of amino acids, the propanoate metabolism, the carbon metabolism and the cell cycle, were significantly enriched. The results provide fundamental evidence for the better understanding of lncRNAs&rsquo, and differentially expressed genes&rsquo, (DEGs) regulatory role in the molecular pathways governing milk production in pigeon crops. To our knowledge, this is the first genome-wide investigation of the lncRNAs in pigeon crop associated with milk production. This study provided valuable resources for differentially expressed lncRNAs and mRNAs, improving our understanding of the molecular mechanism of pigeon milk production.

Background Embryo chicken egg is a nutritional supplement that has been used to enhance physical fitness and promote wound healing according to traditional Chinese medicine for many years. In this study, we evaluated the effects of embryo chicken egg extract (ECE) on the exercise performance and fatigue in mice and the underlying mechanisms. Results The results indicated that ECE can prolong the exhaustive swimming time, decrease lactic acid, blood urea nitrogen, creatine kinase, and malondialdehyde levels, and increase superoxide dismutase, glutathione peroxidase, and glycogen levels. Additionally, ECE can also regulate the balance of oxidative stress via the adenosine monophosphate activated protein kinase/mammalian target of rapamycin signalling pathway. Conclusion Taken together, these results showed that ECE can improve exercise performance and reduce physical fatigue in mice, which indicates that ECE can be used as a potential supplement to reduce physical fatigue. © 2020 Society of Chemical Industry.

Background Beak deformity, typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here. Beak deformity severely impairs the birds’ growth and welfare. Although previous studies shed some light on the genetic regulation of this complex trait, the genetic basis of this malformation remains incompletely understood. Results In this study, single SNP- and pathway-based genome-wide association studies (GWASs) were performed using ROADTRIPS and SNP ratio test (SRT), respectively. A total of 48 birds with deformed beaks (case) and 48 normal birds (control) were genotyped using Affymetrix 600 K HD genotyping arrays. As a result, 95 individuals and 429,539 SNPs were obtained after quality control. The P-value was corrected by a Bonferroni adjustment based on linkage disequilibrium pruning. The single SNP-based association study identified one associated SNP with 5% genome-wide significance and seven suggestively associated SNPs. Four high-confidence genes, LOC421892, TDRD3, RET, and STMN1, were identified as the most promising candidate genes underlying this complex trait in view of their positions, functions, and overlaps with previous studies. The pathway-based association study highlighted the association of six pathways with beak deformity, including the calcium signaling pathway. Conclusions Potentially useful candidate genes and pathways for beak deformity were identified, which should be the subject of further functional characterization. Electronic supplementary material The online version of this article (10.1186/s12864-018-4882-8) contains supplementary material, which is available to authorized users.

Marek&rsquo, s disease (MD) is a T cell lymphoma disease induced by Marek&rsquo, s disease virus (MDV), a highly oncogenic &alpha, herpesvirus primarily affecting chickens. MD is a chronic infectious disease that threatens the poultry industry. However, the mechanisms of genetic resistance for MD are complex and not completely understood. In this study, to identify high-confidence candidate genes of MD genetic resistance, high throughput sequencing (RNA-seq) was used to obtain transcriptomic data of CD4+ T cells isolated from MDV-infected and non-infected groups of two reciprocal crosses of individuals mating by two highly inbred chicken lines (63 MD-resistant and 72 MD-susceptible). After RNA-seq analysis with two biological replicates in each group, we identified 61 and 123 single nucleotide polymorphisms (SNPs) (false discovery rate (FDR) &lt, 0.05) annotated in 39 and 132 genes in intercrosses 63 &times, 72 and 72 &times, 63, respectively, which exhibited allele-specific expression (ASE) in response to MDV infection. Similarly, we identified 62 and 79 SNPs annotated in 66 and 96 genes in infected and non-infected groups, respectively. We identified 534 and 1543 differentially expressed genes (DEGs) (FDR &lt, 0.05) related to MDV infection in intercrosses 63 &times, 63, respectively. We also identified 328 and 20 DEGs in infected and non-infected groups, respectively. The qRT-PCR using seven DEGs further verified our results of RNA-seq analysis. The qRT-PCR of 11 important ASE genes was performed for gene functional validation in CD4+ T cells and tumors. Combining the analyses, six genes (MCL1, SLC43A2, PDE3B, ADAM33, BLB1, and DMB2), especially MCL1, were highlighted as the candidate genes with the potential to be involved in MDV infection. Gene-set enrichment analysis revealed that many ASE genes are linked to T cell activation, T cell receptor (TCR), B cell receptor (BCR), ERK/MAPK, and PI3K/AKT-mTOR signaling pathways, which play potentially important roles in MDV infection. Our approach underlines the importance of comprehensive functional studies for gaining valuable biological insight into the genetic factors behind MD and other complex traits, and our findings provide additional insights into the mechanisms of MD and disease resistance breeding in poultry.

This study was conducted to investigate the effects of replacing in-feed antibiotics with synergistic organic acids on growth performance, health, carcass, and immune and oxidative statuses of broiler chickens under Clostridium perfringens (CP) type A challenge. Two organic acid products were tested: organic acid 1 (OA1), consisting of butyrate, medium-chain fatty acids, organic acids, and phenolics; and organic acid 2 (OA2), consisting of buffered short-chain fatty acids. Six hundred 1-day-old male Arbor Acres broiler chicks were randomly assigned to one of five treatments: Control 1, basal diet, nonchallenged birds; Control 2, basal diet, with CP challenge; antimicrobial growth promoters (AGP), basal diet supplemented with Aureomycin (chlortetracycline), with CP challenge; OA1, basal diet supplemented with OA1, with CP challenge; and OA1OA2, basal diet supplemented with OA1 and OA2, with CP challenge. Each treatment had eight replicate pens of 15 birds. The experiments lasted for 29 days. The disease challenge was performed on days 15-17, with an oral gavage of 0.5 mL of CP culture (2.0 × 108 colony-forming units [CFU]/mL) for each bird. Body weights (BWs), intestinal lesion scores, immune organ indices, and serum malondialdehyde (MDA) concentrations were measured on days 19, 22, and 29, respectively, in three birds per pen. Carcass characteristics were determined on day 29. No treatment-related differences in mortality were noted before (P = 0.28) or after (P = 0.64) challenge or over the whole study period (days 0-28; P = 0.66). On day 19, the BW of Control 2 was lower than other treatments (P0.0001). On day 22, AGP, OA1, and OA1OA2 had higher BW than Control 2 (P = 0.001). The breast muscle yield of OA1 and OA1OA2 was higher than AGP (P0.05). The abdominal fat yield of OA1OA2 was lower than AGP and Control 2 (P0.05). On day 22, the birds fed OA1OA2 showed lower intestinal lesion scores than OA1 (P0.05). No treatment-related differences in immune organ (spleen, thymus, and bursa) indices were noted (P0.05). On day 29, the MDA concentration of OA1 and OA1OA2 was lower than those of Control 1 and AGP (P0.05). In conclusion, the addition of organic acids may protect broiler chickens from severe intestinal lesions and oxidative stress and may help reduce abdominal fat mass deposition. There is potential for organic acid-based products as alternatives for AGP in preventing necrotic enteritis in broilers.

Pigeon belongs to altrices. Squab cannot forage independently. Nutrition can only be obtained from crop milk secreted by male and female pigeon. miRNA could regulate many biological events. However, the roles of miRNA and ceRNA in regulating crop milk production are still unknown. In this study, we investigated the miRNAs expression profile of female pigeon crop, explored the potential key genes, and found the regulatory mechanisms of crop milk production. A total of 71 miRNAs were identified differentially expressed significantly. Meanwhile, miR-20b-5p, miR-146b-5p, miR-21-5p, and miR-26b-5p were found to be the key miRNAs regulating lactation. Target genes of these miRNAs participated mainly in cell development, protein and lipid synthesis, and ion signaling processes, such as cell-cell adhesion, epithelial cell morphogenesis, calcium signaling pathway, protein digestion, and absorption. In the ceRNA network, miR-193-5p was located in the central position, and miR-193-5p/CREBRF/LOC110355588, miR-460b-5p/GRHL2/MSTRG.132954, and miR-193-5p/PIK3CD/LOC110355588 regulatory axes were believed to affect lactation. Collectively, our findings enriched the miRNA expression profile of pigeon and provided novel insights into the microRNA-associated-ceRNA networks regulating crop milk production in pigeon.

Sperm motility is used to predict the semen quality and fertilization ability of breeder roosters. Indigenous chicken breeder roosters show variation in sperm motility, but less has been known about its relationship with other reproductive attributes. In this study, 40- to 44-wk-old Beijing-You breeder roosters with the high and low sperm motility phenotypes (n = 15 in each group) were identified and compared, with regard to their semen characteristics, reproductive hormone concentrations, testicular histomorphology, fertility capacity, and genes expression of hematopoietic prostaglandin D synthase (H-PGDS) and wingless-type MMTV integration site family, member 2 (WNT2). The low sperm motility roosters showed lower semen volume (P = 0.003) and sperm viability (P = 0.008). Like semen donors in the artificial insemination test, the low sperm motility roosters showed lower fertility than the high sperm motility roosters (P < 0.001). No difference in the serum concentration of follicle stimulating hormone (FSH, P = 0.347), luteinizing hormone (LH, P = 0.376), or testosterone (T, P = 0.068) was found between the high and low sperm motility roosters. Furthermore, among roosters with similar BW, the low sperm motility roosters had smaller testis mass (P = 0.037), seminiferous tubules diameter (P = 0.031), spermatogenic epithelium height (P = 0.001), and Johnsen score (P = 0.005) than the high sperm motility ones. Finally, the expression of both H-PGDS and WNT2, which are involved in the prostaglandin D2 and WNT signaling pathways, respectively, was low in the testis of the low sperm motility phenotype roosters (P < 0.05). Thus, the findings of the present study indicated that the testis of low sperm motility showed impaired testicular histomorphology as compared to normal; the BW, testis weight, and serum FSH, LH, and T levels are associated with sperm production, but not with sperm motility, and that low expression of H-PGDS and WNT2 may be related with the abnormal testicular morphology of low sperm motility birds which deserves further functional validation studies.

Sperm motility is the most important indicator in evaluating roosters’ fecundity. However, the genetic mechanisms underlying chicken sperm motility is not yet clear. Long non-coding RNA (lncRNA) play epigenetic roles in reproduction. In this study, RNA sequencing was employed to profile the testis transcriptome (lncRNA and mRNA) of six Beijing-you cocks divergent in sperm motility. In total, 2,597 lncRNAs were identified in the chicken testis, including 1,267 lincRNAs, 975 anti-sense lncRNAs, and 355 intronic lncRNAs. They shared similar features with previous studies. Of these lncRNAs, 124 were differentially expressed. Among 17,690 mRNAs detected in this study, 544 were differentially expressed, including a bunch of genes with known functions on sperm motility. GO annotation analysis revealed these genes were involved in ATP binding, cilium assembly, and oxidation-reduction processes. Integrating analysis of lncRNA and mRNA profiles predicted 10 lncRNA-gene pairs, including 8 co-regulated and 2 inversely-regulated pairs. To the best of our knowledge, this is the first genome-wide investigation of the lncRNAs in the chicken testis associated with sperm motility. Our results provided a catalog of chicken testis lncRNAs and genes worthy of further studies to understand their roles in cocks’ reproductive performance regulation.

Background The beak deformity (crossed beaks) was found in some indigenous chickens of China, such as Beijing-You (BJY), Qingyuan Partridge, and Huxu Chickens. Birds with deformed beaks have reduced feed intake and drinking, impeded growth rate, and poor production performance. Beak deformity reduces the economy of poultry industry and affects animal welfare as well. The genetic basis of this malformation remains incompletely understood. LOC426217, also named claw keratin-like, was the most up-regulated gene in the deformed beaks from a previous digital gene expression (DGE) analysis and was selected as an important candidate gene for further analysis. Results In the present study, quantitative real-time PCR (qRT-PCR) was firstly performed to determine the expression pattern of LOC426217 gene in deformed and normal beaks to verify the DGE results. Tissue-specific expression profile of this gene in 14 tissues was also determined using qRT-PCR. The LOC426217 was amplified from the genomic DNA of 171 deformed and 164 normal beaks, and sequenced to detect the single nucleotide polymorphisms (SNPs). The results showed that LOC426217 was significantly high-expressed in the deformed beaks, which was in good agreement with the DGE results. This gene was specifically high-expressed in beaks than other tissues. Eight SNPs were detected in LOC426217: -62G > T, 24 T > C, 36G > C, 192A > T, 204C > T, 222 T > C, 285G > T, and 363 T > C. Genotype frequency of G-62 T, T24C, G36C, T222C, and T363C loci was significant different between deformed and normal beaks. Haplotype analysis revealed one block with SNPs T24C and G36C, and one block with SNPs A192T, C204T, T222C, and G285T in normal birds, while the block with SNPs G36C and A192T in deformed ones. Conclusions It was concluded from these results that the over-expression of LOC426217 in the beak maybe related to the malformation. The polymorphisms of LOC426217 gene were associated with the beak deformity trait where the SNPs of G-62 T, T24C, G36C, T222C, and T363C loci maybe used as markers. The specific haplotype block in deformed birds may be a potential linkage marker for this trait. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0353-x) contains supplementary material, which is available to authorized users.

This paper, the second from a comprehensive study, describes the effects of varying growth rate by feeding at different planes of nutrition with a constant ME:CP ratio on muscle characteristics and meat quality in 2 distinct broiler breeds of male chickens (Arbor Acres, a commercial line; and Beijing-You, a Chinese nonimproved line). Experimental diets, differing on average by 2% CP, were formulated with high-, medium-, or low-nutrient densities for 3 growing phases. Male hatchlings (216 of each breed) were randomly assigned to 6 pens of 12 birds in each treatment. Altered histological characteristics of muscle fibers, early postmortem muscle metabolism, and meat quality were investigated in the pectoralis major and biceps femoris. At their market age, Arbor Acres broilers had significantly higher concentrations of plasma protein and lipid metabolites, ratios of white to red and intermediate fibers, pH, L* and b* values, and lower concentrations of plasma glucose metabolites, muscle-fiber diameter, muscle contents of energy stores, a* value, drip loss, and shear force than the values found for the Beijing-You chickens (P < 0.01). Higher nutrient density increased the size of the muscle fibers, decreased glycogen reserve, and reduced the rate and extent of acidification in the Arbor Acres chickens, while accelerating transformation of red and intermediate-to-white fibers, enhancing energy stores, and hastening the decrease in pH postmortem in the Beijing-You chickens (P < 0.05). In each breed, most meat quality variables (e.g., shear force, drip loss, and color) were consistent with the histological and biochemical changes caused by the feeding strategy. Together, dietary nutrient density can influence meat quality as a result of altered histological and initial energy and metabolic characteristics of the muscle. Many of the responses to diet are breed and tissue dependent in broiler chickens.

TLR signaling plays a role in Salmonella infection, but less information is available in chickens infected with Salmonella serovar Pullorum. The present study with young chickens, experimentally infected with S. Pullorum, has used real-time quantitative RT-PCR to investigate the relative expression of genes of the TLR4 signaling pathway (TLR4, MyD88, TRAF6 and NF-kappaB) in the spleen and caecum at 1, 3, 7 and 14 days post-infection (dpi). Three-day-old specific-pathogen-free chickens were orally infected with S. Pullorum or saline (controls). In addition to gene expression, the bacterial burden of spleen and caecum was assessed and serum concentrations and total IgG were measured. Significantly more bacteria were found in the caecum than in the spleen. Concentrations of IgG were significantly higher in infected birds at 1 dpi, reached a peak at 3 dpi (P

This study has assessed the association of single nucleotide polymorphisms (SNP) identified in the adipocyte fatty acid binding protein (A-FABP) and heart-type fatty acid binding protein (H-FABP) genes with the content of intramuscular fat (IMF) in a population of male Beijing-You chickens. A previously described SNP in the chicken A-FABP gene had a significant (P < 0.05) effect on IMF content. Chickens inheriting the homozygous BB genotype at A-FABP had a significantly higher content of IMF in thigh muscles and breast muscles than did those inheriting the AA and AB genotypes. A novel SNP, identified here, in the H-FABP gene was also significantly (P < 0.05) associated with IMF content in thigh and breast muscle. Chickens inheriting the genotypes of DD and CD had much higher content of IMF than those inheriting the homozygous genotype of CC. Markers at the A-FABP and H-FABP genes were associated with IMF content in the studied population. Chickens inheriting the BB genotype at A-FABP, along with the CD genotype at H-FABP, produced muscles with a much higher content of IMF when compared with all other genotypes. A weak interaction between A-FABP and H-FABP was detected (P < 0.09) for IMF content in the tested population. The statistical significance of interaction is tentative because of the limited number of observations for some genotypic combinations. Markers identified within the A-FABP and H-FABP genes are suitable for future use in identifying chickens with the genetic potential to produce more desirable muscle with higher IMF content, at least in the population of Beijing-You male chickens.

A study was conducted to evaluate the effects of varying nutrient density with constant ME:CP ratio on growing performance, carcass characteristics, and blood responses in 2 distinct broiler breeds of male chickens (Arbor Acres, a commercial line, and Beijing-You, a Chinese nonimproved line). Experimental diets were formulated with high, medium, or low nutrient densities for 3 growing phases. Starter diets (1 to 21 d) contained 23, 21, and 19% CP with 3,059, 2,793, and 2,527 kcal/kg of ME; grower diets (22 to 35 d) contained 21, 19, and 17% CP with 3,150, 2,850, and 2,550 kcal/kg of ME; and finisher diets (36 to 42 d for Arbor Acres and 36 to 91 d for Beijing-You) had 19, 17, and 15% CP with 3,230, 2,890, and 2,550 kcal/kg of ME. Male hatchlings (216 of each breed) were randomly assigned to 6 replicates of 12 birds in each treatment. Arbor Acres broilers had better (P < 0.001) BW gain, feed conversion ratio (FCR), and carcass yield, but had greater (P < 0.001) abdominal and carcass fat deposition. In both breeds, the higher nutrient density increased (P < 0.05) BW gain, protein efficiency ratio, and energy efficiency ratio while decreasing (P < 0.05) feed intake and FCR. The breed differences were increased for FCR, protein efficiency ratio, and energy efficiency ratio in the starter period and decreased for carcass chemical composition, respectively, by higher nutrient density. These findings indicate that 1) genetic improvement has a significant effect on broiler responses to dietary nutrient density, 2) performance differences between breeds are lessened with diets of low nutrient density, 3) carcass quality differences are less when birds were fed diets of high nutrient density, 4) carcass composition is hardly modified by nutrient density and both breeds exhibit similar metabolite responses to dietary concentrations, and 5) optimal diets are deduced for these breeds for the 3 growing phases.

This study examined the association between expression of heart- and adipocyte-fatty acid binding-protein genes (H- and A-FABP) with intramuscular fat percentage (IFP) in two Chinese chicken breeds (Beijingyou [BJY] and Jingxing [JX]). The results showed that age and breed had significant effects on the FABP expression. A-FABP mRNA levels were dramatically higher in BJY than in JX chickens and in males than in females. The results indicate that transcription of H- and A-FABP genes was significantly correlated with IFP in two breeds of chicken.

This study was conducted to estimate genetic parameters of meat quality-related traits by a MTDFREML procedure, using 1,069 purebred Beijing-You full-sib male chickens derived from the first 2 generations of divergent selection for the percentage of intramuscular fat (IMF) and selection for increased inosine-5'-monophosphate content (IMP) in breast meat. The results show that estimated heritability of IMP was moderate (0.23), and heritability of IMF was low (0.11). Other traits with high heritabilities, ranging between 0.56 and 0.79, were BW, abdominal fat weight (AFW), breast meat yield, ratio of breast meat yield to evisceration weight (BMP), leg muscle yield, comb weight, and ratio of comb weight to BW (CWP). Moderate heritabilities for the ratio of AFW to BW (AFP) and leg muscle yield to evisceration weight were estimated, 0.24 and 0.32, respectively. Lower significant phenotypic correlations of IMP with BMP and ratio of leg muscle weight to evisceration weight were discovered (P < 0.05), whereas IMF exhibited slightly positive, though significant, phenotypic correlations with BW (0.11) and AFP (0.27). Genetic correlations of IMP with BW and CWP were negative (-0.38 and -0.62, respectively), whereas a high positive genetic correlation was found between IMP and BMP (0.57). It was found that IMF had high genetic correlations with BW (0.75) and AFW (0.66) and moderate correlations with AFP (0.32) and CWP (0.40). A low positive genetic correlation was estimated between IMP and IMF (0.27). In conclusion, both IMP and IMF contents in chicken meat have the potential to be increased through genetic selection with little or no positive effect on BW. Furthermore, close managerial control of growth rate (and BW) will be needed to assure high quality of chicken meat so that increased IMP and IMF can be obtained with less abdominal fat deposited.

Folate, an essential vitamin participating in 1-carbon metabolism leading to a methyl donor function, is a key factor inducing epigenetic changes. This study sought to determine if folate influences the methylation level of cytosine-guanine (CpG) islands in the promoters of critical adipogenic genes in chickens, and how this might affect gene expression and differentiation of preadipocytes in vitro. Preadipocytes were treated with 0 to 16 mg/L of folate during the induction of differentiation, and cell proliferation and lipid accumulation were assessed. The folate supplementation resulted in enhanced cell proliferation and decreased content of lipid per adipocyte at d 6 of differentiation. The effects of folate on relative expression of genes critical for adipocyte differentiation and 1-carbon metabolism were measured by quantitative reverse-transcription PCR. Folate caused a dose-dependent decrease in transcript abundance of peroxisome proliferator-activated receptor γ (PPARγ), CCAAT/enhancer-binding protein α (C/EBPα) gene expression, and the downstream enzyme fatty acid synthase; in contrast, expression of DNA (cytosine-5)-methyltransferase and methylenetetrahydrofolate reductase was obviously upregulated at d 6 of differentiation (P < 0.05). The DNA methylation was examined with the bisulfite sequencing PCR method. Overall CpG methylation in the C/EBPα gene promoter region was 21.8% lower (P < 0.05) and the gene's expression was 2.7-fold higher in the absence of folate, compared with cells treated with 16 mg/L of folate, whereas methylation of the PPARγ promoter was not affected. Overall, the results show that folate increased the proliferation of adipocytes but reduced per-cell lipid accumulation, thereby influencing differentiation; it increased expression of genes involved in 1-carbon metabolism resulting in greater methylation of the C/EBPα promoter during differentiation and decreased that gene's expression, perhaps accounting for decreased expression of PPARγ.

Frequencies of up to 3% of beak deformity (normally a crossed beak) occur in some indigenous chickens in China, such as and Beijing-You. Chickens with deformed beaks have reduced feed intake, growth rate, and abnormal behaviors. Beak deformity represents an economic as well as an animal welfare problem in the poultry industry. Because the genetic basis of beak deformity remains incompletely understood, the present study sought to identify important genes and metabolic pathways involved in this phenotype. Digital gene expression analysis was performed on deformed and normal beaks collected from Beijing-You chickens to detect global gene expression differences. A total of >11 million cDNA tags were sequenced, and 5,864,499 and 5,648,877 clean tags were obtained in the libraries of deformed and normal beaks, respectively. In total, 1,156 differentially expressed genes (DEG) were identified in the deformed beak with 409 being up-regulated and 747 down-regulated in the deformed beaks. qRT-PCR using eight genes was performed to verify the results of DGE profiling. Gene ontology (GO) analysis highlighted that genes of the keratin family on GGA25 were abundant among the DEGs. Pathway analysis showed that many DEGs were linked to the biosynthesis of unsaturated fatty acids and glycerolipid metabolism. Combining the analyses, 11 genes (MUC, LOC426217, BMP4, ACAA1, LPL, ALDH7A1, GLA, RETSAT, SDR16C5, WWOX, and MOGAT1) were highlighted as potential candidate genes for beak deformity in chickens. Some of these genes have been identified previously, while others have unknown function with respect to thus phenotype. To the best of our knowledge, this is the first genome-wide study to investigate the transcriptome differences in the deformed and normal beaks of chickens. The DEGs identified here are worthy of further functional characterization.

By estimating the genetic parameters of various semen quality traits in Beijing-You chickens, this study aims to elucidate the inheritance patterns of these traits and the correlations between them to facilitate setting up appropriate breeding strategies for enhanced semen quality. Semen samples were collected from 518 Beijing-You roosters at 43 wk of age from 3 selection lines related to meat flavor traits. Seven semen quality traits, consisting of semen volume, pH, and color, and sperm viability, motility, percent deformity, and concentration, were determined. Sizeable variations (18-24% CV) were observed for all traits, except for semen pH. The effects of semen collection time and origin of the chickens (line) were analyzed to optimize the proper models for estimating genetic parameters for each trait. The multiple-trait derivative-free restricted maximum likelihood method was used for estimating variance components. The results revealed that sperm viability, motility, and percent deformity exhibited high heritabilities (h(2) = 0.52, 0.85, and 0.60, respectively). Semen volume, semen color, and sperm concentration had moderate heritabilities (h(2) = 0.28, 0.19, and 0.12, respectively). Semen pH showed low heritability (h(2) = 0.03). Genetic and phenotypic correlations between sperm motility and viability were positive and high (rA = 0.88 and rP = 0.59). In addition, these 2 traits were genetically negatively correlated with percent deformity. This implied the possibility of reducing sperm deformity, which is difficult to measure, by indirect selection. It is concluded from this study that semen quality can be improved by selection. The traits with high variations and heritabilities such as semen volume are promising traits for selection to improve semen quality and likely reproductive performance of native chicken breeds.

Intramuscular fat (IMF) is a crucial factor for the meat quality of chickens. With the aim of studying the molecular mechanisms underlying IMF deposition in chickens, the expression profiles of five candidate transcription factors involved in lipid metabolism in several tissues were examined in Beijing-You (BJY) chickens at five ages (0, 4, 8, 14 and 20 wk). Results showed that accumulation of IMF in breast (IMFbr), thigh (IMFth) and abdominal fat weight increased significantly (P

The associations between polymorphisms of five genes, calpain 1 (CAPN1), follicle stimulating hormone beta (FSHB), follicle stimulating hormone receptor (FSHR), peroxisome proliferator-activated receptor gamma (PPARG), and retinol binding protein 7 (RBP7), and live weight, carcass composition, and meat-quality traits were estimated from two meat-type chickens lines (n=311). Except for the variants of the FSHR gene, 11 SNPs of the other four genes and two diplotypes of PPARG were associated with one or more traits excluding shear factor (SF). SNP C31566680T of the CAPN1 gene was significantly associated with live weight (LW) carcass traits. The SNP A4580859C of FSHB gene was significantly associated with breast muscle weight (BrW) and LW. One of the PPARG SNPs, C5070948T, was associated with intramuscular fat content in breast (IMFbr). Diplotype P1 of the PPARG gene was significantly associated with LW and all carcass traits. P3 were significantly associated with abdominal fat weight (AbFW). SNPs in RBP7 were only associated with BrW. These results indicate that the four genes were associated with these traits and have promise as genetic markers for future marker-assisted selection. Supplementary materials for this paper are available online.

Body composition and meat quality traits are important economic traits of chickens. The development of high-throughput genotyping platforms and relevant statistical methods have enabled genome-wide association studies in chickens. In order to identify molecular markers and candidate genes associated with body composition and meat quality traits, genome-wide association studies were conducted using the Illumina 60 K SNP Beadchip to genotype 724 Beijing-You chickens. For each bird, a total of 16 traits were measured, including carcass weight (CW), eviscerated weight (EW), dressing percentage, breast muscle weight (BrW) and percentage (BrP), thigh muscle weight and percentage, abdominal fat weight and percentage, dry matter and intramuscular fat contents of breast and thigh muscle, ultimate pH, and shear force of the pectoralis major muscle at 100 d of age. The SNPs that were significantly associated with the phenotypic traits were identified using both simple (GLM) and compressed mixed linear (MLM) models. For nine of ten body composition traits studied, SNPs showing genome wide significance (P

Transcripts and protein for follicle-stimulating hormone receptor (FSHR) were demonstrated in abdominal adipose tissue of female chickens. There was no expression of the Fsh gene, but FSH and FSHR colocalized, suggesting that FSH was receptor bound. Partial correlations indicted that changes in abdominal fat (AF) content were most directly correlated with Fshr mRNA expression, and the latter was directly correlated with tissue FSH content. These relationships were consistent with FSH inducing Fshr mRNA expression and with the finding that FSH influenced the accumulation of AF in chickens, a novel role for the hormone. Chicken preadipocytes responded linearly to doubling concentrations of FSH in Fshr mRNA expression and quantities of FSHR and lipid, without discernable effect on proliferation. Cells exposed to FSH more rapidly acquired adipocyte morphology. Treatment of young chickens with chicken FSH (4 mIU/day, subcutaneous, days 7–13) did not significantly decrease live weight but increased AF weight by 54.61%, AF as a percentage of live weight by 55.45%, and FSHR transcripts in AF by 222.15% (2 h after injection). In cells stimulated by FSH, genes related to lipid metabolism, including Rdh10, Dci, RarB, Lpl, Acsl3, and Dgat2, were expressed differentially, compared with no FSH. Several pathways of retinal and fatty acid metabolism, and peroxisome proliferator-activated receptor (PPAR) signaling changed. In conclusion, FSH stimulates lipid biosynthesis by upregulating Fshr mRNA expression in abdominal adipose tissue of chickens. Several genes involved in fatty acid and retinal metabolism and the PPAR signaling pathway mediate this novel function of FSH.

Toll-like receptors (TLRs) signaling pathways are the first lines in defense against Salmonella enteritidis (S. enteritidis) infection but the molecular mechanism underlying susceptibility to S. enteritidis infection in chicken remains unclear. SPF chickens injected with S. enteritidis were partitioned into two groups, one consisted of those from Salmonella-susceptible chickens (died within 5 d after injection, n = 6), the other consisted of six Salmonella-resistant chickens that survived for 15 d after injection. The present study shows that the bacterial load in susceptible chickens was significantly higher than that in resistant chickens and TLR4, TLR2-1 and TLR21 expression was strongly diminished in the leukocytes of susceptible chickens compared with those of resistant chickens. The induction of expression of pro-inflammatory cytokine genes, IL-6 and IFN-β, was greatly enhanced in the resistant but not in susceptible chickens. Contrasting with the reduced expression of TLR genes, those of the zinc finger protein 493 (ZNF493) gene and Toll-interacting protein (TOLLIP) gene were enhanced in the susceptible chickens. Finally, the expression of TLR4 in peripheral blood mononuclear cells (PBMCs) infected in vitro with S. enteritidis increased significantly as a result of treatment with 5-Aza-2-deoxycytidine (5-Aza-dc) while either 5-Aza-dc or trichostatin A was effective in up-regulating the expression of TLR21 and TLR2-1. DNA methylation, in the predicted promoter region of TLR4 and TLR21 genes, and an exonic CpG island of the TLR2-1 gene was significantly higher in the susceptible chickens than in resistant chickens. Taken together, the results demonstrate that ZNF493-related epigenetic modification in leukocytes probably accounts for increased susceptibility to S. enteritidis in chickens by diminishing the expression and response of TLR4, TLR21 and TLR2-1.

On the basis of meat quality traits, muscle fiber characteristics, and nutrient components and contents in chickens at market age, 120-d-old Beijing-you (BJY) chickens (the Chinese local breed) had distinct breast muscle features when compared with 42-d-old Arbor Acres (AA) chickens (the genetically improved broiler line). The phospholipid (P0.05) and essential fatty acid (P0.05) contents in BJY chickens were significantly higher than those in AA chickens. No differences (P0.05) were found between the breeds in the contents of polyunsaturated fatty acids, unsaturated fatty acids, protein, or amino acids. Breast muscle fiber diameter was significantly smaller (~55.76%) and fiber density was higher (~174.86%) in BJY chickens than in AA chickens (P0.05). In this study, breast muscle from 120-d-old BJY chickens was judged to have better quality of phospholipids and essential fatty acid contents and muscle fiber characteristics than breast muscle from 42-d-old AA chickens.

The 3-hydroxyl-3-methylglutaryl Coenzyme A reductase (HMGCR) gene was examined for polymorphisms in Beijing-you chickens. A "T" base insert was detected at nucleotide 2749 of the 3-UTR region of the HMGCR gene and was used as the basis for distinguishing a B allele, distinct from the A. Serum and muscle contents of total cholesterol. LDL-cholesterol in serum was significantly lower in AB birds and lowest in BB birds. Real-time PCR showed that the same trends across genotypes occurred in an abundance of HMGCR transcripts in liver, but there was no difference in contents of HMGCR mRNA in breast or thigh muscles. Hepatic expression and serum LDL-cholesterol were meaningfully correlated (partial, with total serum cholesterol held constant, r = 0.923). In muscle, similar genotypic differences were found for the abundance of the LDL receptor (LDLR) transcript. Cholesterol content in breast muscle related to LDLR expression (partial correlation with serum LDL-cholesterol held constant, r = 0.719); the equivalent partial correlation in thigh muscle was not significant. The results indicated that the B allele significantly reduces hepatic abundance of HMGCR transcripts, probably accounting for genotypic differences in serum cholesterol. In muscle, the cholesterol content appeared to reflect differences in LDLR expression with apparent mechanistic differences between breast and thigh.

Background Intramuscular fat (IMF) is one of the important factors influencing meat quality, however, for chickens, the molecular regulatory mechanisms underlying this trait have not yet been determined. In this study, a systematic identification of candidate genes and new pathways related to IMF deposition in chicken breast tissue has been made using gene expression profiles of two distinct breeds: Beijing-you (BJY), a slow-growing Chinese breed possessing high meat quality and Arbor Acres (AA), a commercial fast-growing broiler line. Results Agilent cDNA microarray analyses were conducted to determine gene expression profiles of breast muscle sampled at different developmental stages of BJY and AA chickens. Relative to d 1 when there is no detectable IMF, breast muscle at d 21, d 42, d 90 and d 120 (only for BJY) contained 1310 differentially expressed genes (DEGs) in BJY and 1080 DEGs in AA. Of these, 34–70 DEGs related to lipid metabolism or muscle development processes were examined further in each breed based on Gene Ontology (GO) analysis. The expression of several DEGs was correlated, positively or negatively, with the changing patterns of lipid content or breast weight across the ages sampled, indicating that those genes may play key roles in these developmental processes. In addition, based on KEGG pathway analysis of DEGs in both BJY and AA chickens, it was found that in addition to pathways affecting lipid metabolism (pathways for MAPK & PPAR signaling), cell junction-related pathways (tight junction, ECM-receptor interaction, focal adhesion, regulation of actin cytoskeleton), which play a prominent role in maintaining the integrity of tissues, could contribute to the IMF deposition. Conclusion The results of this study identified potential candidate genes associated with chicken IMF deposition and imply that IMF deposition in chicken breast muscle is regulated and mediated not only by genes and pathways related to lipid metabolism and muscle development, but also by others involved in cell junctions. These findings establish the groundwork and provide new clues for deciphering the molecular mechanisms underlying IMF deposition in poultry. Further studies at the translational and posttranslational level are now required to validate the genes and pathways identified here.