Chicken Lines Research Articles

MicroRNA gga-miR-10a-mediated transcriptional regulation of the immune genes in necrotic enteritis afflicted chickens

miRNAs are involved in both adaptive and innate immune systems of host animals; and play important roles in many immune-related pathways. The systemic biological roles of gga-miR-10a-5p chicken microRNA on immune response were investigated in two necrotic enteritis (NE) induced chicken lines, Marek's disease (MD) resistant (line 6.3) and susceptible (line 7.2). We determined the expression patterns of gga-miR-10a in the intestinal mucosal layer of chickens upon NE induction, and identified the target genes (MyD88, and SKP1) related to the host immune response to pathogens. We found that gga-miR-10a expression in the intestinal mucosal layer of MD-resistant chicken line 6.3 gga-miR-10a was significantly down-regulated (p < 0.01) during NE. Overexpression analysis of gga-miR-10a and reporter gene analysis using a wild- or mutant-type MyD88 3′ untranslated region (3′ UTR)-luciferase construct in chicken macrophage cell line HD11 and chicken fibroblast cell line OU2 showed that gga-miR-10a acted as a direct translational repressor of MyD88 by targeting the 3′ UTR of this gene. Furthermore, miR-10a indirectly negatively influenced the expression of signaling molecules related to the MyD88-dependent pathway, including TRAF6, TAK1, and NF-κB1 at both transcriptional and translational levels. Downstream of the MyD88-dependent pathway, several proinflammatory cytokines such as IL-1β, IFN-γ, IL-12p40, TNFSF15, and LITAF were down-regulated by overexpression of gga-miR-10a. These results suggest that gga-miR-10a is an important regulator of the Toll-like receptor signaling pathway. The findings of this study improve our understanding of the biological functions of miR-10a and the mechanisms underlying the TLR signaling pathway upon NE afflicted chickens, as well improving the overall understanding of the immune system function in domestic animals.

The Novel Avian Leukosis Virus Subgroup K Shares Its Cellular Receptor with Subgroup A.

Avian leukosis virus subgroup K (ALV-K) is composed of newly emerging isolates, which, in sequence analyses, cluster separately from the well-characterized subgroups A, B, C, D, E, and J. However, it remains unclear whether ALV-K represents an independent ALV subgroup with regard to receptor usage, host range, and superinfection interference. In the present study, we examined the host range of the Chinese infectious isolate JS11C1, an ALV-K prototype, and we found substantial overlap of species that were either resistant or susceptible to ALV-A and JS11C1. Ectopic expression of the chicken tva gene in mammalian cells conferred susceptibility to JS11C1, while genetic ablation of the tva gene rendered chicken DF-1 cells resistant to infection by JS11C1. Thus, tva expression is both sufficient and necessary for JS11C1 entry. Receptor sharing was also manifested in superinfection interference, with preinfection of cells with ALV-A, but not ALV-B or ALV-J, blocking subsequent JS11C1 infection. Finally, direct binding of JS11C1 and Tva was demonstrated by preincubation of the virus with soluble Tva, which substantially decreased viral infectivity in susceptible chicken cells. Collectively, these findings indicate that JS11C1 represents a new and bona fide ALV subgroup that utilizes Tva for cell entry and binds to a site other than that for ALV-A.IMPORTANCE ALV consists of several subgroups that are particularly characterized by their receptor usage, which subsequently dictates the host range and tropism of the virus. A few newly emerging and highly pathogenic Chinese ALV strains have recently been suggested to be an independent subgroup, ALV-K, based solely on their genomic sequences. Here, we performed a series of experiments with the ALV-K strain JS11C1, which showed its dependence on the Tva cell surface receptor. Due to the sharing of this receptor with ALV-A, both subgroups were able to interfere with superinfection. Because ALV-K could become an important pathogen and a significant threat to the poultry industry in Asia, the identification of a specific receptor could help in the breeding of resistant chicken lines with receptor variants with decreased susceptibility to the virus.

Transfer of natural auto-antibodies via egg yolk in chickens divergently selected for natural antibodies binding keyhole limpet hemocyanin

Barcodes of natural auto-antibody (NAAb) profiles based on staining intensity of isotypes binding numbers of self-(tissue) antigen fragments were suggested as parameters for immune diversity, and related to genetic background and health status in man, rodents and poultry. Here, hens, eggs and hatchlings from chicken lines divergently selected and bred for high (H line) or low (L line) total natural antibodies (NAb) levels in plasma binding keyhole limpet hemocyanin (KLH) at 16 weeks of age were tested for their NAAb repertoire binding chicken liver homogenate (CLH) fragments using quantitative Western immunoblotting. The aims of this study were 1. to detect line differences between the H and L line adult hens, eggs and hatchlings for the IgM and IgG isotypes binding CLH fragments, 2. study the presence of NAAb of both isotypes in yolk and albumen, as well as in hatchlings to detect a maternal NAAb transfer route via the egg to the hatchling, and 3. study whether new self-antigen binding isotypes and idiotypes are present in the hatchling.NAAb binding CLH fragments were found in plasma of adult hens (both IgM and IgG), in yolk (IgG only), and hatchlings (mostly IgG, but low levels of IgM). Auto-profiles of IgM showed homogeneity, while IgG profiles were heterogenic between individual hens and individual hatchlings. Significant higher levels as indicated by staining intensity and number of stained CLH fragments were found in plasma of hens genetically selected for high levels of NAb binding KLH. Lines could be clustered based on their auto-profiles indicating that profiles of self-binding IgM and IgG antibodies are genetically based. Visual comparison, clustering and correlation of hens and their hatchlings showed similarities for the IgG, but not the IgM isotype, indicating maternal transfer of IgG NAAb via the yolk. The IgM profile in the hatchlings on the other hand might represent neonatal self-binding antibody formation. As a consequence, hatchlings initially depend for self-binding antibodies on maternal IgG provision during early life.

Differential immune response to Eimeria maxima infection in fast‐ and slow‐growing broiler genotypes

Very little has been reported comparing resistance to coccidiosis in fast or slow growing broilers, the latter of which are becoming more prevalent in the broiler industry. We examined mRNA expression in the intestines of fast and slow growing broilers following Eimeria infection. We show that by day 13 post-infection (d pi) with 2500 or 7000 oocysts of Eimeria maxima, slower-growing (Ranger Classic) broilers significantly (P<0.01) upregulated expression of proinflammatory cyclooxygenase genes (LTB4DH, PTSG1 and PTSG2) above that detected in fast growing (Ross 308) broilers. Expression of CD8α mRNA was downregulated in Ross 308 at day 6d pi with either 2500 or 7000 oocysts of Emaxima (P<0.05), compared to uninfected controls, but was not differentially expressed in Ranger Classic. CD4 genes were not differentially expressed in either chicken line infected with either infectious oocyst dose at d6 pi, compared to uninfected controls. However, at d13 pi, CD4 expression was significantly upregulated in both chicken lines infected with either infectious oocystdose, compared to uninfected controls (P<0.05) but this was significantly greater in Ranger Classic broilers compared to Ross 308 (P<0.05). At d13 pi, expression of CD3 chains (required for T lymphocyte activation) was significantly increased in Ranger Classic compared to Ross 308, infected with either oocyst dose (P<0.05-0.01). Expression of IL-2 and IL-15 mRNA, required for T lymphocyte proliferation was also significantly upregulated, or maintained longer, in Ranger Classic broilers compared to Ross 308. These differences in immune response to Emaxima corresponded with a reduction in Emaxima genome detected in the intestines of Ranger Classic compared to Ross 308.

Bone parameters and organ morphometry of two broiler chicken lines exposed to heat for different periods

The objective of this study was to evaluate the effects of different times of exposure to heat on bone parameters and organ morphometry of Cobb Slow® and Hubbard Flex® broilers exposed to high temperatures for 1, 2 or 3 h daily, from 14 days of age. A total of 1120 one-day-old male chicks (half of each line; average weight of 44 g) were housed into 32 cages with 35 birds each, in a randomized-block experimental design. From the first to the 13th day of age, the birds remained under the thermal conditions recommended for their lines; thereafter, from the 14th day, the shed was separated into four parallel sections of 5.60 × 10.20 × 2.8 m delimited by double-sided plastic curtains along the width of the shed. Cyclic heat stress was generated by average temperatures of 36 ºC from 14-20 days, 35 °C from 21-27 days, 34 °C from 28-34 days and 33 °C from 35-42 days. The total length, width, density and mineral matter of the tibia; the size of the duodenum, jejunum and ileum; and the weights of the bursa of Fabricius and spleen were measured. No interaction effect between thermal environment and line was observed. Heat stress for up to 3 h daily, from the 14th to the 41st day of age, led to a longer but narrower tibia. There was no influence on small intestine morphometry. The Hubbard line presented longer and wider tibiae as well as higher relative and absolute weights of the bursa. In conclusion, heat stress from 2 h daily modifies the structure of the tibia in broilers, which increases in length and reduces in width, but heat exposure has no influence on the small intestine or lymphoid organs. The Hubbard line shows better tibia development than the Cobb line as well as different primary lymphoid responses, represented by a heavier bursa.

DNA methylation of the PLIN1 promoter downregulates expression in chicken lines.

Evidence suggests that Perilipin-1 (PLIN1) is subject to functional regulation by epigenetic modifications in women with obesity. However, whether chicken PLIN1 expression is regulated by DNA methylation is unknown. Here, Sequenom MassARRAY and real-time polymerase chain reaction (PCR) were conducted to analyze the promoter methylation status and expression of the PLIN1 gene in Northeast Agricultural University broiler lines divergently selected for abdominal fat content. We found that chicken PLIN1 expression was significantly higher in adipose tissue of fat-line broilers than in lean lines at 1–7 weeks of age, and was significantly positively correlated with abdominal fat percentage (AFP) in chicken adipose development (Pearson's , ). The region analyzed for DNA methylation was from to bp upstream of the translation start codon ATG, and had five CpG sites, where only the DNA methylation levels of CpG5 located at position bp were significantly higher in lean compared to fat chickens at 5 and 6 weeks () and were significantly negatively correlated with PLIN1 mRNA levels and AFP (). These results shed new light on the regulation of hypertrophic growth in chicken adipose development.

Domestication of Campylobacter jejuni NCTC 11168.

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterized isolates among laboratories has run in parallel with research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C . jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates, identified previously to have aberrant phenotypes, varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37 °C, invasion of chicken and human cell lines, and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. This article contains data hosted by Microreact.

Genomic Analysis Reveals Pleiotropic Alleles at EDN3 and BMP7 Involved in Chicken Comb Color and Egg Production.

Artificial selection is often associated with numerous changes in seemingly unrelated phenotypic traits. The genetic mechanisms of correlated phenotypes probably involve pleiotropy or linkage of genes related to such phenotypes. Dongxiang blue-shelled chicken, an indigenous chicken breed of China, has segregated significantly for the dermal hyperpigmentation phenotype. Two lines of the chicken have been divergently selected with respect to comb color for over 20 generations. The red comb line chicken produces significantly higher number of eggs than the dark comb line chicken. The objective of this study was to explore potential mechanisms involved in the relationship between comb color and egg production among chickens. Based on the genome-wide association study results, we identified a genomic region on chromosome 20 involving EDN3 and BMP7, which is associated with hyperpigmentation of chicken comb. Further analyses by selection signatures in the two divergent lines revealed that several candidate genes, including EDN3, BMP7, BPIFB3, and PCK1, closely located on chromosome 20 are involved in the development of neural crest cell and reproductive system. The two genes EDN3 and BMP7 have known roles in regulating both ovarian function and melanogenesis, indicating the pleiotropic effect on hyperpigmentation and egg production in blue-shelled chickens. Association analysis for egg production confirmed the pleiotropic effect of selected loci identified by selection signatures. The study provides insights into phenotypic evolution due to genetic variation across the genome. The information might be useful in the current breeding efforts to develop improved breeds for egg production.

Marek's Disease Virus Infection Induced Mitochondria Changes in Chickens.

Mitochondria are crucial cellular organelles in eukaryotes and participate in many cell processes including immune response, growth development, and tumorigenesis. Marek’s disease (MD), caused by an avian alpha-herpesvirus Marek’s disease virus (MDV), is characterized with lymphomas and immunosuppression. In this research, we hypothesize that mitochondria may play roles in response to MDV infection. To test it, mitochondrial DNA (mtDNA) abundance and gene expression in immune organs were examined in two well-defined and highly inbred lines of chickens, the MD-susceptible line 72 and the MD-resistant line 63. We found that mitochondrial DNA contents decreased significantly at the transformation phase in spleen of the MD-susceptible line 72 birds in contrast to the MD-resistant line 63. The mtDNA-genes and the nucleus-genes relevant to mtDNA maintenance and transcription, however, were significantly up-regulated. Interestingly, we found that POLG2 might play a potential role that led to the imbalance of mtDNA copy number and gene expression alteration. MDV infection induced imbalance of mitochondrial contents and gene expression, demonstrating the indispensability of mitochondria in virus-induced cell transformation and subsequent lymphoma formation, such as MD development in chicken. This is the first report on relationship between virus infection and mitochondria in chicken, which provides important insights into the understanding on pathogenesis and tumorigenesis due to viral infection.

The Role of Tryptophan-Kynurenine in Feather Pecking in Domestic Chicken Lines.

Research into the role of tryptophan (TRP) breakdown away from the serotonergic to the kynurenine (KYN) pathway by stimulating the brain-endocrine-immune axis system interaction has brought new insight into potential etiologies of certain human behavioral and mental disorders. TRP is involved in inappropriate social interactions, such as feather-destructive pecking behavior (FP) in birds selected for egg laying. Therefore, our goal was to determine the effect of social disruption stress on FP and the metabolism of the amino acids TRP, phenylalanine (PHE), tyrosine (TYR), their relevant ratios, and on large neutral amino acids which are competitors with regard to their transport across the blood-brain barriers, at least in the human system, in adolescent birds selected for and against FP behavior. We used 160 laying hens selected for high (HFP) or low (LFP) FP activity and an unselected control line (UC). Ten pens with 16 individuals each (4 HFP birds; 3 LFP birds; 9 UC birds) were used. At 16 weeks of age, we disrupted the groups twice in 5 pens by mixing individuals with unfamiliar birds to induce social stress. Blood plasma was collected before and after social disruption treatments, to measure amino acid concentrations. Birds FP behavior was recorded before and after social disruption treatments. HFP birds performed significantly more FP and had lower KYN/TRP ratios. We detected significantly higher FP activity and significantly lower plasma PHE/TYR ratios and a trend to lower KYN/TRP ratios in socially disrupted compared to control pens. This might indicate that activating insults for TRP catabolism along the KYN axis in laying hens differs compared to humans and points toward the need for a more detailed analysis of regulatory mechanisms to understand the role of TRP metabolism for laying hen immune system and brain function.

Effects of Elevated Grids on Growing Male Chickens Differing in Growth Performance

Pullets, i. e., chickens of layer lines are often raised in housings equipped with perches. In contrast, broiler chickens most often are raised in a barren environment that lacks any three-dimensional structures, even though broilers also are motivated to use elevated structures. In addition, environmental enrichment may improve welfare problems in broiler chickens, such as skeletal disorders or contact dermatitis. Due to ethical reasons, currently there are attempts to fatten the male chickens of layer strains or to use dual purpose strains. However, there is only limited knowledge on the behavior of these chickens until now. The aim of this study was to test the use of elevated grids and their effect on animal-based indicators (e.g., physical condition). In two successive trials, we kept a total of 1,217 male chickens from three strains (Lohmann Dual, Lohmann Brown Plus, Ross 308) that show differences in growth performance in 24 pens (two trials × three strains × eight pens). In half of the pens, grids were offered at three different heights (enriched groups); in the other half of the pens, no elevated structures were installed (control groups). We recorded the number of birds using the grids at the different heights as well as locomotor activity, walking ability, plumage cleanliness, and the footpad health of chickens. Chickens with low and medium growth performance preferred the highest grids during both the light and dark periods. In contrast, fast-growing chickens used the lowest grid more frequently. Fast-growing chickens kept in the enriched pens tended to have a higher level of locomotor activity and reduced chest cleanliness. Chickens from the medium growth performance strain showed better walking ability when kept in the enriched pens. Enrichment did not affect any of the welfare measures in the slow-growing chickens. These findings suggest that elevated structures may improve chicken welfare, particularly for medium growing chickens. For fast-growing chickens we found evidence for an improvement of animal-based indicators although they used the elevated structures less. However, regardless of growth performance, elevated grids offer the birds an opportunity to rest in a species-specific manner.

Immune responses upon in ovo HVT-IBD vaccination vary between different chicken lines

The genotype of chickens is assumed to be associated with variable immune responses. In this study a modern, moderate performing dual-purpose chicken line (DT) was compared with a high-performing layer-type (LT) as well as a broiler-type (BT) chicken line. One group of each genotype was vaccinated in ovo with a recombinant herpesvirus of turkeys expressing the virus protein VP2 of the infectious bursal disease virus (HVT-IBD) while one group of each genotype was left HVT-IBD unvaccinated (control group). Genotype associated differences in innate and adapted immune responses between the groups were determined over five weeks post hatch. HVT-IBD vaccination significantly enhanced humoral immune responses against subsequently applied live vaccines compared to non-HVT-IBD vaccinated groups at some of the investigated time points (P < 0.05). In addition HVT-IBD vaccination had depending on the genotype a significant impact on splenic macrophage as well as bursal CD4+ T-cell numbers (P < 0.05). On the other hand, the detectable genotype influence on Interferon (IFN) γ and nitric oxide (NO) release of ex vivo stimulated spleen cells was independent of HVT-IBD vaccination. The results of our study suggest considering a genotype specific vaccination regime in the field.

Innate Immune Genes Associated With Newcastle Disease Virus Load in Chick Embryos From Inbred and Outbred Lines.

Newcastle disease virus (NDV) causes substantial economic losses to smallholder farmers in low- and middle-income countries with high levels of morbidity and mortality in poultry flocks. Previous investigations have suggested differing levels of susceptibility to NDV between specific inbred lines and amongst breeds of chickens, however, the mechanisms contributing to this remain poorly understood. Studies have shown that some of these differences in levels of susceptibility to NDV infection may be accounted for by variability in the innate immune response amongst various breeds of poultry to NDV infection. Recent studies, in inbred Fayoumi and Leghorn lines, uncovered conserved, breed-dependent, and subline-dependent responses. To better understand the role of innate immune genes in engendering a protective immune response, we assessed the transcriptional responses to NDV of three highly outbred Tanzanian local chicken ecotypes, the Kuchi, the Morogoro Medium, and the Ching’wekwe. Hierarchical clustering and principal coordinate analysis of the gene expression profiles of 21-day old chick embryos infected with NDV clustered in an ecotype-dependent manner and was consistent with the relative viral loads for each of the three ecotypes. The Kuchi and Morogoro Medium exhibit significantly higher viral loads than the Ching’wekwe. The results show that the outbred ecotypes with increased levels of expression of CCL4, NOS2, and SOCS1 also had higher viral loads. The higher expression of SOCS1 is inconsistent with the expression in inbred lines. These differences may uncover new mechanisms or pathways in these populations that may have otherwise been overlooked when examining the response in highly inbred lines. Taken together, our findings provide insights on the specific conserved and differentially expressed innate immune-related genes involved the response of highly outbred chicken lines to NDV. This also suggests that several of the specific innate immunity related genes identified in the current investigation may serve as markers for the selection of chickens with reduced susceptibility to NDV.

RNA-seq analysis of viral gene expression in the skin of Marek’s disease virus infected chickens

Marek’s disease virus (MDV), a highly cell-associated oncogenic avian α-herpesvirus, is the causative agent of malignant transformation of T cells in domestic chickens. The latently infected CD4+CD8− T cells carry the virus through the blood stream and establish lymphomas in the skin, visceral organs and peripheral nerves. The feather follicle epithelium (FFE) is the only anatomical site where fully infectious enveloped virions are produced and eventually disseminated into the environment to infect contact birds. Therefore, skin and FFE play a critical role as being the common source of re-infection of birds sharing the same habitat. The molecular mechanism involved in the replication and assembly of MDV in the FFE leading to the production and release of cell-free infectious virus particles is unknown and to date no viral or host gene has been implicated in the process. To examine alterations in the expression pattern of viral genes, we performed RNA-seq on the skin samples of Marek’s disease virus-infected susceptible chickens at 10, 20, and 30 days post infection. For comparative analysis of the expression patterns of viral genes between the skin and spleen of the MD-susceptible and resistant lines, Real-Time RT-PCR was employed. In total, RNA-seq based analysis identified 42 viral genes that were differentially expressed in the skin of infected birds. Majority of the identified genes are involved in DNA replication, capsid, tegument, and envelop formation. Comparative analysis between the skin and spleen of MD-susceptible and resistant chicken lines, revealed significantly higher expression of the genes in the skin of either lines than the spleen. Furthermore, much higher expression of the genes was observed in the skin of the susceptible line than the resistant line.

Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing.

Simple SummaryImmunoglobulin Y (IgY) is the major antibody produced by hens and it endows their offspring with effective humoral immunity against the pathogens. In previous research, we identified 13 genomic regions that were significantly associated with the serum IgY level or antibody responses to sheep red-blood-cells, but the specific mutations in these regions have not been reported. Therefore, we screened for variations in these regions in White Leghorn and Beijing-You chickens with high and low IgY. Our study identified 35,154 mutations and 829 Indels which were associated with IgY levels in both lines. Many non-synonymous mutations were located in crucial genes related to the host immune function, indicating the possible involvement of these genes in controlling IgY levels.Based on the results of our previous genome-wide association study (GWAS), a comprehensive analysis on single nucleotide polymorphisms (SNPs) was performed on White Leghorn and Beijing-You chickens with high and low IgY levels in defined genomic regions using the capture-sequencing approach. High and low IgY chickens showed substantial genetic variations. In total, more than 30,000 SNPs were found in all four chicken groups, among which 1045 were non-synonymous mutations resulting in amino acids alterations. In total, 23,309 Indels were identified. Among the 1169 Indels that were found only in Beijing-You chickens, 702 were shared between high and low IgY chickens compared with the reference genome. There were 1016 Indels specific to the White Leghorn chickens, among which 188 were high IgY-specific, 134 were low IgY-specific and 694 were shared between the high and low IgY chicken lines. Many genetic mutations were located in the regulatory regions of important immunomodulatory genes, including TAP1, TAP2 and BF1. Our findings provide an in-depth understanding of genetic mutations in chicken microchromosomes.

Mapping of QTL for chicken body weight, carcass composition, and meat quality traits in a slow-growing line

Slow-growing chicken lines are valuable genetic resources for the development of well-perceived alternative free-range production. While there is no constraint on increasing growth rate, breeding programs have to evolve in order to include new traits improving the positioning of such lines in the growing market for parts and processed products. In this study, we used dense genotyping to fine map QTL for chicken growth, body composition, and meat quality traits in view of developing new tools for selection of a slow-growing line. The dataset included a total of 836 birds (10 sires, 87 dams, 739 descendants) and 40,203 SNP. QTL for the 15 traits analyzed were detected by 3 different methods, i.e., linkage and linkage disequilibrium haplotype-based analysis (LDLA), family-based single marker association (FASTA), and Bayesian multi-marker regression (Bayes Cπ). After filtering for QTL redundancy, we found 16, 16, and 9 QTL when using the FASTA, LDLA, and Bayes Cπ methods, respectively, with a threshold of 2.49 × 10-5 for FASTA and LDLA, and a Bayes factor of 150 for the Bayes Cπ analysis. They comprised 17 QTL for body weight, 9 QTL for body composition, and 15 QTL for breast meat quality or behavior at slaughter. The 3 methods agreed in the detection of highly significant QTL such as that detected on GGA24 for body weight at 3, 6, and 9 wk, and the 2 QTL detected on GGA17 and GGA18 for breast meat yield. Several significant QTL were also detected for the different components of breast meat quality. This study provided new locations for investigation in order to improve our understanding of the genetic architecture of growth, carcass composition, and meat quality in the chicken and to develop molecular tools for the selection of these traits in a slow-growing line.

Genome-wide association study for plasma very low-density lipoprotein concentration in chicken.

The plasma very low-density lipoprotein (VLDL) concentration is an effective blood biochemical indicator that could be used to select lean chicken lines. In the current study, we used Genome-wide association study (GWAS) method to detect SNPs with significant effects on plasma VLDL concentration. As a result, 38 SNPs significantly associated with plasma VLDL concentration were identified using at least one of the three mixed linear model (MLM) packages, including GRAMMAR, EMMAX and GEMMA. Nearly, all these SNPs with significant effects on plasma VLDL concentration (except Gga_rs16160897) have significantly different allele frequencies between lean and fat lines. The 1-Mb regions surrounding these 38 SNPs were extracted, and twelve important regions were obtained after combining the overlaps. A total of 122 genes in these twelve important regions were detected. Among these genes, LRRK2, ABCD2, TLR4, E2F1, SUGP1, NCAN, KLF2 and RAB8A were identified as important genes for plasma VLDL concentration based on their basic functions. The results of this study may supply useful information to select lean chicken lines.

The seminal acrosin-inhibitor ClTI1/SPINK2 is a fertility-associated marker in the chicken.

The seminal plasma is a very complex fluid, which surrounds sperm in semen. It contains numerous proteins including proteases and protease inhibitors that regulate proteolytic processes associated with protein activation and degradation. We previously identified a seminal protein, chicken liver trypsin inhibitor 1 (ClTI‐1) over expressed in semen of roosters with high fertility, suggesting a role in male fertility. In the present study, we showed that ClTI‐1 gene is actually SPINK2. Using normal healthy adult roosters, we showed that SPINK2 amount in seminal plasma was positively correlated with male fertility in chicken lines with highly contrasted genetic backgrounds (broiler and layer lines). Using affinity chromatography combined to mass spectrometry analysis and kinetic assays, we demonstrated for the first time that two chicken acrosin isoforms (acrosin and acrosin‐like proteins) are the physiological serine protease targets of SPINK2 inhibitor. SPINK2 transcript was overexpressed all along the male tract, and the protein was present in the lumen as expected for secreted proteins. Altogether, these data emphasize the role of seminal SPINK2 Kazal‐type inhibitor as an important actor of fertility in birds through its inhibitory action on acrosin isoforms proteins.

A Novel Regulator of Preadipocyte Differentiation, Transcription Factor TCF21, Functions Partially Through Promoting LPL Expression.

The transcription factor TCF21 has been previously shown to be specifically expressed in white preadipocytes in mice. However, the exact biological function of TCF21 in the context of adipogenesis remains unknown. In the current study, we used chicken lines selected based on their abdominal fat content, and observed a significant decrease in TCF21 mRNA and protein levels in the abdominal fat of lean broilers relative to fat broilers. Moreover, TCF21 expression increased throughout preadipocyte differentiation in vitro. We also found that TCF21 knockdown and over-expression attenuated and promoted preadipocyte differentiation, respectively, as evidenced by appropriate changes in lipid droplet accumulation and altered expressions of C/EBPa, LPL, and A-FABP. Additional chromatin immunoprecipitation analyses and luciferase assays demonstrated that TCF21 promotes the transcription of LPL by directly binding to the E-box motif in the LPL promoter. Together, these results show that TCF21 is a novel regulator of preadipocyte differentiation, in part by directly promoting LPL expression.

Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3

BackgroundThe interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity. Their biological activity is well documented in several animal species, but their genetic variation and biological mechanism is less well understood, particularly in avian species.ResultsHere we report the complete sequence of the domestic chicken Gallus gallus IFITM locus from a wide variety of chicken breeds to examine the detailed pattern of genetic variation of the locus on chromosome 5, including the flanking genes ATHL1 and B4GALNT4. We have generated chIFITM sequences from commercial breeds (supermarket-derived chicken breasts), indigenous chickens from Nigeria (Nsukka) and Ethiopia, European breeds and inbred chicken lines from the Pirbright Institute, totalling of 206 chickens. Through mapping of genetic variants to the latest chIFITM consensus sequence our data reveal that the chIFITM locus does not show structural variation in the locus across the populations analysed, despite spanning diverse breeds from different geographic locations. However, single nucleotide variants (SNVs) in functionally important regions of the proteins within certain groups of chickens were detected, in particular the European breeds and indigenous birds from Ethiopia and Nigeria. In addition, we also found that two out of four SNVs located in the chIFITM1 (Ser36 and Arg77) and chIFITM3 (Val103) proteins were simultaneously under positive selection.ConclusionsTogether these data suggest that IFITM genetic variation may contribute to the capacities of different chicken populations to resist virus infection.