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Currently, Avian Hepatitis E virus (aHEV) has emerged as a significant concern within the poultry industry, leading to elevated mortality rates characterized by enlarged livers and spleens in affected flocks. The pathological progression involves hepatic lipidosis, exudate release into the coelomic cavity, and eventual liver fracture accompanied by hemorrhages. Despite its impact, there remains a notable dearth of comprehensive information on the pathobiology and epidemiology of the virus and associated disease. This study focused on aHEV infections in commercial layers, its seroprevalence, virus isolation, designing a new diagnostic tool for detection of viral RNA, and the identification of circulating genotypes. Utilizing a commercial ELISA test, we observed approximately 30% seropositivity among all collected serum samples. In addition, we detected a positive correlation between aHEV titers and the age of the birds. Regarding viral load distribution, gallbladders exhibited the highest loads compared to the livers and spleens. The genotyping strategy was able to detect genotype 2 viruses, and for the first time in the U.S. identified genotype 3, which has significantly altered the previously established epidemiological understanding of this virus in the country. Despite efforts to isolate the virus in SPF eggs, our results were not successful. In conclusion, all these findings highlight the importance of continuing aHEV research to strengthen control strategies in the poultry sector.

This study aimed to characterise three Ghanaian local chicken ecotypes, namely, Interior Savannah, Forest, and Coastal Savannah, based on morphological data and single nucleotide polymorphism (SNP) genotypes. Morphological data including body weight, shank length, body girth, back length, thigh length, beak length, comb length, and wattle length were collected from 250 local chickens. DNA isolated from blood of 1,440 local chickens was used for SNP genotyping with the Affymetrix chicken 600k SNP chip. Principal component analysis showed that Forest and Coastal Savannah birds were closely related. Generally, all three ecotypes exhibited high genetic diversity, especially birds from the Interior Savannah zone. Morphological characterisation showed that ecotype (p = 0.016) and sex (p = 0.000) had significant effects on body weight. Birds of the Interior Savannah ecotype were the heaviest (p = 0.004), with mean weights of 1.23 kg for females and 1.40 kg for males. Sex also had a strong significant effect on most of the morphological measurements, but the sex * ecotype interaction effect was not significant. Very few of the feather phenotypes previously reported to be associated with heat resistance-frizzle (2%) and naked neck (1.6%)-were found in the studied populations. It is concluded that the three local ecotypes are genetically diverse but with similar morphological features and the information provided would be useful for future selection decisions.

Infectious bronchitis virus (IBV) is a respiratory virus causing atropism in multiple body systems of chickens. Recently, the California 1737/04 (CA1737/04) IBV strain was identified as one of the circulating IBV variants among poultry operations in North America. Here, the pathogenicity and tissue tropism of CA1737/04 IBV strain in specific-pathogen-free (SPF) hens were characterized in comparison to Massachusetts (Mass) IBV. In 30 weeks-old SPF hens, Mass or CA1737/04 IBV infections were carried out, while the third group was maintained as a control group. Following infection, we evaluated clinical signs, egg production, viral shedding, serology, necropsy examination, and histopathology during a period of 19 days. Also, certain tissue affinity parameters were investigated, which involved the localization of viral antigens and the detection of viral RNA copies in designated tissues. Our findings indicate that infection with CA1737/04 or Mass IBV strain could induce significant clinical signs, reduced egg production, and anti-IBV antibodies locally in oviduct wash and systemically in serum. Both IBV strains showed detectable levels of viral RNA copies and induced pathology in respiratory, renal, enteric, and reproductive tissues. However, the CA1737/04 IBV strain had higher pathogenicity, higher tissue tropism, and higher replication in the kidney, large intestine, and different segments of the oviduct compared to the Mass IBV strain. Both IBV strains shed viral genome from the cloacal route, however, the Mass IBV infected hens shed higher IBV genome loads via the oropharyngeal route compared to CA1737/04 IBV-infected hens. Overall, the current findings could contribute to a better understanding of CA1737/04 IBV pathogenicity in laying hens.

Heat stress results in significant economic losses to the poultry industry. Genetics plays an important role in chickens adapting to the warm environment. Physiological parameters such as hematochemical parameters change in response to heat stress in chickens. To explore the genetics of heat stress resilience in chickens, a genome-wide association study (GWAS) was conducted using Hy-Line Brown layer chicks subjected to either high ambient temperature or combined high temperature and Newcastle disease virus infection. Hematochemical parameters were measured during three treatment phases: acute heat stress, chronic heat stress, and chronic heat stress combined with NDV infection. Significant changes in blood parameters were recorded for 11 parameters (sodium (Na+, potassium (K+), ionized calcium (iCa2+), glucose (Glu), pH, carbon dioxide partial pressure (PCO2), oxygen partial pressure (PO2), total carbon dioxide (TCO2), bicarbonate (HCO3), base excess (BE), and oxygen saturation (sO2)) across the three treatments. The GWAS revealed 39 significant SNPs (p < 0.05) for seven parameters, located on Gallus gallus chromosomes (GGA) 1, 3, 4, 6, 11, and 12. The significant genomic regions were further investigated to examine if the genes within the regions were associated with the corresponding traits under heat stress. A candidate gene list including genes in the identified genomic regions that were also differentially expressed in chicken tissues under heat stress was generated. Understanding the correlation between genetic variants and resilience to heat stress is an important step towards improving heat tolerance in poultry.

Infectious bronchitis virus (IBV) induces severe economic losses in chicken farms due to the emergence of new variants leading to vaccine breaks. The studied IBV strains belong to Massachusetts (Mass), Canadian 4/91, and California (Cal) 1737 genotypes that are prevalent globally. This study was designed to compare the impact of these three IBV genotypes on primary and secondary lymphoid organs. For this purpose, one-week-old specific pathogen-free chickens were inoculated with Mass, Canadian 4/91, or Cal 1737 IBV variants, keeping a mock-infected control. We examined the IBV replication in primary and secondary lymphoid organs. The molecular, histopathological, and immunohistochemical examinations revealed significant differences in lesion scores and viral distribution in these immune organs. In addition, we observed B-cell depletion in the bursa of Fabricius and the spleen with a significant elevation of T cells in these organs. Further studies are required to determine the functional consequences of IBV replication in lymphoid organs.

Information on the genetic architecture of the production traits of indigenous African chicken is limited. We performed a genome-wide association study using imputed Affymetrix Axiom® 600K SNP-chip genotypes on 1,113 chickens from three agroecological zones of Ghana. After quality control, a total of 382,240 SNPs remained. Variance components and heritabilities for some growth, carcass and internal organ traits were estimated. The genetic and phenotypic correlations among these traits were also estimated. The estimated heritabilities of body weight at week 22 (BW22), average daily gain (ADG), dressed weight, breast weight, thigh weight, wing weight, drumstick weight, and neck weight were high and ranged from 0.50 to 0.69. Estimates of heritabilities for head weight, shank weight, and gizzard weight were moderate (0.31-0.35) while those of liver weight, back weight, dressing percentage, and heart weight were low (0.13-0.21). The estimated heritabilities of dressed weight, breast weight, wing weight, drumstick weight, neck weight, shank weight, and gizzard weight, corrected for BW22, were moderate (0.29-0.38), while the remaining traits had low heritability estimates (0.13-0.21). A total of 58 1-Mb SNP windows on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 13, 18, and 33 each explained more than 1% of the genetic variance for at least one of these traits. These genomic regions contained many genes previously reported to have effects on growth, carcass, and internal organ traits of chickens, including EMX2, CALCUL1, ACVR1B, CACNB1, RB1, MLNR, FOXO1, NCARPG, LCORL, LAP3, LDB2, KPNA3, and CAB39L. The moderate to high heritability estimates and high positive genetic correlations suggest that BW22, ADG, dressed weight, breast weight, thigh weight, wing weight, drumstick weight, and neck weight could be improved through selective breeding.

Herein, we report the complete genome for an avian infectious bronchitis virus isolated from cecal tonsils of California layers in 2021. This whole-genome sequence belongings to genotype GVIII, previously classified as a unique variant.

Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

In May 2018, an outbreak of virulent Newcastle disease (vND) affected backyard and commercial premises in Southern California. The re-occurrence of these outbreaks since the 1970s suggests that some poultry communities may not have reliable and stable resources available regarding biosecurity and disease prevention. Therefore, staff at the University of California, Davis (UCD) School of Veterinary Medicine (SVM), and the California Department of Food and Agriculture (CDFA) began organizing educational events and learning more about the gamefowl breeder community through a needs assessment exercise, during which local feedstores and neighborhoods were also visited. Focus groups were organized with breeders in various cities within the regional quarantine area, established by the CDFA during the vND outbreak. The focus groups were aimed at creating open communication networks with gamefowl breeders in the affected area, as well as to learn about their current sources of information, learning preferences, and current management practices. With the input from gamefowl breeders, as well as funding and input from the CDFA and the United States Department of Agriculture (USDA), a quality assurance program called the "Gamefowl Wellness Program" was established. Educational content was created and published through the UCD Gamefowl Wellness Program poultry health website. Additionally, with the help of the CDFA, the USDA, and pharmaceutical companies, Newcastle disease vaccines and training for their application were provided to feedstores with gamefowl breeder clientele. Nurturing trust with these poultry communities allowed us to receive the information needed to develop effective outreach strategies that could better serve them. Responding to community concerns might be a way to garner the trust necessary to prevent or at least promptly detect foreign animal disease outbreaks.

The novel severe acute respiratory syndrome (SARS) coronavirus, SARS-CoV-2, is responsible for the global COVID-19 pandemic. Effective interventions are urgently needed to mitigate the effects of COVID-19 and likely require multiple strategies. Egg-extracted antibody therapies are a low-cost and scalable strategy to protect at-risk individuals from SARS-CoV-2 infection. Commercial laying hens were hyperimmunized against the SARS-CoV-2 S1 protein using three different S1 recombinant proteins and three different doses. Sera and egg yolk were collected at three and six weeks after the second immunization for enzyme-linked immunosorbent assay and plaque-reduction neutralization assay to determine antigen-specific antibody titers and neutralizing antibody titers, respectively. In this study we demonstrate that hens hyperimmunized against the SARS-CoV-2 recombinant S1 and receptor binding domain (RBD) proteins produced neutralizing antibodies against SARS-CoV-2. We further demonstrate that antibody production was dependent on the dose and type of antigen administered. Our data suggests that antibodies purified from the egg yolk of hyperimmunized hens can be used as immunoprophylaxis in humans at risk of exposure to SARS-CoV-2.

In May 2018, an outbreak of virulent Newcastle disease (vND) affected backyard and commercial premises in Southern California. The re-occurrence of these outbreaks since the 1970s suggests that some poultry communities may not have reliable and stable resources available regarding biosecurity and disease prevention. Therefore, staff at the University of California, Davis (UCD) School of Veterinary Medicine (SVM), and the California Department of Food and Agriculture (CDFA) began organizing educational events and learning more about the gamefowl breeder community through a needs assessment exercise, during which local feedstores and neighborhoods were also visited. Focus groups were organized with breeders in various cities within the regional quarantine area, established by the CDFA during the vND outbreak. The focus groups were aimed at creating open communication networks with gamefowl breeders in the affected area, as well as to learn about their current sources of information, learning preferences, and current management practices. With the input from gamefowl breeders, as well as funding and input from the CDFA and the United States Department of Agriculture (USDA), a quality assurance program called the "Gamefowl Wellness Program" was established. Educational content was created and published through the UCD Gamefowl Wellness Program poultry health website. Additionally, with the help of the CDFA, the USDA, and pharmaceutical companies, Newcastle disease vaccines and training for their application were provided to feedstores with gamefowl breeder clientele. Nurturing trust with these poultry communities allowed us to receive the information needed to develop effective outreach strategies that could better serve them. Responding to community concerns might be a way to garner the trust necessary to prevent or at least promptly detect foreign animal disease outbreaks.

Infectious bronchitis virus (IBV) is a highly variable RNA virus that affects chickens worldwide. Due to its inherited tendency to suffer point mutations and recombination events during viral replication, emergent IBV strains have been linked to nephropathogenic and reproductive disease that are more severe than typical respiratory disease, leading, in some cases, to mortality, severe production losses, and/or unsuccessful vaccination. QX and DMV/1639 strains are examples of the above-mentioned IBV evolutionary pathway and clinical outcome. In this study, our purpose was to systematically compare whole genomes of QX and DMV strains looking at each IBV gene individually. Phylogenetic analyses and amino acid site searches were performed in datasets obtained from GenBank accounting for all IBV genes and using our own relevant sequences as a basis. The QX dataset studied is more genetically diverse than the DMV dataset, partially due to the greater epidemiological diversity within the five QX strains used as a basis compared to the four DMV strains from our study. Historically, QX strains have emerged and spread earlier than DMV strains in Europe and Asia. Consequently, there are more QX sequences deposited in GenBank than DMV strains, assisting in the identification of a larger pool of QX strains. It is likely that a similar evolutionary pattern will be observed among DMV strains as they develop and spread in North America.

The novel severe acute respiratory syndrome (SARS) coronavirus, SARS-CoV-2, is responsible for the global COVID-19 pandemic. Effective interventions are urgently needed to mitigate the effects of COVID-19 and likely require multiple strategies. Egg-extracted antibody therapies are a low-cost and scalable strategy to protect at-risk individuals from SARS-CoV-2 infection. Commercial laying hens were hyperimmunized against the SARS-CoV-2 S1 protein using three different S1 recombinant proteins and three different doses. Sera and egg yolk were collected at three and six weeks after the second immunization for enzyme-linked immunosorbent assay and plaque-reduction neutralization assay to determine antigen-specific antibody titers and neutralizing antibody titers, respectively. In this study we demonstrate that hens hyperimmunized against the SARS-CoV-2 recombinant S1 and receptor binding domain (RBD) proteins produced neutralizing antibodies against SARS-CoV-2. We further demonstrate that antibody production was dependent on the dose and type of antigen administered. Our data suggests that antibodies purified from the egg yolk of hyperimmunized hens can be used as immunoprophylaxis in humans at risk of exposure to SARS-CoV-2.

Newcastle disease is a devastating poultry disease that often causes significant economic losses in poultry in the developing countries of Africa, Asia, as well as South and Central America. Velogenic Newcastle disease virus (NDV) outbreaks are associated with high mortalities, which can threaten household livelihoods, especially in the rural areas, and lead to loss of high-quality proteins in the form of meat and eggs, as well as household purchasing power. In this study, we exposed unvaccinated Ghanaian and Tanzanian chickens of six local ecotypes to velogenic NDV strains, measured NDV response traits, sequenced their DNA on a genotyping-by-sequencing platform, and performed variance component analyses. The collected phenotypes included: growth rates (pre- and post-exposure); lesion scores (gross lesion severity) in the trachea, proventriculus, intestine, and cecal tonsils; natural antibody levels; anti-NDV antibody levels at 7 days post exposure (dpe); tear and cloacal viral load at 2, 4, and 6 dpe; and survival time. Heritability estimates were low to moderate, ranging from 0.11 for average lesion scores to 0.36 for pre-exposure growth rate. Heritability estimates for survival time were 0.23 and 0.27 for the Tanzanian and Ghanaian ecotypes, respectively. Similar heritability estimates were observed when data were analyzed either separately or combined for the two countries. Survival time was genetically negatively correlated with lesion scores and with viral load. Results suggested that response to mesogenic or velogenic NDV of these local chicken ecotypes could be improved by selective breeding. Chickens that are more resilient to velogenic NDV can improve household livelihoods in developing countries.

The possible link between hIAPP accumulation and β-cell death in diabetic patients has inspired numerous studies focusing on amyloid structures and aggregation pathways of this hormone. Recent studies have reported on the importance of early oligomeric intermediates, the many roles of their interactions with lipid membrane, pH, insulin, and zinc on the mechanism of aggregation of hIAPP. The challenges posed by the transient nature of amyloid oligomers, their structural heterogeneity, and the complex nature of their interaction with lipid membranes have resulted in the development of a wide range of biophysical and chemical approaches to characterize the aggregation process. While the cellular processes and factors activating hIAPP-mediated cytotoxicity are still not clear, it has recently been suggested that its impaired turnover and cellular processing by proteasome and autophagy may contribute significantly toward toxic hIAPP accumulation and, eventually, β-cell death. Therefore, studies focusing on the restoration of hIAPP proteostasis may represent a promising arena for the design of effective therapies. In this review we discuss the current knowledge of the structures and pathology associated with hIAPP self-assembly and point out the opportunities for therapy that a detailed biochemical, biophysical, and cellular understanding of its aggregation may unveil.

Newcastle disease (ND) has a great impact on poultry health and welfare with its most virulent (velogenic) strain. In addition, issues exacerbated by the increase in global temperatures necessitates a greater understanding of the host immune response when facing a combination of biotic and abiotic stress factors in poultry production. Previous investigations have revealed that the host immune response is tissue-specific. The goal of this study was to identify genes and/or signaling pathways associated with immune response to NDV (Newcastle disease virus) in the trachea, an essential organ where NDV replicate after the infection, by profiling the tissue specific transcriptome response in two genetically distinct inbred chicken lines when exposed to both abiotic and biotic stressors. Fayoumis appear to be able to respond more effectively (lower viral titer, higher antibody levels, immune gene up-regulation) and earlier than Leghorns. Our results suggest NDV infection in Fayoumis appears to elicit proinflammatory processes, and pathways such as the inhibition of cell viability, cell proliferation of lymphocytes, and transactivation of RNA, more rapidly than in Leghorns. These differences in immune response converge at later timepoints which may indicate that Leghorns eventually regulate its immune response to infection. The profiling of the gene expression response in the trachea adds to our understanding of the chicken host response to NDV infection and heat stress on a whole genome level and provides potential candidate genes and signaling pathways for further investigation into the characterization of the time-specific and pathway specific responses in Fayoumis and Leghorns.

Infectious bronchitis virus (IBV) induces respiratory and urogenital disease in chickens. Although IBV replicates in the gastrointestinal tract, enteric lesions are uncommon. We have reported a case of runting-stunting syndrome in commercial broilers from which an IBV variant was isolated from the intestines. The isolate, CalEnt, demonstrated an enteric tissue tropism in chicken embryos and SPF chickens experimentally. Here, we determined the full genome of CalEnt and compared it to other IBV strains, in addition to comparing the pathobiology of CalEnt and M41 in commercial broilers. Despite the high whole-genome identity to other IBV strains, CalEnt is rather unique in its nucleotide composition. The S gene phylogenetic analyses showed great similarity between CalEnt and Cal 99. Clinically, vent staining was slightly more frequent in CalEnt-infected birds than those challenged with M41. Furthermore, IBV IHC detection was more evident and the viral shedding in feces was overall higher with the CalEnt challenge compared with M41. Despite underlying intestinal lesions caused by coccidiosis and salmonellosis vaccination, microscopic lesions in CalEnt-infected chickens were more severe than in M41-infected chickens or controls, supporting the enteric tropism of CalEnt. Further studies in SPF chickens are needed to determine the pathogenesis of the virus, its molecular mechanisms for the enteric tropism, and its influence in intestinal health.

Infectious bronchitis virus (IBV) induces respiratory and urogenital disease in chickens. Although IBV replicates in the gastrointestinal tract, enteric lesions are uncommon. We have reported a case of runting-stunting syndrome in commercial broilers from which an IBV variant was isolated from the intestines. The isolate, CalEnt, demonstrated an enteric tissue tropism in chicken embryos and SPF chickens experimentally. Here, we determined the full genome of CalEnt and compared it to other IBV strains, in addition to comparing the pathobiology of CalEnt and M41 in commercial broilers. Despite the high whole-genome identity to other IBV strains, CalEnt is rather unique in its nucleotide composition. The S gene phylogenetic analyses showed great similarity between CalEnt and Cal 99. Clinically, vent staining was slightly more frequent in CalEnt-infected birds than those challenged with M41. Furthermore, IBV IHC detection was more evident and the viral shedding in feces was overall higher with the CalEnt challenge compared with M41. Despite underlying intestinal lesions caused by coccidiosis and salmonellosis vaccination, microscopic lesions in CalEnt-infected chickens were more severe than in M41-infected chickens or controls, supporting the enteric tropism of CalEnt. Further studies in SPF chickens are needed to determine the pathogenesis of the virus, its molecular mechanisms for the enteric tropism, and its influence in intestinal health.

Newcastle disease (ND) has a great impact on poultry health and welfare with its most virulent (velogenic) strain. In addition, issues exacerbated by the increase in global temperatures necessitates a greater understanding of the host immune response when facing a combination of biotic and abiotic stress factors in poultry production. Previous investigations have revealed that the host immune response is tissue-specific. The goal of this study was to identify genes and/or signaling pathways associated with immune response to NDV (Newcastle disease virus) in the trachea, an essential organ where NDV replicate after the infection, by profiling the tissue specific transcriptome response in two genetically distinct inbred chicken lines when exposed to both abiotic and biotic stressors. Fayoumis appear to be able to respond more effectively (lower viral titer, higher antibody levels, immune gene up-regulation) and earlier than Leghorns. Our results suggest NDV infection in Fayoumis appears to elicit proinflammatory processes, and pathways such as the inhibition of cell viability, cell proliferation of lymphocytes, and transactivation of RNA, more rapidly than in Leghorns. These differences in immune response converge at later timepoints which may indicate that Leghorns eventually regulate its immune response to infection. The profiling of the gene expression response in the trachea adds to our understanding of the chicken host response to NDV infection and heat stress on a whole genome level and provides potential candidate genes and signaling pathways for further investigation into the characterization of the time-specific and pathway specific responses in Fayoumis and Leghorns.

Newcastle disease (ND) is one of the most challenging infectious diseases affecting poultry production in Africa, causing major economic losses. To date, Newcastle disease virus isolates from several African countries have been grouped into class II NDV genotypes I, IV, V, VI, VII, XI, XIII, XIV, XVII, XVIII and XXI. Although ND is endemic in many African countries, information on circulating genotypes is still scarce. In Tanzania, outbreaks with genotypes V and XIII have been reported. In West and Central Africa, genotypes XIV, XVII, and XVIII are the most predominant. To investigate other genotypes circulating in Tanzania and Ghana, we performed molecular genotyping on isolates from Tanzania and Ghana using the MinION, a third-generation portable sequencing device from Oxford Nanopore Technologies. Using the MinION, we successfully sequenced the NDV F gene hypervariable region of 24 isolates from Tanzania and four samples from Ghana. In Tanzania, genotypes V, VII and XIII were detected. All isolates from Ghana belonged to genotype XVIII. The data obtained in this study reflect the genetic diversity of NDV in Africa and highlight the importance of surveillance for monitoring the distribution of NDV genotypes and viral evolution.

Two environmental factors, Newcastle disease and heat stress, are concurrently negatively impacting poultry worldwide and warrant greater attention into developing genetic resistance within chickens. Using two genetically distinct and highly inbred layer lines, Fayoumi and Leghorn, we explored how different genetic backgrounds affect the bursal response to a treatment of simultaneous Newcastle disease virus (NDV) infection at 6 days postinfection (dpi) while under chronic heat stress. The bursa is a primary lymphoid organ within birds and is crucial for the development of B cells. We performed RNA-seq and ChIP-seq targeting histone modifications on bursa tissue. Differential gene expression revealed that Leghorn, compared to Fayoumi, had significant down-regulation in genes involved in cell proliferation, cell cycle, and cell division. Interestingly, we also found greater differences in histone modification levels in response to treatment in Leghorns than Fayoumis, and biological processes enriched in associated target genes of H3K27ac and H3K4me1 were similarly associated with cell cycle and receptor signaling of lymphocytes. Lastly, we found candidate variants between the two genetic lines within exons of differentially expressed genes and regulatory elements with differential histone modification enrichment between the lines, which provides a strong foundation for understanding the effects of genetic variation on NDV resistance under heat stress. This study provides further understanding of the cellular mechanisms affected by NDV infection under heat stress in chicken bursa and identified potential genes and regulatory regions that may be targets for developing genetic resistance within chickens.

Newcastle disease (ND) is a global threat to domestic poultry, especially in rural areas of Africa and Asia, where the loss of entire backyard local chicken flocks often threatens household food security and income. To investigate the genetics of Ghanaian local chicken ecotypes to Newcastle disease virus (NDV), in this study, three popular Ghanaian chicken ecotypes (regional populations) were challenged with a lentogenic NDV strain at 28 days of age. This study was conducted in parallel with a similar study that used three popular Tanzanian local chicken ecotypes and after two companion studies in the United States, using Hy-line Brown commercial laying birds. In addition to growth rate, NDV response traits were measured following infection, including anti-NDV antibody levels [pre-infection and 10 days post-infection (dpi)], and viral load (2 and 6 dpi). Genetic parameters were estimated, and two genome-wide association study analysis methods were used on data from 1,440 Ghanaian chickens that were genotyped on a chicken 600K Single Nucleotide Polymorphism (SNP) chip. Both Ghana and Tanzania NDV challenge studies revealed moderate to high (0.18 - 0.55) estimates of heritability for all traits, except viral clearance where the heritability estimate was not different from zero for the Tanzanian ecotypes. For the Ghana study, 12 quantitative trait loci (QTL) for growth and/or response to NDV from single-SNP analyses and 20 genomic regions that explained more than 1% of genetic variance using the Bayes B method were identified. Seven of these windows were also identified as having at least one significant SNP in the single SNP analyses for growth rate, anti-NDV antibody levels, and viral load at 2 and 6 dpi. An important gene for growth during stress, CHORDC1 associated with post-infection growth rate was identified as a positional candidate gene, as well as other immune related genes, including VAV2, IL12B, DUSP1, and IL17B. The QTL identified in the Ghana study did no

Heat stress results in reduced productivity, anorexia, and mortality in chickens. The objective of the study was to identify genes and signal pathways associated with heat stress and Newcastle disease virus (NDV) infection in the liver of chickens through RNA-seq analysis, using two highly inbred chicken lines (Leghorn and Fayoumi). All birds were held in the same environment until 14 days of age. On day 14, half the birds were exposed to 38 °C with 50% relative humidity for 4 h, then 35 °C until the end of the experiment. The remaining birds were kept at 25 °C throughout the experiment. The heat-treated birds were inoculated at 21 days of age with 107 EID50 (One EID50 unit is the amount of virus that will infect 50 percent of inoculated embryos) NDV La Sota strain to investigate the effects of both heat stress and NDV infection. Physiological parameters were recorded as blood phenotypes at three stages: acute heat (AH), chronic heat (CH1), and chronic heat combined with NDV infection (CH&NDV), at 4 h, 7 days, and 10 days post-initiation of heat treatment, respectively. Our previous work revealed that the heat-resilient Fayoumi line maintained a more stable acid-base balance in their blood compared to the Leghorn line. Liver samples were harvested on both AH and CH&NDV to characterize the transcriptome profiles of these two inbred lines. Both genetic lines and treatments had large impact on the liver transcriptome. Fayoumi birds had more differentially expressed genes (DEGs) than Leghorn birds for both treatments. Metabolic and immune-related genes were on the DEG list, with Fayoumi having more immune-related DEGs than Leghorns, which was confirmed by gene functional enrichment analysis. Weighted correlation network analysis (WGCNA) indicated that the driver genes such as Solute Carrier Family genes could be very important for stabilizing the acid-base balance in Fayoumi birds during heat stress. Therefore, candidate genes such solute carrier family genes co

Disease has large negative impacts on poultry production. A more comprehensive understanding of host-pathogen interaction can lead to new and improved strategies to maintain health. In particular, host genetic factors can lead to a more effective response to pathogens, hereafter termed resistance. Fayoumi and Leghorn chicken lines have demonstrated relative resistance and susceptibility, respectively, to the Newcastle disease virus (NDV) vaccine strain and many other pathogens. This biological model was used to better understand the host response to a vaccine strain of NDV across three tissues and time points, using RNA-seq. Analyzing the Harderian gland, trachea, and lung tissues together using weighted gene co-expression network analysis (WGCNA) identified important genes that were co-expressed and associated with parameters including: genetic line, days post-infection (dpi), challenge status, sex, and tissue. Pathways and driver genes, such as EIF2AK2, MPEG1, and TNFSF13B, associated with challenge status, dpi, and genetic line were of particular interest as candidates for disease resistance. Overall, by jointly analyzing the three tissues, this study identified genes and gene networks that led to a more comprehensive understanding of the whole animal response to lentogenic NDV than that obtained by analyzing the tissues individually.

BackgroundFree-range local chickens (FRLC) farming is an important activity in Tanzania, however, they have not been well-characterized. This study aimed to phenotypically characterize three Tanzanian FRLCs and to determine their population structure. A total of 389 mature breeder chickens (324 females and 65 males) from three popular Tanzanian FRLC ecotypes (Kuchi, Morogoro-medium and Ching'wekwe) were used for the phenotypic characterization. Progenies of these chickens were utilized to assess population structure. The ecotypes were collected from four geographical zones across Tanzania: Lake, Central, Northern and Coastal zones. Body weights and linear measurements were obtained from the mature breeders, including body, neck, shanks, wingspan, chest girth, and shank girth. Descriptive statistics were utilized to characterize the chickens. Correlations between the linear measurements and differences among the means of measured linear traits between ecotypes and between sexes were assessed. A total of 1399 progeny chicks were genotyped using a chicken 600 K high density single nucleotide polymorphism (SNP) panel for determination of population structure.ResultsThe means for most traits were significantly higher in Kuchi relative to Ching'wekwe and Morogoro-medium. However, shank length and shank girth were similar between Kuchi and Morogoro-medium females. All traits were correlated with the exception of shank girth in Morogoro-medium. Admixture analyses revealed that Morogoro-medium and Ching'wekwe clustered together as one population, separate from Kuchi.ConclusionsPhenotypic traits could be used to characterize FRLCs, however, there were variations in traits among individuals within ecotypes; therefore, complementary genomic methods should be considered to improve the characterization for selective breeding.

The chicken immune system has provided an immense contribution to basic immunology knowledge by establishing major landmarks and discoveries that defined concepts widely used today. One of many special features on chickens is the presence of a compact and simple major histocompatibility complex (MHC). Despite its simplicity, the chicken MHC maintains the essential counterpart genes of the mammalian MHC, allowing for a strong association to be detected between the MHC and resistance or susceptibility to infectious diseases. This association has been widely studied for several poultry infectious diseases, including infectious bronchitis. In addition to the MHC and its linked genes, other non-MHC loci may play a role in the mechanisms underlying such resistance. It has been reported that innate immune responses, such as macrophage function and inflammation, might be some of the factors driving resistance or susceptibility, consequently influencing the disease outcome in an individual or a population. Information about innate immunity and genetic resistance can be helpful in developing effective preventative measures for diseases such as infectious bronchitis, to which a systemic antibody response is often not associated with disease protection. In this review, we summarize the importance of the chicken MHC in poultry disease resistance, particularly to infectious bronchitis virus (IBV) infections and the role played by innate immunity and inflammation on disease outcome. We highlight how future studies focusing on the MHC and non-MHC genes can potentially bring clarity to observed resistance in some chicken B haplotype lines.

As a major infectious disease in chickens, Newcastle disease virus (NDV) causes considerable economic losses in the poultry industry, especially in developing countries where there is limited access to effective vaccination. Therefore, enhancing resistance to the virus in commercial chickens through breeding is a promising way to promote poultry production. In this study, we investigated gene expression changes at 2 and 6 days post inoculation (dpi) at day 21 with a lentogenic NDV in a commercial egg-laying chicken hybrid using RNA sequencing analysis. By comparing NDV-challenged and non-challenged groups, 526 differentially expressed genes (DEGs) (false discovery rate (FDR) < 0.05) were identified at 2 dpi, and only 36 at 6 dpi. For the DEGs at 2 dpi, Ingenuity Pathway Analysis predicted inhibition of multiple signaling pathways in response to NDV that regulate immune cell development and activity, neurogenesis, and angiogenesis. Up-regulation of interferon induced protein with tetratricopeptide repeats 5 (IFIT5) in response to NDV was consistent between the current and most previous studies. Sprouty RTK signaling antagonist 1 (SPRY1), a DEG in the current study, is in a significant quantitative trait locus associated with virus load at 6 dpi in the same population. These identified pathways and DEGs provide potential targets to further study breeding strategy to enhance NDV resistance in chickens.

Disease has large negative impacts on poultry production. A more comprehensive understanding of host-pathogen interaction can lead to new and improved strategies to maintain health. In particular, host genetic factors can lead to a more effective response to pathogens, hereafter termed resistance. Fayoumi and Leghorn chicken lines have demonstrated relative resistance and susceptibility, respectively, to the Newcastle disease virus (NDV) vaccine strain and many other pathogens. This biological model was used to better understand the host response to a vaccine strain of NDV across three tissues and time points, using RNA-seq. Analyzing the Harderian gland, trachea, and lung tissues together using weighted gene co-expression network analysis (WGCNA) identified important genes that were co-expressed and associated with parameters including: genetic line, days post-infection (dpi), challenge status, sex, and tissue. Pathways and driver genes, such as EIF2AK2, MPEG1, and TNFSF13B, associated with challenge status, dpi, and genetic line were of particular interest as candidates for disease resistance. Overall, by jointly analyzing the three tissues, this study identified genes and gene networks that led to a more comprehensive understanding of the whole animal response to lentogenic NDV than that obtained by analyzing the tissues individually.

Newcastle disease (ND) is a global threat to domestic poultry, especially in rural areas of Africa and Asia, where the loss of entire backyard local chicken flocks often threatens household food security and income. To investigate the genetics of Ghanaian local chicken ecotypes to Newcastle disease virus (NDV), in this study, three popular Ghanaian chicken ecotypes (regional populations) were challenged with a lentogenic NDV strain at 28 days of age. This study was conducted in parallel with a similar study that used three popular Tanzanian local chicken ecotypes and after two companion studies in the United States, using Hy-line Brown commercial laying birds. In addition to growth rate, NDV response traits were measured following infection, including anti-NDV antibody levels [pre-infection and 10 days post-infection (dpi)], and viral load (2 and 6 dpi). Genetic parameters were estimated, and two genome-wide association study analysis methods were used on data from 1,440 Ghanaian chickens that were genotyped on a chicken 600K Single Nucleotide Polymorphism (SNP) chip. Both Ghana and Tanzania NDV challenge studies revealed moderate to high (0.18 - 0.55) estimates of heritability for all traits, except viral clearance where the heritability estimate was not different from zero for the Tanzanian ecotypes. For the Ghana study, 12 quantitative trait loci (QTL) for growth and/or response to NDV from single-SNP analyses and 20 genomic regions that explained more than 1% of genetic variance using the Bayes B method were identified. Seven of these windows were also identified as having at least one significant SNP in the single SNP analyses for growth rate, anti-NDV antibody levels, and viral load at 2 and 6 dpi. An important gene for growth during stress, CHORDC1 associated with post-infection growth rate was identified as a positional candidate gene, as well as other immune related genes, including VAV2, IL12B, DUSP1, and IL17B. The QTL identified in the Ghana study did no

Newcastle disease (ND) is one of the most challenging infectious diseases affecting poultry production in Africa, causing major economic losses. To date, Newcastle disease virus isolates from several African countries have been grouped into class II NDV genotypes I, IV, V, VI, VII, XI, XIII, XIV, XVII, XVIII and XXI. Although ND is endemic in many African countries, information on circulating genotypes is still scarce. In Tanzania, outbreaks with genotypes V and XIII have been reported. In West and Central Africa, genotypes XIV, XVII, and XVIII are the most predominant. To investigate other genotypes circulating in Tanzania and Ghana, we performed molecular genotyping on isolates from Tanzania and Ghana using the MinION, a third-generation portable sequencing device from Oxford Nanopore Technologies. Using the MinION, we successfully sequenced the NDV F gene hypervariable region of 24 isolates from Tanzania and four samples from Ghana. In Tanzania, genotypes V, VII and XIII were detected. All isolates from Ghana belonged to genotype XVIII. The data obtained in this study reflect the genetic diversity of NDV in Africa and highlight the importance of surveillance for monitoring the distribution of NDV genotypes and viral evolution.

As a major infectious disease in chickens, Newcastle disease virus (NDV) causes considerable economic losses in the poultry industry, especially in developing countries where there is limited access to effective vaccination. Therefore, enhancing resistance to the virus in commercial chickens through breeding is a promising way to promote poultry production. In this study, we investigated gene expression changes at 2 and 6 days post inoculation (dpi) at day 21 with a lentogenic NDV in a commercial egg-laying chicken hybrid using RNA sequencing analysis. By comparing NDV-challenged and non-challenged groups, 526 differentially expressed genes (DEGs) (false discovery rate (FDR) < 0.05) were identified at 2 dpi, and only 36 at 6 dpi. For the DEGs at 2 dpi, Ingenuity Pathway Analysis predicted inhibition of multiple signaling pathways in response to NDV that regulate immune cell development and activity, neurogenesis, and angiogenesis. Up-regulation of interferon induced protein with tetratricopeptide repeats 5 (IFIT5) in response to NDV was consistent between the current and most previous studies. Sprouty RTK signaling antagonist 1 (SPRY1), a DEG in the current study, is in a significant quantitative trait locus associated with virus load at 6 dpi in the same population. These identified pathways and DEGs provide potential targets to further study breeding strategy to enhance NDV resistance in chickens.

Heat stress results in reduced productivity, anorexia, and mortality in chickens. The objective of the study was to identify genes and signal pathways associated with heat stress and Newcastle disease virus (NDV) infection in the liver of chickens through RNA-seq analysis, using two highly inbred chicken lines (Leghorn and Fayoumi). All birds were held in the same environment until 14 days of age. On day 14, half the birds were exposed to 38 °C with 50% relative humidity for 4 h, then 35 °C until the end of the experiment. The remaining birds were kept at 25 °C throughout the experiment. The heat-treated birds were inoculated at 21 days of age with 107 EID50 (One EID50 unit is the amount of virus that will infect 50 percent of inoculated embryos) NDV La Sota strain to investigate the effects of both heat stress and NDV infection. Physiological parameters were recorded as blood phenotypes at three stages: acute heat (AH), chronic heat (CH1), and chronic heat combined with NDV infection (CH&NDV), at 4 h, 7 days, and 10 days post-initiation of heat treatment, respectively. Our previous work revealed that the heat-resilient Fayoumi line maintained a more stable acid-base balance in their blood compared to the Leghorn line. Liver samples were harvested on both AH and CH&NDV to characterize the transcriptome profiles of these two inbred lines. Both genetic lines and treatments had large impact on the liver transcriptome. Fayoumi birds had more differentially expressed genes (DEGs) than Leghorn birds for both treatments. Metabolic and immune-related genes were on the DEG list, with Fayoumi having more immune-related DEGs than Leghorns, which was confirmed by gene functional enrichment analysis. Weighted correlation network analysis (WGCNA) indicated that the driver genes such as Solute Carrier Family genes could be very important for stabilizing the acid-base balance in Fayoumi birds during heat stress. Therefore, candidate genes such solute carrier family genes co

Two environmental factors, Newcastle disease and heat stress, are concurrently negatively impacting poultry worldwide and warrant greater attention into developing genetic resistance within chickens. Using two genetically distinct and highly inbred layer lines, Fayoumi and Leghorn, we explored how different genetic backgrounds affect the bursal response to a treatment of simultaneous Newcastle disease virus (NDV) infection at 6 days postinfection (dpi) while under chronic heat stress. The bursa is a primary lymphoid organ within birds and is crucial for the development of B cells. We performed RNA-seq and ChIP-seq targeting histone modifications on bursa tissue. Differential gene expression revealed that Leghorn, compared to Fayoumi, had significant down-regulation in genes involved in cell proliferation, cell cycle, and cell division. Interestingly, we also found greater differences in histone modification levels in response to treatment in Leghorns than Fayoumis, and biological processes enriched in associated target genes of H3K27ac and H3K4me1 were similarly associated with cell cycle and receptor signaling of lymphocytes. Lastly, we found candidate variants between the two genetic lines within exons of differentially expressed genes and regulatory elements with differential histone modification enrichment between the lines, which provides a strong foundation for understanding the effects of genetic variation on NDV resistance under heat stress. This study provides further understanding of the cellular mechanisms affected by NDV infection under heat stress in chicken bursa and identified potential genes and regulatory regions that may be targets for developing genetic resistance within chickens.

The chicken immune system has provided an immense contribution to basic immunology knowledge by establishing major landmarks and discoveries that defined concepts widely used today. One of many special features on chickens is the presence of a compact and simple major histocompatibility complex (MHC). Despite its simplicity, the chicken MHC maintains the essential counterpart genes of the mammalian MHC, allowing for a strong association to be detected between the MHC and resistance or susceptibility to infectious diseases. This association has been widely studied for several poultry infectious diseases, including infectious bronchitis. In addition to the MHC and its linked genes, other non-MHC loci may play a role in the mechanisms underlying such resistance. It has been reported that innate immune responses, such as macrophage function and inflammation, might be some of the factors driving resistance or susceptibility, consequently influencing the disease outcome in an individual or a population. Information about innate immunity and genetic resistance can be helpful in developing effective preventative measures for diseases such as infectious bronchitis, to which a systemic antibody response is often not associated with disease protection. In this review, we summarize the importance of the chicken MHC in poultry disease resistance, particularly to infectious bronchitis virus (IBV) infections and the role played by innate immunity and inflammation on disease outcome. We highlight how future studies focusing on the MHC and non-MHC genes can potentially bring clarity to observed resistance in some chicken B haplotype lines.

BackgroundFree-range local chickens (FRLC) farming is an important activity in Tanzania, however, they have not been well-characterized. This study aimed to phenotypically characterize three Tanzanian FRLCs and to determine their population structure. A total of 389 mature breeder chickens (324 females and 65 males) from three popular Tanzanian FRLC ecotypes (Kuchi, Morogoro-medium and Ching'wekwe) were used for the phenotypic characterization. Progenies of these chickens were utilized to assess population structure. The ecotypes were collected from four geographical zones across Tanzania: Lake, Central, Northern and Coastal zones. Body weights and linear measurements were obtained from the mature breeders, including body, neck, shanks, wingspan, chest girth, and shank girth. Descriptive statistics were utilized to characterize the chickens. Correlations between the linear measurements and differences among the means of measured linear traits between ecotypes and between sexes were assessed. A total of 1399 progeny chicks were genotyped using a chicken 600 K high density single nucleotide polymorphism (SNP) panel for determination of population structure.ResultsThe means for most traits were significantly higher in Kuchi relative to Ching'wekwe and Morogoro-medium. However, shank length and shank girth were similar between Kuchi and Morogoro-medium females. All traits were correlated with the exception of shank girth in Morogoro-medium. Admixture analyses revealed that Morogoro-medium and Ching'wekwe clustered together as one population, separate from Kuchi.ConclusionsPhenotypic traits could be used to characterize FRLCs, however, there were variations in traits among individuals within ecotypes; therefore, complementary genomic methods should be considered to improve the characterization for selective breeding.

Newcastle disease virus (NDV) is a highly contagious avian pathogen that poses a tremendous threat to poultry producers in endemic zones due to its epidemic potential. To investigate host genetic resistance to NDV while under the effects of heat stress, a genome-wide association study (GWAS) was performed on Hy-Line Brown layer chickens that were challenged with NDV while under high ambient temperature to identify regions associated with host viral titer, circulating anti-NDV antibody titer, and body weight change. A single nucleotide polymorphism (SNP) on chromosome 1 was associated with viral titer at two days post-infection (dpi), while 30 SNPs spanning a quantitative trait loci (QTL) on chromosome 24 were associated with viral titer at 6 dpi. Immune related genes, such as CAMK1d and CCDC3 on chromosome 1, associated with viral titer at 2 dpi, and TIRAP, ETS1, and KIRREL3, associated with viral titer at 6 dpi, were located in two QTL regions for viral titer that were identified in this study. This study identified genomic regions and candidate genes that are associated with response to NDV during heat stress in Hy-Line Brown layer chickens. Regions identified for viral titer on chromosome 1 and 24, at 2 and 6 dpi, respectively, included several genes that have key roles in regulating the immune response.

We conducted an experiment in Southeast Santa Cruz, Patagonia, Argentina in order to evaluate losses of lambs respect to natural grassland, and evolution of live weight from January to May during two years (2015-2016 and 2017-2018) in a mixed pasture of orchardgrass (Dactylis glomerata) and intermediate wheatgrass (Agropyron intermedium (Host) Beauvois.Three flocks of marked ewes that came from three different paddocks were chosen randomly and evaluated. Live weight (PV) and ranges of PV were determined on three dates (January, February-March-April-May). Pasture’s available aerial biomass, the living(VM) and dead material, crude protein and dry matter digestibility were determined on three dates(December, March and May). Evolution of animal PV during the period was analyzed using regressions. Lamb PV was analyzed in relation to MV and nutritional variables through correlations. The work included records of rainfall and temperatures. Animal losses in the pasture were reduced (< 5%) respect to natural grassland (18%) in both years. Animal performance included loss of PV and maintenance of range of initial and final PV (1st year) and improvements in both parameters (2nd year). We conclude that management of animals in pastures generates a global benefit and increased efficiency in the productive system although animal performance depends on the maturative state of the pasture, that are in turn influenced by water conditions of the environment., En el SE de Santa Cruz, se desarrolló un trabajo con el objetivo de evaluar las pérdidas de corderas de reposición respecto al campo natural y la evolución del peso vivo desde enero a mayo durante dos años (2015-2016 y 2017-2018) en una pastura mezcla de pasto ovillo (Dactylis glomerata) y agropiro intermedio (Agropyron intermedium (Host) Beauvois. Tres lotes de corderas señaladas provenientes de tres campos fueron elegidas al azar y evaluadas. En los animales identificados se determinó en tres fechas (enero, febrero-marzo y abril-mayo) el peso vivo (PV), ganancias y rangos de PV. La pastura se muestreo en tres fechas (diciembre, marzo y mayo) para determinar la biomasa aérea disponible, el material vivo (MV) y muerto, la proteína bruta y digestibilidad de la materia seca. El análisis estadístico relaciono el PV de los animales con los días mediante regresiones y el PV de las corderas con el MV y las variables nutricionales mediante correlaciones. El trabajo incluyó registros de lluvias y temperaturas. En ambos años, se redujeron las pérdidas de animales en la pastura (< al 5%) respecto al campo natural (18%). La perfomance animal incluyó pérdidas de PV y mantenimiento del rango de PV inicial y final (1° año) y mejoras en ambos parámetros (2° año). Se concluye que el manejo aplicado genera un beneficio global y una mayor eficiencia en el sistema productivo aunque el desempeño animal depende del estado madurativo de la pastura influenciado por las condiciones hídricas ambientales.

We conducted an experiment in Southeast Santa Cruz, Patagonia, Argentina in order to evaluate losses of lambs respect to natural grassland, and evolution of live weight from January to May during two years (2015-2016 and 2017-2018) in a mixed pasture of orchardgrass (Dactylis glomerata) and intermediate wheatgrass (Agropyron intermedium (Host) Beauvois.Three flocks of marked ewes that came from three different paddocks were chosen randomly and evaluated. Live weight (PV) and ranges of PV were determined on three dates (January, February-March-April-May). Pasture’s available aerial biomass, the living(VM) and dead material, crude protein and dry matter digestibility were determined on three dates(December, March and May). Evolution of animal PV during the period was analyzed using regressions. Lamb PV was analyzed in relation to MV and nutritional variables through correlations. The work included records of rainfall and temperatures. Animal losses in the pasture were reduced (< 5%) respect to natural grassland (18%) in both years. Animal performance included loss of PV and maintenance of range of initial and final PV (1st year) and improvements in both parameters (2nd year). We conclude that management of animals in pastures generates a global benefit and increased efficiency in the productive system although animal performance depends on the maturative state of the pasture, that are in turn influenced by water conditions of the environment., En el SE de Santa Cruz, se desarrolló un trabajo con el objetivo de evaluar las pérdidas de corderas de reposición respecto al campo natural y la evolución del peso vivo desde enero a mayo durante dos años (2015-2016 y 2017-2018) en una pastura mezcla de pasto ovillo (Dactylis glomerata) y agropiro intermedio (Agropyron intermedium (Host) Beauvois. Tres lotes de corderas señaladas provenientes de tres campos fueron elegidas al azar y evaluadas. En los animales identificados se determinó en tres fechas (enero, febrero-marzo y abril-mayo) el peso vivo (PV), ganancias y rangos de PV. La pastura se muestreo en tres fechas (diciembre, marzo y mayo) para determinar la biomasa aérea disponible, el material vivo (MV) y muerto, la proteína bruta y digestibilidad de la materia seca. El análisis estadístico relaciono el PV de los animales con los días mediante regresiones y el PV de las corderas con el MV y las variables nutricionales mediante correlaciones. El trabajo incluyó registros de lluvias y temperaturas. En ambos años, se redujeron las pérdidas de animales en la pastura (< al 5%) respecto al campo natural (18%). La perfomance animal incluyó pérdidas de PV y mantenimiento del rango de PV inicial y final (1° año) y mejoras en ambos parámetros (2° año). Se concluye que el manejo aplicado genera un beneficio global y una mayor eficiencia en el sistema productivo aunque el desempeño animal depende del estado madurativo de la pastura influenciado por las condiciones hídricas ambientales.

Newcastle Disease (ND) is a continuing global threat to domestic poultry, especially in developing countries, where severe outbreaks of velogenic ND virus (NDV) often cause major economic losses to households. Local chickens are of great importance to rural family livelihoods through provision of high-quality protein. To investigate the genetic basis of host response to NDV, three popular Tanzanian chicken ecotypes (regional populations) were challenged with a lentogenic (vaccine) strain of NDV at 28 days of age. Various host response phenotypes, including anti-NDV antibody levels (pre-infection and 10 days post-infection, dpi), and viral load (2 and 6 dpi) were measured, in addition to growth rate. We estimated genetic parameters and conducted genome-wide association study analyses by genotyping 1399 chickens using the Affymetrix 600K chicken SNP chip. Estimates of heritability of the evaluated traits were moderate (0.18-0.35). Five quantitative trait loci (QTL) associated with growth and/or response to NDV were identified by single-SNP analyses, with some regions explaining ≥1% of genetic variance based on the Bayes-B method. Immune related genes, such as ETS1, TIRAP, and KIRREL3, were located in regions associated with viral load at 6 dpi. The moderate estimates of heritability and identified QTL indicate that NDV response traits may be improved through selective breeding of chickens to enhance increased NDV resistance and vaccine efficacy in Tanzanian local ecotypes.

We conducted an experiment in Southeast Santa Cruz, Patagonia, Argentina in order to evaluate losses of lambs respect to natural grassland, and evolution of live weight from January to May during two years (2015-2016 and 2017-2018) in a mixed pasture of orchardgrass (Dactylis glomerata) and intermediate wheatgrass (Agropyron intermedium (Host) Beauvois.Three flocks of marked ewes that came from three different paddocks were chosen randomly and evaluated. Live weight (PV) and ranges of PV were determined on three dates (January, February-March-April-May). Pasture’s available aerial biomass, the living(VM) and dead material, crude protein and dry matter digestibility were determined on three dates(December, March and May). Evolution of animal PV during the period was analyzed using regressions. Lamb PV was analyzed in relation to MV and nutritional variables through correlations. The work included records of rainfall and temperatures. Animal losses in the pasture were reduced (< 5%) respect to natural grassland (18%) in both years. Animal performance included loss of PV and maintenance of range of initial and final PV (1st year) and improvements in both parameters (2nd year). We conclude that management of animals in pastures generates a global benefit and increased efficiency in the productive system although animal performance depends on the maturative state of the pasture, that are in turn influenced by water conditions of the environment., En el SE de Santa Cruz, se desarrolló un trabajo con el objetivo de evaluar las pérdidas de corderas de reposición respecto al campo natural y la evolución del peso vivo desde enero a mayo durante dos años (2015-2016 y 2017-2018) en una pastura mezcla de pasto ovillo (Dactylis glomerata) y agropiro intermedio (Agropyron intermedium (Host) Beauvois. Tres lotes de corderas señaladas provenientes de tres campos fueron elegidas al azar y evaluadas. En los animales identificados se determinó en tres fechas (enero, febrero-marzo y abril-mayo) el peso vivo (PV), ganancias y rangos de PV. La pastura se muestreo en tres fechas (diciembre, marzo y mayo) para determinar la biomasa aérea disponible, el material vivo (MV) y muerto, la proteína bruta y digestibilidad de la materia seca. El análisis estadístico relaciono el PV de los animales con los días mediante regresiones y el PV de las corderas con el MV y las variables nutricionales mediante correlaciones. El trabajo incluyó registros de lluvias y temperaturas. En ambos años, se redujeron las pérdidas de animales en la pastura (< al 5%) respecto al campo natural (18%). La perfomance animal incluyó pérdidas de PV y mantenimiento del rango de PV inicial y final (1° año) y mejoras en ambos parámetros (2° año). Se concluye que el manejo aplicado genera un beneficio global y una mayor eficiencia en el sistema productivo aunque el desempeño animal depende del estado madurativo de la pastura influenciado por las condiciones hídricas ambientales.

Newcastle disease virus (NDV) is a highly contagious avian pathogen that poses a tremendous threat to poultry producers in endemic zones due to its epidemic potential. To investigate host genetic resistance to NDV while under the effects of heat stress, a genome-wide association study (GWAS) was performed on Hy-Line Brown layer chickens that were challenged with NDV while under high ambient temperature to identify regions associated with host viral titer, circulating anti-NDV antibody titer, and body weight change. A single nucleotide polymorphism (SNP) on chromosome 1 was associated with viral titer at two days post-infection (dpi), while 30 SNPs spanning a quantitative trait loci (QTL) on chromosome 24 were associated with viral titer at 6 dpi. Immune related genes, such as CAMK1d and CCDC3 on chromosome 1, associated with viral titer at 2 dpi, and TIRAP, ETS1, and KIRREL3, associated with viral titer at 6 dpi, were located in two QTL regions for viral titer that were identified in this study. This study identified genomic regions and candidate genes that are associated with response to NDV during heat stress in Hy-Line Brown layer chickens. Regions identified for viral titer on chromosome 1 and 24, at 2 and 6 dpi, respectively, included several genes that have key roles in regulating the immune response.

Newcastle Disease (ND) is a continuing global threat to domestic poultry, especially in developing countries, where severe outbreaks of velogenic ND virus (NDV) often cause major economic losses to households. Local chickens are of great importance to rural family livelihoods through provision of high-quality protein. To investigate the genetic basis of host response to NDV, three popular Tanzanian chicken ecotypes (regional populations) were challenged with a lentogenic (vaccine) strain of NDV at 28 days of age. Various host response phenotypes, including anti-NDV antibody levels (pre-infection and 10 days post-infection, dpi), and viral load (2 and 6 dpi) were measured, in addition to growth rate. We estimated genetic parameters and conducted genome-wide association study analyses by genotyping 1399 chickens using the Affymetrix 600K chicken SNP chip. Estimates of heritability of the evaluated traits were moderate (0.18-0.35). Five quantitative trait loci (QTL) associated with growth and/or response to NDV were identified by single-SNP analyses, with some regions explaining ≥1% of genetic variance based on the Bayes-B method. Immune related genes, such as ETS1, TIRAP, and KIRREL3, were located in regions associated with viral load at 6 dpi. The moderate estimates of heritability and identified QTL indicate that NDV response traits may be improved through selective breeding of chickens to enhance increased NDV resistance and vaccine efficacy in Tanzanian local ecotypes.

We conducted an experiment in Southeast Santa Cruz, Patagonia, Argentina in order to evaluate losses of lambs respect to natural grassland, and evolution of live weight from January to May during two years (2015-2016 and 2017-2018) in a mixed pasture of orchardgrass (Dactylis glomerata) and intermediate wheatgrass (Agropyron intermedium (Host) Beauvois.Three flocks of marked ewes that came from three different paddocks were chosen randomly and evaluated. Live weight (PV) and ranges of PV were determined on three dates (January, February-March-April-May). Pasture’s available aerial biomass, the living(VM) and dead material, crude protein and dry matter digestibility were determined on three dates(December, March and May). Evolution of animal PV during the period was analyzed using regressions. Lamb PV was analyzed in relation to MV and nutritional variables through correlations. The work included records of rainfall and temperatures. Animal losses in the pasture were reduced (< 5%) respect to natural grassland (18%) in both years. Animal performance included loss of PV and maintenance of range of initial and final PV (1st year) and improvements in both parameters (2nd year). We conclude that management of animals in pastures generates a global benefit and increased efficiency in the productive system although animal performance depends on the maturative state of the pasture, that are in turn influenced by water conditions of the environment., En el SE de Santa Cruz, se desarrolló un trabajo con el objetivo de evaluar las pérdidas de corderas de reposición respecto al campo natural y la evolución del peso vivo desde enero a mayo durante dos años (2015-2016 y 2017-2018) en una pastura mezcla de pasto ovillo (Dactylis glomerata) y agropiro intermedio (Agropyron intermedium (Host) Beauvois. Tres lotes de corderas señaladas provenientes de tres campos fueron elegidas al azar y evaluadas. En los animales identificados se determinó en tres fechas (enero, febrero-marzo y abril-mayo) el peso vivo (PV), ganancias y rangos de PV. La pastura se muestreo en tres fechas (diciembre, marzo y mayo) para determinar la biomasa aérea disponible, el material vivo (MV) y muerto, la proteína bruta y digestibilidad de la materia seca. El análisis estadístico relaciono el PV de los animales con los días mediante regresiones y el PV de las corderas con el MV y las variables nutricionales mediante correlaciones. El trabajo incluyó registros de lluvias y temperaturas. En ambos años, se redujeron las pérdidas de animales en la pastura (< al 5%) respecto al campo natural (18%). La perfomance animal incluyó pérdidas de PV y mantenimiento del rango de PV inicial y final (1° año) y mejoras en ambos parámetros (2° año). Se concluye que el manejo aplicado genera un beneficio global y una mayor eficiencia en el sistema productivo aunque el desempeño animal depende del estado madurativo de la pastura influenciado por las condiciones hídricas ambientales.

We conducted an experiment in Southeast Santa Cruz, Patagonia, Argentina in order to evaluate losses of lambs respect to natural grassland, and evolution of live weight from January to May during two years (2015-2016 and 2017-2018) in a mixed pasture of orchardgrass (Dactylis glomerata) and intermediate wheatgrass (Agropyron intermedium (Host) Beauvois.Three flocks of marked ewes that came from three different paddocks were chosen randomly and evaluated. Live weight (PV) and ranges of PV were determined on three dates (January, February-March-April-May). Pasture’s available aerial biomass, the living(VM) and dead material, crude protein and dry matter digestibility were determined on three dates(December, March and May). Evolution of animal PV during the period was analyzed using regressions. Lamb PV was analyzed in relation to MV and nutritional variables through correlations. The work included records of rainfall and temperatures. Animal losses in the pasture were reduced (< 5%) respect to natural grassland (18%) in both years. Animal performance included loss of PV and maintenance of range of initial and final PV (1st year) and improvements in both parameters (2nd year). We conclude that management of animals in pastures generates a global benefit and increased efficiency in the productive system although animal performance depends on the maturative state of the pasture, that are in turn influenced by water conditions of the environment., En el SE de Santa Cruz, se desarrolló un trabajo con el objetivo de evaluar las pérdidas de corderas de reposición respecto al campo natural y la evolución del peso vivo desde enero a mayo durante dos años (2015-2016 y 2017-2018) en una pastura mezcla de pasto ovillo (Dactylis glomerata) y agropiro intermedio (Agropyron intermedium (Host) Beauvois. Tres lotes de corderas señaladas provenientes de tres campos fueron elegidas al azar y evaluadas. En los animales identificados se determinó en tres fechas (enero, febrero-marzo y abril-mayo) el peso vivo (PV), ganancias y rangos de PV. La pastura se muestreo en tres fechas (diciembre, marzo y mayo) para determinar la biomasa aérea disponible, el material vivo (MV) y muerto, la proteína bruta y digestibilidad de la materia seca. El análisis estadístico relaciono el PV de los animales con los días mediante regresiones y el PV de las corderas con el MV y las variables nutricionales mediante correlaciones. El trabajo incluyó registros de lluvias y temperaturas. En ambos años, se redujeron las pérdidas de animales en la pastura (< al 5%) respecto al campo natural (18%). La perfomance animal incluyó pérdidas de PV y mantenimiento del rango de PV inicial y final (1° año) y mejoras en ambos parámetros (2° año). Se concluye que el manejo aplicado genera un beneficio global y una mayor eficiencia en el sistema productivo aunque el desempeño animal depende del estado madurativo de la pastura influenciado por las condiciones hídricas ambientales.

We conducted an experiment in Southeast Santa Cruz, Patagonia, Argentina in order to evaluate losses of lambs respect to natural grassland, and evolution of live weight from January to May during two years (2015-2016 and 2017-2018) in a mixed pasture of orchardgrass (Dactylis glomerata) and intermediate wheatgrass (Agropyron intermedium (Host) Beauvois.Three flocks of marked ewes that came from three different paddocks were chosen randomly and evaluated. Live weight (PV) and ranges of PV were determined on three dates (January, February-March-April-May). Pasture’s available aerial biomass, the living(VM) and dead material, crude protein and dry matter digestibility were determined on three dates(December, March and May). Evolution of animal PV during the period was analyzed using regressions. Lamb PV was analyzed in relation to MV and nutritional variables through correlations. The work included records of rainfall and temperatures. Animal losses in the pasture were reduced (< 5%) respect to natural grassland (18%) in both years. Animal performance included loss of PV and maintenance of range of initial and final PV (1st year) and improvements in both parameters (2nd year). We conclude that management of animals in pastures generates a global benefit and increased efficiency in the productive system although animal performance depends on the maturative state of the pasture, that are in turn influenced by water conditions of the environment., En el SE de Santa Cruz, se desarrolló un trabajo con el objetivo de evaluar las pérdidas de corderas de reposición respecto al campo natural y la evolución del peso vivo desde enero a mayo durante dos años (2015-2016 y 2017-2018) en una pastura mezcla de pasto ovillo (Dactylis glomerata) y agropiro intermedio (Agropyron intermedium (Host) Beauvois. Tres lotes de corderas señaladas provenientes de tres campos fueron elegidas al azar y evaluadas. En los animales identificados se determinó en tres fechas (enero, febrero-marzo y abril-mayo) el peso vivo (PV), ganancias y rangos de PV. La pastura se muestreo en tres fechas (diciembre, marzo y mayo) para determinar la biomasa aérea disponible, el material vivo (MV) y muerto, la proteína bruta y digestibilidad de la materia seca. El análisis estadístico relaciono el PV de los animales con los días mediante regresiones y el PV de las corderas con el MV y las variables nutricionales mediante correlaciones. El trabajo incluyó registros de lluvias y temperaturas. En ambos años, se redujeron las pérdidas de animales en la pastura (< al 5%) respecto al campo natural (18%). La perfomance animal incluyó pérdidas de PV y mantenimiento del rango de PV inicial y final (1° año) y mejoras en ambos parámetros (2° año). Se concluye que el manejo aplicado genera un beneficio global y una mayor eficiencia en el sistema productivo aunque el desempeño animal depende del estado madurativo de la pastura influenciado por las condiciones hídricas ambientales.

We conducted an experiment in Southeast Santa Cruz, Patagonia, Argentina in order to evaluate losses of lambs respect to natural grassland, and evolution of live weight from January to May during two years (2015-2016 and 2017-2018) in a mixed pasture of orchardgrass (Dactylis glomerata) and intermediate wheatgrass (Agropyron intermedium (Host) Beauvois.Three flocks of marked ewes that came from three different paddocks were chosen randomly and evaluated. Live weight (PV) and ranges of PV were determined on three dates (January, February-March-April-May). Pasture’s available aerial biomass, the living(VM) and dead material, crude protein and dry matter digestibility were determined on three dates(December, March and May). Evolution of animal PV during the period was analyzed using regressions. Lamb PV was analyzed in relation to MV and nutritional variables through correlations. The work included records of rainfall and temperatures. Animal losses in the pasture were reduced (< 5%) respect to natural grassland (18%) in both years. Animal performance included loss of PV and maintenance of range of initial and final PV (1st year) and improvements in both parameters (2nd year). We conclude that management of animals in pastures generates a global benefit and increased efficiency in the productive system although animal performance depends on the maturative state of the pasture, that are in turn influenced by water conditions of the environment., En el SE de Santa Cruz, se desarrolló un trabajo con el objetivo de evaluar las pérdidas de corderas de reposición respecto al campo natural y la evolución del peso vivo desde enero a mayo durante dos años (2015-2016 y 2017-2018) en una pastura mezcla de pasto ovillo (Dactylis glomerata) y agropiro intermedio (Agropyron intermedium (Host) Beauvois. Tres lotes de corderas señaladas provenientes de tres campos fueron elegidas al azar y evaluadas. En los animales identificados se determinó en tres fechas (enero, febrero-marzo y abril-mayo) el peso vivo (PV), ganancias y rangos de PV. La pastura se muestreo en tres fechas (diciembre, marzo y mayo) para determinar la biomasa aérea disponible, el material vivo (MV) y muerto, la proteína bruta y digestibilidad de la materia seca. El análisis estadístico relaciono el PV de los animales con los días mediante regresiones y el PV de las corderas con el MV y las variables nutricionales mediante correlaciones. El trabajo incluyó registros de lluvias y temperaturas. En ambos años, se redujeron las pérdidas de animales en la pastura (< al 5%) respecto al campo natural (18%). La perfomance animal incluyó pérdidas de PV y mantenimiento del rango de PV inicial y final (1° año) y mejoras en ambos parámetros (2° año). Se concluye que el manejo aplicado genera un beneficio global y una mayor eficiencia en el sistema productivo aunque el desempeño animal depende del estado madurativo de la pastura influenciado por las condiciones hídricas ambientales.

We conducted an experiment in Southeast Santa Cruz, Patagonia, Argentina in order to evaluate losses of lambs respect to natural grassland, and evolution of live weight from January to May during two years (2015-2016 and 2017-2018) in a mixed pasture of orchardgrass (Dactylis glomerata) and intermediate wheatgrass (Agropyron intermedium (Host) Beauvois.Three flocks of marked ewes that came from three different paddocks were chosen randomly and evaluated. Live weight (PV) and ranges of PV were determined on three dates (January, February-March-April-May). Pasture’s available aerial biomass, the living(VM) and dead material, crude protein and dry matter digestibility were determined on three dates(December, March and May). Evolution of animal PV during the period was analyzed using regressions. Lamb PV was analyzed in relation to MV and nutritional variables through correlations. The work included records of rainfall and temperatures. Animal losses in the pasture were reduced (< 5%) respect to natural grassland (18%) in both years. Animal performance included loss of PV and maintenance of range of initial and final PV (1st year) and improvements in both parameters (2nd year). We conclude that management of animals in pastures generates a global benefit and increased efficiency in the productive system although animal performance depends on the maturative state of the pasture, that are in turn influenced by water conditions of the environment., En el SE de Santa Cruz, se desarrolló un trabajo con el objetivo de evaluar las pérdidas de corderas de reposición respecto al campo natural y la evolución del peso vivo desde enero a mayo durante dos años (2015-2016 y 2017-2018) en una pastura mezcla de pasto ovillo (Dactylis glomerata) y agropiro intermedio (Agropyron intermedium (Host) Beauvois. Tres lotes de corderas señaladas provenientes de tres campos fueron elegidas al azar y evaluadas. En los animales identificados se determinó en tres fechas (enero, febrero-marzo y abril-mayo) el peso vivo (PV), ganancias y rangos de PV. La pastura se muestreo en tres fechas (diciembre, marzo y mayo) para determinar la biomasa aérea disponible, el material vivo (MV) y muerto, la proteína bruta y digestibilidad de la materia seca. El análisis estadístico relaciono el PV de los animales con los días mediante regresiones y el PV de las corderas con el MV y las variables nutricionales mediante correlaciones. El trabajo incluyó registros de lluvias y temperaturas. En ambos años, se redujeron las pérdidas de animales en la pastura (< al 5%) respecto al campo natural (18%). La perfomance animal incluyó pérdidas de PV y mantenimiento del rango de PV inicial y final (1° año) y mejoras en ambos parámetros (2° año). Se concluye que el manejo aplicado genera un beneficio global y una mayor eficiencia en el sistema productivo aunque el desempeño animal depende del estado madurativo de la pastura influenciado por las condiciones hídricas ambientales.

Aggregation is a sequence-specific process, nucleated by short aggregation-prone regions (APRs) that can be exploited to induce aggregation of proteins containing the same APR. Here, we find that most APRs are unique within a proteome, but that a small minority of APRs occur in many proteins. When aggregation is nucleated in bacteria by such frequently occurring APRs, it leads to massive and lethal inclusion body formation containing a large number of proteins. Buildup of bacterial resistance against these peptides is slow. In addition, the approach is effective against drug-resistant clinical isolates of Escherichia coli and Acinetobacter baumannii, reducing bacterial load in a murine bladder infection model. Our results indicate that redundant APRs are weak points of bacterial protein homeostasis and that targeting these may be an attractive antibacterial strategy., Funding Agencies|European Research Council under the European Unions Horizon Framework Programme ERC [647458]; Flanders Institute for Biotechnology (VIB); University of Leuven ("Industrieel Onderzoeksfonds"); Funds for Scientific Research Flanders (FWO); Flanders Agency for innovation by Science and Technology (IWT, SBO) [60839]; Federal Office for Scientific Affairs of Belgium (Belspo), IUAP [P7/16]; Erasmus Mundus fellowship; DBOF grant from KULeuven Research fund; Goran Gustafsson Foundation; Swedish Research council; Swedish Foundation for Strategic Research; Swedish Alzheimer Foundation

Aggregation is a sequence-specific process, nucleated by short aggregation-prone regions (APRs) that can be exploited to induce aggregation of proteins containing the same APR. Here, we find that most APRs are unique within a proteome, but that a small minority of APRs occur in many proteins. When aggregation is nucleated in bacteria by such frequently occurring APRs, it leads to massive and lethal inclusion body formation containing a large number of proteins. Buildup of bacterial resistance against these peptides is slow. In addition, the approach is effective against drug-resistant clinical isolates of Escherichia coli and Acinetobacter baumannii, reducing bacterial load in a murine bladder infection model. Our results indicate that redundant APRs are weak points of bacterial protein homeostasis and that targeting these may be an attractive antibacterial strategy., Funding Agencies|European Research Council under the European Unions Horizon Framework Programme ERC [647458]; Flanders Institute for Biotechnology (VIB); University of Leuven ("Industrieel Onderzoeksfonds"); Funds for Scientific Research Flanders (FWO); Flanders Agency for innovation by Science and Technology (IWT, SBO) [60839]; Federal Office for Scientific Affairs of Belgium (Belspo), IUAP [P7/16]; Erasmus Mundus fellowship; DBOF grant from KULeuven Research fund; Goran Gustafsson Foundation; Swedish Research council; Swedish Foundation for Strategic Research; Swedish Alzheimer Foundation

Newcastle disease virus (NDV) is a devastating worldwide poultry pathogen with major implications for global food security. In this study, two highly inbred and genetically distinct chicken lines, Fayoumis and Leghorns, were exposed to a lentogenic strain of NDV, while under the effects of heat stress, in order to understand the genetic mechanisms of resistance during high ambient temperatures. Fayoumis, which are relatively more resistant to pathogens than Leghorns, had larger numbers of differentially expressed genes (DEGs) during the early stages of infection when compared to Leghorns and subsequently down-regulated their immune response at the latter stages to return to homeostasis. Leghorns had very few DEGs across all observed time points, with the majority of DEGs involved with metabolic and glucose-related functions. Proteomic analysis corroborates findings made within Leghorns, while also identifying interesting candidate genes missed by expression profiling. Poor correlation between changes observed in the proteomic and transcriptomic datasets highlights the potential importance of integrative approaches to understand the mechanisms of disease response. Overall, this study provides novel insights into global protein and expression profiles of these two genetic lines, and provides potential genetic targets involved with NDV resistance during heat stress in poultry.