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Browsing by Author "Ashwell, Christopher M."

Now showing 1 - 11 of 11
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    A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens
    Feng, Chungang; Gao, Yu; Dorshorst, Benjamin J.; Song, Chi; Gu, Xiaorong; Li, Qingyuan; Li, Jinxiu; Liu, Tongxin; Rubin, Carl-Johan; Zhao, Yiqiang; Wang, Yanqiang; Fei, Jing; Li, Huifang; Chen, Kuanwei; Qu, Hao; Shu, Dingming; Ashwell, Christopher M.; Da, Yang; Andersson, Leif; Hu, Xiaoxiang; Li, Ning (PLoS, 2014-08)
    Silky-feather has been selected and fixed in some breeds due to its unique appearance. This phenotype is caused by a single recessive gene (hookless, h). Here we map the silky-feather locus to chromosome 3 by linkage analysis and subsequently fine-map it to an 18.9 kb interval using the identical by descent (IBD) method. Further analysis reveals that a C to G transversion located upstream of the prenyl (decaprenyl) diphosphate synthase, subunit 2 (PDSS2) gene is causing silky-feather. All silky-feather birds are homozygous for the G allele. The silky-feather mutation significantly decreases the expression of PDSS2 during feather development in vivo. Consistent with the regulatory effect, the C to G transversion is shown to remarkably reduce PDSS2 promoter activity in vitro. We report a new example of feather structure variation associated with a spontaneous mutation and provide new insight into the PDSS2 function.
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    Corticotrophin Releasing Hormone Modulation of Feed Intake, Gastric Motility, and Behavior in Low and High Body Weight Selected Lines of Chickens
    Cline, Mark A. (Virginia Tech, 2005-05-04)
    The effect of intracerebroventricular (ICV) injection of corticotrophin releasing hormone (CRH) and related compounds on appetite, behavior, and gastric motility in lines of chickens, one selected for low body weight (LWS) and the other high body weight (HWS), was determined. Nucleotide sequence and expression patterns of the CRHr2 receptor, involved in appetite regulation, were also determined. Some individuals of the LWS line are anorexics and many die simply from not eating while some individuals in the HWS line are compulsive eaters and exhibit obesity. CRH is a 41 residue peptide that initiates an organism's stress response and is a potent inhibitor of appetite. An ICV injection of CRH dose-dependently decreased feed intake in both lines but did not effect water intake. When CRH receptor antagonists were ICV injected an increase in feed intake in the LWS line but not in the HWS line was observed, however the appetite reducing effect of CRH was attenuated in the HWS line but not in the LWS line. The LWS line has higher concentration of corticosterone than does the HWS line. In both lines at all times treatment with CRH caused an increase in locomotion and no CRH-treated chicks from either line slept post injection. Chicks from the LWS line that were treated with CRH exhibited other anxiety related behaviors sooner than the HWS line. The LWS line showed a liner increase in crop emptying time as the dose of ICV CRH increased. The HWS line responded with a quadratic dose response to CRH treatment. Polymorphisms in the CRHr2 receptor were found in both lines in the same positions, thus we concluded these differences do not significantly contribute to body weight differences. However, differences detected in expression patterns between lines for the CRHr2 receptor may contribute to their different body weights. We conclude that differences in the CRH system, its concentrations and differential receptor action, of these two lines may be partly responsible for their altered body weight phenotype.
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    Genetic analysis of production, physiological, and egg quality traits in heat-challenged commercial white egg-laying hens using 600k SNP array data
    Rowland, Kaylee; Ashwell, Christopher M.; Persia, Michael E.; Rothschild, Max F.; Schmidt, Carl J.; Lamont, Susan J. (2019-06-25)
    Background Heat stress negatively affects the welfare and production of chickens. High ambient temperature is considered one of the most ubiquitous abiotic environmental challenges to laying hens around the world. In this study, we recorded several production traits, feed intake, body weight, digestibility, and egg quality of 400 commercial white egg-laying hens before and during a 4-week heat treatment. For the phenotypes that had estimated heritabilities (using 600k SNP chip data) higher than 0, SNP associations were tested using the same 600k genotype data. Results Seventeen phenotypes had heritability estimates higher than 0, including measurements at various time points for feed intake, feed efficiency, body weight, albumen weight, egg quality expressed in Haugh units, egg mass, and also for change in egg mass from prior to heat exposure to various time points during the 4-week heat treatment. Quantitative trait loci (QTL) were identified for 10 of these 17 phenotypes. Some of the phenotypes shared QTL including Haugh units before heat exposure and after 4 weeks of heat treatment. Conclusions Estimated heritabilities differed from 0 for 17 traits, which indicates that they are under genetic control and that there is potential for improving these traits through selective breeding. The association of different QTL with the same phenotypes before heat exposure and during heat treatment indicates that genomic control of traits under heat stress is distinct from that under thermoneutral conditions. This study contributes to the knowledge on the genomic control of response to heat stress in laying hens.
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    Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens
    Lillie, Mette; Sheng, Zheya; Honaker, Christa F.; Dorshorst, Benjamin J.; Ashwell, Christopher M.; Siegel, Paul B.; Carlborg, Örjan (2017-01-18)
    Background Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation. Here we implement a pooled genome re-sequencing approach to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells. Results We observed wide genome involvement in response to this selection regime. Many genomic regions were highly differentiated resulting from this experimental selection regime, an involvement of up to 20% of the chicken genome (208.8 Mb). While genetic drift has certainly contributed to this, we implement gene ontology, association analysis and population simulations to increase our confidence in candidate selective sweeps. Three strong candidate genes, MHC, SEMA5A and TGFBR2, are also presented. Conclusions The extensive genomic changes highlight the polygenic genetic architecture of antibody response in these chicken populations, which are derived from a common founder population, demonstrating the extent of standing immunogenetic variation available at the onset of selection.
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    Genomic and Physiological Differences for Ghrelin and Leptin Receptor in Lines of Chickens Selected for High and Low Body Weight
    Kuo, Alice Yi-Wen (Virginia Tech, 2003-12-08)
    Autonomic nervous system (ANS) activity is related to body weight regulation. Based on the hypothesis that Most Obesities kNown Are Low In Sympathetic Activity (MONA LISA), it has been suggested that most obese subjects and animals have low sympathetic nervous system activity. Leptin, leptin receptor, and ghrelin genes influence the ANS regulation of body weight and food intake. The aim of this study was to investigate whether there are differences in leptin, the leptin receptor, or ghrelin regulation between lines of chickens selected for high (HWS) or low body weight (LWS). Intraperitoneal injections of reserpine were administrated to chickens from the HWS and LWS lines. Body weight and food intake were then compared to evaluate ANS regulation. While reserpine caused a transitory decrease in food intake and body weight in both lines, the magnitude of the change was greater in the HWS than in the LWS chickens. However, chickens from the LWS line exhibited greater catecholamine and indoleamine level changes in response to reserpine than those from the HWS line. Therefore, HWS chickens were more sensitive to the body weight-reducing effects of reserpine than LWS lines, while LWS chickens appeared to have greater sympathetic nervous system activity. Food and water intakes were differentially affected in HWS and LWS chickens in response to intracerebroventricular administration of human recombinant leptin. Leptin caused a linear decrease in food intake in the LWS line, but no effect on food intake in the HWS lines. The HWS chickens tended to have reduced water intake following leptin administration. These results suggest that the leptin receptor, or the down-stream neuropeptide regulation pathway mediating the effect of leptin; may be different between chickens from the HWS and LWS lines. Leptin, insulin like growth factor (IGF)-1, and IGF-2 concentrations in the plasma of HWS and LWS lines of chickens were evaluated. Leptin, IGF-1 and IGF-2 levels were significantly higher in the LWS than HWS chickens. The HWS female leptin concentrations were significantly lower than in HWS males or LWS females. Male chickens had greater IGF-1 concentrations in the plasma than female chickens. However, the concentration of IGF-2 did not differ between sexes. The difference in leptin concentrations in these lines and sexes may explain the differences in age of sexual maturity. Different IGF-1 and IGF-2 concentrations may be involved in the obese and anorexic conditions, fast and slow growth, and high and low food consumption found in these two lines of chickens. Differences in the gene sequence of the leptin receptor were observed in HWS and LWS lines of chickens. A single nucleotide polymorphism (SNP) in the intron between exon 8 and 9 introduced a restriction site for the enzyme Sel I in the HWS, but not the LWS line. Two SNP were detected in the leptin receptor cDNA region at nucleotides 189 and 234. At nucleotide 189, the LWS line has both a homozygous (T-T) and heterozygous (C-T), whereas the HWS line has only homozygous (T-T) form. The SNP found in nucleotide 234 introduces a restriction site Mse I in the HWS, but not the LWS line. These specific changes may be directly involved or closely linked to differences between the two lines in either the coding or regulatory domains of the leptin receptor. Differences in the leptin receptor gene expression between HWS and LWS lines of chickens in various organs and ages were observed. Leptin receptor expression in the whole brain was significantly different between sexes at 28 days-of-age in the HWS and LWS lines. The LWS line had higher leptin receptor gene expression in the liver at 2 days-of-age than at 56 and 363 days-of-age, but no differences were observed in the HWS line. In addition, at 2 days-of age, liver leptin receptor gene expression was higher in LWS than HWS chickens, but the reverse was observed at 363 days-of age. In adipose tissue, leptin receptor expression was higher in the LWS than HWS line. Leptin receptor expression in adipose tissue was greater at 363, than 28 and 56 days-of-ages. Our results showed that changes in the regulation of leptin and the leptin receptor were associated with sex, age, and growth. Differences in the ghrelin gene in the HWS and LWS lines under different feeding conditions were investigated. Both HWS and LWS chickens have six extra base pairs in the 5'-untranslated region. The LWS male ghrelin gene expression was significantly lower than in the LWS female and HWS male. The 84 day-old males had lower gene expression than 84 day-old females and 363 day-old males. When comparing different feeding methods, females allowed ad libitum feed consumption had a lower cycle threshold cycle number (CT) ratio than males allowed ad libitum feeding or fasted females. However, the inflection point cycle number of ad libitum fed females was lower than that of the ad libitum fed males, but greater than the fasted females. Ghrelin gene expression was different between the two lines of chickens, and the expression of ghrelin in chickens was influenced by body weight selection, sex, age, and feeding condition.
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    Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure
    Fleming, Damarius S.; Weigend, Steffen; Simianer, Henner; Weigend, Annett; Rothschild, Max F.; Schmidt, Carl J.; Ashwell, Christopher M.; Persia, Michael E.; Reecy, James; Lamont, Susan J. (Genetics Society of America, 2017-05)
    Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed FST, integrated haplotype score (iHS), and runs of homozygosity (ROH) procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27) and Northern European (chromosome 2) birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population's indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions.
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    A Genomic Duplication is Associated with Ectopic Eomesodermin Expression in the Embryonic Chicken Comb and Two Duplex-comb Phenotypes
    Dorshorst, Benjamin J.; Harun-Or-Rashid, Mohammad; Bagherpoor, Alireza Jian; Rubin, Carl-Johan; Ashwell, Christopher M.; Gourichon, David; Tixier-Boichard, Michele; Hallböök, Finn; Andersson, Leif (PLoS, 2015-03)
    Duplex-comb (D) is one of three major loci affecting comb morphology in the domestic chicken. Here we show that the two Duplex-comb alleles, V-shaped (D*V) and Buttercup (D*C), are both associated with a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene (EOMES). EOMES is a T-box transcription factor that is involved in mesoderm specification during gastrulation. In D*V and D*C chicken embryos we find that EOMES is ectopically expressed in the ectoderm of the comb-developing region as compared to wild-type embryos. The confinement of the ectopic expression of EOMES to the ectoderm is in stark contrast to the causal mechanisms underlying the two other major comb loci in the chicken (Rose-comb and Pea-comb) in which the transcription factors MNR2 and SOX5 are ectopically expressed strictly in the mesenchyme. Interestingly, the causal mutations of all three major comb loci in the chicken are now known to be composed of large-scale structural genomic variants that each result in ectopic expression of transcription factors. The Duplex-comb locus also illustrates the evolution of alleles in domestic animals, which means that alleles evolve by the accumulation of two or more consecutive mutations affecting the phenotype. We do not yet know whether the V-shaped or Buttercup allele correspond to the second mutation that occurred on the haplotype of the original duplication event.
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    Identification of quantitative trait loci for body temperature, body weight, breast yield, and digestibility in an advanced intercross line of chickens under heat stress
    Van Goor, Angelica G.; Bolek, Kevin J.; Ashwell, Christopher M.; Persia, Michael E.; Rothschild, Max F.; Schmidt, Carl J.; Lamont, Susan J. (2015-12-17)
    Background Losses in poultry production due to heat stress have considerable negative economic consequences. Previous studies in poultry have elucidated a genetic influence on response to heat. Using a unique chicken genetic resource, we identified genomic regions associated with body temperature (BT), body weight (BW), breast yield, and digestibility measured during heat stress. Identifying genes associated with a favorable response during high ambient temperature can facilitate genetic selection of heat-resilient chickens. Methods Generations F18 and F19 of a broiler (heat-susceptible) × Fayoumi (heat-resistant) advanced intercross line (AIL) were used to fine-map quantitative trait loci (QTL). Six hundred and thirty-one birds were exposed to daily heat cycles from 22 to 28 days of age, and phenotypes were measured before heat treatment, on the 1st day and after 1 week of heat treatment. BT was measured at these three phases and BW at pre-heat treatment and after 1 week of heat treatment. Breast muscle yield was calculated as the percentage of BW at day 28. Ileal feed digestibility was assayed from digesta collected from the ileum at day 28. Four hundred and sixty-eight AIL were genotyped using the 600 K Affymetrix chicken SNP (single nucleotide polymorphism) array. Trait heritabilities were estimated using an animal model. A genome-wide association study (GWAS) for these traits and changes in BT and BW was conducted using Bayesian analyses. Candidate genes were identified within 200-kb regions around SNPs with significant association signals. Results Heritabilities were low to moderate (0.03 to 0.35). We identified QTL for BT on Gallus gallus chromosome (GGA)14, 15, 26, and 27; BW on GGA1 to 8, 10, 14, and 21; dry matter digestibility on GGA19, 20 and 21; and QTL of very large effect for breast muscle yield on GGA1, 15, and 22 with a single 1-Mb window on GGA1 explaining more than 15 % of the genetic variation. Conclusions This is the first study to estimate heritabilities and perform GWAS using this AIL for traits measured during heat stress. Significant QTL as well as low to moderate heritabilities were found for each trait, and these QTL may facilitate selection for improved animal performance in hot climatic conditions.
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    Immunomodulatory effects of heat stress and lipopolysaccharide on the bursal transcriptome in two distinct chicken lines
    Monson, Melissa S.; Van Goor, Angelica G.; Ashwell, Christopher M.; Persia, Michael E.; Rothschild, Max F.; Schmidt, Carl J.; Lamont, Susan J. (2018-08-30)
    Background Exposure to heat stress suppresses poultry immune responses, which can increase susceptibility to infectious diseases and, thereby, intensify the negative effects of heat on poultry welfare and performance. Identifying genes and pathways that are affected by high temperatures, especially heat-induced changes in immune responses, could provide targets to improve disease resistance in chickens. This study utilized RNA-sequencing (RNA-seq) to investigate transcriptome responses in the bursa of Fabricius, a primary immune tissue, after exposure to acute heat stress and/or subcutaneous immune stimulation with lipopolysaccharide (LPS) in a 2 × 2 factorial design: Thermoneutral + Saline, Heat + Saline, Thermoneutral + LPS and Heat + LPS. All treatments were investigated in two chicken lines: a relatively heat- and disease-resistant Fayoumi line and a more susceptible broiler line. Results Differential expression analysis determined that Heat + Saline had limited impact on gene expression (N = 1 or 63 genes) in broiler or Fayoumi bursa. However, Thermoneutral + LPS and Heat + LPS generated many expression changes in Fayoumi bursa (N = 368 and 804 genes). Thermoneutral + LPS was predicted to increase immune-related cell signaling and cell migration, while Heat + LPS would activate mortality-related functions and decrease expression in WNT signaling pathways. Further inter-treatment comparisons in the Fayoumi line revealed that heat stress prevented many of the expression changes caused by LPS. Although fewer significant expression changes were observed in the broiler bursa after exposure to Thermoneutral + LPS (N = 59 genes) or to Heat + LPS (N = 146 genes), both treatments were predicted to increase cell migration. Direct comparison between lines (broiler to Fayoumi) confirmed that each line had distinct responses to treatment. Conclusions Transcriptome analysis identified genes and pathways involved in bursal responses to heat stress and LPS and elucidated that these effects were greatest in the combined treatment. The interaction between heat and LPS was line dependent, with suppressive expression changes primarily in the Fayoumi line. Potential target genes, especially those involved in cell migration and immune signaling, can inform future research on heat stress in poultry and could prove useful for improving disease resistance.
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    Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress
    Van Goor, Angelica G.; Ashwell, Christopher M.; Persia, Michael E.; Rothschild, Max F.; Schmidt, Carl J.; Lamont, Susan J. (2016-04-14)
    Background Heat stress in poultry results in considerable economic losses and is a concern for both animal health and welfare. Physiological changes occur during periods of heat stress, including changes in blood chemistry components. A highly advanced intercross line, created from a broiler (heat susceptible) by Fayoumi (heat resistant) cross, was exposed to daily heat cycles for seven days starting at 22 days of age. Blood components measured pre-heat treatment and on the seventh day of heat treatment included pH, pCO2, pO2, base excess, HCO3, TCO2, K, Na, ionized Ca, hematocrit, hemoglobin, sO2, and glucose. A genome-wide association study (GWAS) for these traits and their calculated changes was conducted to identify quantitative trait loci (QTL) using a 600 K SNP panel. Results There were significant increases in pH, base excess, HCO3, TCO2, ionized Ca, hematocrit, hemoglobin, and sO2, and significant decreases in pCO2 and glucose after 7 days of heat treatment. Heritabilities ranged from 0.01-0.21 for pre-heat measurements, 0.01-0.23 for measurements taken during heat, and 0.00-0.10 for the calculated change due to heat treatment. All blood components were highly correlated within measurement days, but not correlated between measurement days. The GWAS revealed 61 QTL for all traits, located on GGA (Gallus gallus chromosome) 1, 3, 6, 9, 10, 12–14, 17, 18, 21–28, and Z. A functional analysis of the genes in these QTL regions identified the Angiopoietin pathway as significant. The QTL that co-localized for three or more traits were on GGA10, 22, 26, 28, and Z and revealed candidate genes for birds’ response to heat stress. Conclusions The results of this study contribute to our knowledge of levels and heritabilities of several blood components of chickens under thermoneutral and heat stress conditions. Most components responded to heat treatment. Mapped QTL may serve as markers for genomic selection to enhance heat tolerance in poultry. The Angiopoietin pathway is likely involved in the response to heat stress in chickens. Several candidate genes were identified, giving additional insight into potential mechanisms of physiologic response to high ambient temperatures.
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    Unique genetic responses revealed in RNA-seq of the spleen of chickens stimulated with lipopolysaccharide and short-term heat
    Van Goor, Angelica G.; Ashwell, Christopher M.; Persia, Michael E.; Rothschild, Max F.; Schmidt, Carl J.; Lamont, Susan J. (PLOS, 2017-02-06)
    Climate change and disease have large negative impacts on poultry production, but little is known about the interactions of responses to these stressors in chickens. Fayoumi (heat and disease resistant) and broiler (heat and disease susceptible) chicken lines were stimulated at 22 days of age, using a 2x2x2 factorial design including: breed (Fayoumi or broiler), inflammatory stimulus (lipopolysaccharide (LPS) or saline), and temperature (35°C or 25°C). Transcriptional changes in spleens were analyzed using RNA-sequencing on the Illumina HiSeq 2500. Thirty-two individual cDNA libraries were sequenced (four per treatment) and an average of 22 million reads were generated per library. Stimulation with LPS induced more differentially expressed genes (DEG, log2 fold change ≥ 2 and FDR ≤ 0.05) in the broiler (N = 283) than the Fayoumi (N = 85), whereas heat treatment resulted in fewer DEG in broiler (N = 22) compared to Fayoumi (N = 107). The double stimulus of LPS+heat induced the largest numbers of changes in gene expression, for which broiler had 567 DEG and Fayoumi had 1471 DEG of which 399 were shared between breeds. Further analysis of DEG revealed pathways impacted by these stressors such as Remodelling of Epithelial Adherens Junctions due to heat stress, Granulocyte Adhesion and Diapedesis due to LPS, and Hepatic Fibrosis/Hepatic Stellate Cell Activation due to LPS+heat. The genes and pathways identified provide deeper understanding of the response to the applied stressors and may serve as biomarkers for genetic selection for heat and disease tolerant chickens.