Christa F. Honaker

Extra-phosphoric effects of superdoses of a novel microbial phytase

An experiment was conducted to evaluate the influence of a novel microbial phytase on broiler performance from d 0 to 42 and tibia ash at d 21. Male Cobb 500 broilers (n = 2,016) were fed 1 of 7 experimental diets: positive control (PC) formulated to meet or exceed nutrient recommendations; PC plus dicalcium phosphate (PC+DCP) formulated to provide Ca and P at 0.10% above the PC; PC plus 500 U/kg of microbial phytase (PC+500); negative control (NC) with Ca and P reduced from the PC by 0.16 and 0.15%, respectively; and NC plus 500 (NC+500), 1,000 (NC+1,000), or 1,500 (NC+1,500) U/kg of microbial phytase. Diets were fed in 3 phases from d 0 to 21, d 22 to 42, and d 43 to 49 to 32 birds/pen and 9 replicate pens/diet. From d 0 to 21, broilers fed the NC diet had decreased (P ≤ 0.05) BW gain and tibia ash compared with broilers fed all other diets, except tibia ash in birds fed PC+500. Phytase supplementation at 500, 1,000, or 1,500 U/kg to the NC improved (P ≤ 0.05) BW gain and tibia ash comparable with the PC. Feed conversion ratio (FCR) was improved (P ≤ 0.05) in broilers fed NC+1,500 compared with broilers fed all other diets. From d 0 to 49, growth performance was not influenced (P > 0.05) by diet. However, FCR was improved (P ≤ 0.05) in broilers fed 1,500 U/kg of microbial phytase compared with broilers fed the PC, PC+DCP, and NC. There were no differences in performance or tibia ash between broilers fed the PC or PC+DCP, which would indicate the PC diet was sufficient in Ca and P. Therefore, the improvements in FCR in the NC+1500 may be associated with mitigation of the antinutrient effects of phytate rather than improved P utilization.

Body Weight Selection Affects Quantitative Genetic Correlated Responses in Gut Microbiota

The abundance of gut microbiota can be viewed as a quantitative trait, which is affected by the genetics and environment of the host. To quantify the effects of host genetics, we calculated the heritability of abundance of specific microorganisms and genetic correlations among them in the gut microbiota of two lines of chickens maintained under the same husbandry and dietary regimes. The lines, which originated from a common founder population, had undergone >50 generations of selection for high (HW) or low (LW) 56-day body weight and now differ by more than 10-fold in body weight at selection age. We identified families of Paenibacillaceae, Streptococcaceae, Helicobacteraceae, and Burkholderiaceae that had moderate heritabilities. Although there were no obvious phenotypic correlations among gut microbiota, significant genetic correlations were observed. Moreover, the effects were modified by genetic selection for body weight, which altered the quantitative genetic background of the host. Heritabilities for Bacillaceae, Flavobacteriaceae, Helicobacteraceae, Comamonadaceae, Enterococcaceae, and Streptococcaceae were moderate in LW line and little to zero in the HW line. These results suggest that loci associated with these microbiota families, while exhibiting genetic variation in LW, have been fixed in HW line. Also, long term selection for body weight has altered the genetic correlations among gut microbiota. No microbiota families had significant heritabilities in both the LW and HW lines suggesting that the presence and/or absence of a particular microbiota family either has a strong growth promoting or inhibiting effect, but not both. These results demonstrate that the quantitative genetics of the host have considerable influence on the gut microbiota.

Sex-linked barring in chickens is controlled by the CDKN2A/B tumour suppressor locus.

Sex‐linked barring, a common plumage colour found in chickens, is characterized by black and white barred feathers. Previous studies have indicated that the white bands are caused by an absence of melanocytes in the feather follicle during the growth of this region. Here, we show that Sex‐linked barring is controlled by the CDKN2A/B locus, which encodes the INK4b and ARF transcripts. We identified two non‐coding mutations in CDKN2A that showed near complete association with the phenotype. In addition, two missense mutations were identified at highly conserved sites, V9D and R10C, and every bird tested with a confirmed Sex‐linked barring phenotype carried one of these missense mutations. Further work is required to determine if one of these or a combined effect of two or more CDKN2A mutations is causing Sex‐linked barring. This novel finding provides the first evidence that the tumour suppressor locus CDKN2A/B can affect pigmentation phenotypes and sheds new light on the functional significance of this gene.

Phenotypic responses of chickens to long-term selection for high or low antibody titers to sheep red blood cells

A long-term bidirectional selection experiment was conducted to study antibody response to SRBC. Lines, high antibody selection (HAS) and low antibody selection (LAS), originating from the same White Leghorn base population had undergone 37 generations of selection for either high or low antibody response 5 d after a single intravenous injection of 0.1 mL of a 0.25% suspension of SRBC antigen. Subpopulations, where selection was relaxed, were maintained as contemporaries with the selected lines from generations 16 to 24 [high antibody relaxed (HAR) and low antibody relaxed (LAR)] and 24 to 37. Body weights were obtained at 4, 24, and 38 wk of age and at the onset of lay (BW at first egg). Also measured were age in days to first egg, percentages of hen-day ovulations and normal egg production, and percentages of normal and defective eggs from total ovulation (PNE and PDE). Selection lead to a large divergence in antibody titers between the selected lines, with a plateau reached in line LAS. Line HAS and HAR females displayed higher antibody titers, lower BW4, and matured at older ages than those from LAS and LAR (P < 0.05). Correlations between BW at 4 wk and antibody titers were different between the selected lines, being positive in line LAS and negative in line HAS. Quadratic regression models fit well with antibody titers, BW4, and PNE, with limiting values for these traits calculated based on regression curves. For line HAS, plots showed that an increased tendency of antibody titers was followed by decreased BW4 and increased PNE. For line LAS, however, antibody titers and BW4 decreased in parallel while PNE increased. It appears that at the phenotypic level there was a resource balance between immune response, growth, and reproductive traits, which during long-term selection, individuals altered their dynamic of resource allocations to satisfy certain needs.

Effect of incubation temperature on nutrient transporters and small intestine morphology of broiler chickens

This study evaluated the effects of elevated incubation temperature on posthatch nutrient transporter gene expression, integrity of the intestinal epithelium, organ development, and performance in Ross 308 broiler chickens. Ross × Ross 308 fertile eggs (n = 900) were incubated at different eggshell temperatures during development. From embryonic day (ED) 1 to ED12, all eggs were incubated at 37.1°C, whereas from ED13 to ED21, the eggs were divided into 2 groups for incubation at 37.4°C (S) or 39.6°C (H). Performance characteristics were measured at day of hatch (DOH) and d 7, 14, 21, 30, and 42. Small intestine and residual yolk sacs were collected at DOH and d 2, 4, 6, and 10 and weighed individually. Intestinal samples from the duodenum, jejunum, and ileum were evaluated for mucosal morphology and relative nutrient transporter gene expression. No significant differences were found in performance or organ weights. The intestinal morphology results showed a temperature × age interaction in duodenum villus height (P = 0.02) and crypt depth (P = 0.05) and in ileum villus height-to-crypt depth ratios (P = 0.02). There was a main effect of temperature, resulting in deeper crypts (P = 0.02) in the jejunum of chicks incubated at H compared with S. In the nutrient gene expression evaluation, peptide transporter (PepT1) showed a temperature × age interaction. On DOH and d 2, 4, and 10, PepT1 expression was similar between chicks incubated at S and H. However, on d 6, chicks incubated at S had significantly higher expression of PepT1 than those incubated at H. This study presents the effects of elevated incubation temperature on small intestine morphology and relative expression of nutrient transporter mRNA in high-yield broiler chicks, which can be important for the availability of nutrients and distribution of energy.

Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance

Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB, both novel mutations in Gallus, allowed us to estimate a molecular rate of 3.13 × 10−7 mutations/site/year (95% confidence interval 3.75 × 10−8–1.12 × 10−6). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 individuals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods.

Chickens from lines artificially selected for juvenile low and high body weight differ in glucose homeostasis and pancreas physiology

Artificial selection of White Plymouth Rock chickens for juvenile (day 56) body weight resulted in two divergent genetic lines: hypophagic low weight (LWS) chickens and hyperphagic obese high weight (HWS) chickens, with the latter more than 10-fold heavier than the former at selection age. A study was designed to investigate glucose regulation and pancreas physiology at selection age in LWS chickens and HWS chickens. Oral glucose tolerance and insulin sensitivity tests revealed differences in threshold sensitivity to insulin and glucose clearance rate between the lines. Results from real-time PCR showed greater pancreatic mRNA expression of four glucose regulatory genes (preproinsulin, PPI; preproglucagon, PPG; glucose transporter 2, GLUT2; and pancreatic duodenal homeobox 1, Pdx1) in LWS chickens, than HWS chickens. Histological analysis of the pancreas revealed that HWS chickens have larger pancreatic islets, less pancreatic islet mass, and more pancreatic inflammation than LWS chickens, all of which presumably contribute to impaired glucose metabolism.

Gut Microbiota Co-microevolution with Selection for Host Humoral Immunity

To explore coevolution between the gut microbiota and the humoral immune system of the host, we used chickens as the model organism. The host populations were two lines (HAS and LAS) developed from a common founder that had undergone 40 generations of divergent selection for antibody titers to sheep red blood cells (SRBC) and two relaxed sublines (HAR and LAR). Analysis revealed that microevolution of host humoral immunity contributed to the composition of gut microbiota at the taxa level. Relaxing selection enriched some microorganisms whose functions were opposite to host immunity. Particularly, Ruminococcaceae and Oscillospira enriched in high antibody relaxed (HAR) and contributed to reduction in antibody response, while Lactobacillus increased in low antibody relaxed (LAR) and elevated the antibody response. Microbial functional analysis showed that alterations were involved in pathways relating to the immune system and infectious diseases. Our findings demonstrated co-microevolution relationships of host-microbiota and that gut microorganisms influenced host immunity.

Selection for juvenile body weight in chickens: Standardizing for scaling

&NA; The influence of scaling on phenotypic responses to long‐term selection was evaluated in lines of chickens selected for high (HWS) and low (LWS) 8‐week body weight. The focus of the experiment was on phenotypic correlations between means and standard deviations, and unadjusted vs. standardized responses. Traits measured were body weight at 4 (BW4) and 8 wk (BW8). Correlations between means and standard deviations for BW8 (the selected trait) were positive and greater for BW4 in LWS than HWS. In both lines, scaling masked the degree more than the pattern of response; however, after standardization, it was greater in LWS than HWS. Selection changed the standard deviation units of juvenile BW with a 2‐fold difference in BW8 for both HWS and LWS in which the latter reached a physiological limit. Standardization is a robust method to adjust for scaling, thus enhancing the interpretability of responses in long‐term selection experiments. Because of changes in variances associated with those in phenotypic means, this method to correct for part‐whole correlations was useful.

Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci

The Virginia chicken lines have been divergently selected for juvenile body weight for more than 50 generations. Today, the high- and low-weight lines show a >12-fold difference for the selected trait, 56-d body weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several quantitative trait loci (QTL) contributing to weight differences between the lines were mapped in an F2-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the genetic diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to explore regions associated with 56-d body weight. The approach revealed several statistically and population structure independent associations and increased the mapping resolution. Further, most QTL were also found to contain multiple independent associations to markers that were not fixed in the founder populations, implying a complex underlying architecture due to the combined effects of multiple, linked loci perhaps located on independent haplotypes that still segregate in the selected lines.