Parameters of the chicken genome (Gallus gallus)

As more information on the chicken genome is gathered, it is becoming increasingly more important to be able to correlate genetic and physical maps. Quantitation of the chicken karyotype is important in establishing parameters which define the genome. Here we report on the physical lengths of the chicken macrochromosomes and establish the DNA content of each, thus identifying implicitly how much of the genome is represented by the microchromosomal component. For the first time, genetic and physical data on the chicken karyotype are presented in relation to one another.     

It's not too Late for the Harpy Eagle (Harpia harpyja): High Levels Of Genetic Diversity and Differentiation Can Fuel Conservation Programs

Background

The harpy eagle (Harpia harpyja) is the largest Neotropical bird of prey and is threatened by human persecution and habitat loss and fragmentation. Current conservation strategies include local education, captive rearing and reintroduction, and protection or creation of trans-national habitat blocks and corridors. Baseline genetic data prior to reintroduction of captive-bred stock is essential for guiding such efforts but has not been gathered previously.

Methodology/Findings

We assessed levels of genetic diversity, population structure and demographic history for harpy eagles using samples collected throughout a large portion of their geographic distribution in Central America (n = 32) and South America (n = 31). Based on 417 bp of mitochondrial control region sequence data, relatively high levels of haplotype and nucleotide diversity were estimated for both Central and South America, although haplotype diversity was significantly higher for South America. Historical restriction of gene flow across the Andes (i.e. between our Central and South American subgroups) is supported by coalescent analyses, the haplotype network and significant F _ST values, however reciprocally monophyletic lineages do not correspond to geographical locations in maximum likelihood analyses. A sudden population expansion for South America is indicated by a mismatch distribution analysis, and further supported by significant (p<0.05) negative values of Fu and Li''s D_F and F, and Fu''s F _S. This expansion, estimated at approximately 60 000 years BP (99 000–36 000 years BP 95% CI), encompasses a transition from a warm and dry time period prior to 50 000 years BP to an interval of maximum precipitation (50 000–36 000 years BP). Notably, this time period precedes the climatic and habitat changes associated with the last glacial maximum. In contrast, a multimodal distribution of haplotypes was observed for Central America suggesting either population equilibrium or a recent decline.

Significance

High levels of mitochondrial genetic diversity in combination with genetic differentiation among subgroups within regions and between regions highlight the importance of local population conservation in order to preserve maximal levels of genetic diversity in this species. Evidence of historically restricted female-mediated gene flow is an important consideration for captive-breeding programs.     

Neurogenic inflammation in the chicken (Gallus gallus var domesticus)

1. Neurogenic inflammation has been studied in the anaesthetized adult hen using a variety of different stimuli.2. Plasma extravasation was produced following antidromic stimulation of the external mandibular ramus of the trigeminal nerve which innervates the skin at the angle of the jaw and the anterior part of the wattle.3. Stimulation of the wattle by external application of mustard oil, thermal and mechanical stimuli, as well as intradermal injection of substance P and bradykinin, all produced plasma extravasation.4. These results demonstrate that, in contrast to previous findings in the pigeon, at least in the trigeminal of the chicken peripheral C-fibre nociceptors have similar physiological characteristics in relation to the neurogenic inflammatory mechanism to those seen in mammals.     

Development of drinking mechanisms in the chicken (Gallus gallus) (Aves)

Summary Development of the drinking mechanism from the day of hatching to the 4 week old chick was studied in relation to the growth of the oropharynx and drinking performance. Results indicate that due to scaling effects in the growing oropharynx, physical factors require the development of extra mechanisms. The swallowing mechanism to transport water from the pharynx into the esophagus during the tip up phase is already present in hatchlings, and does not change during ontogeny. The mechanism for water intake during the immersion phase changes considerably. Hatchlings display pecking behavior towards water. Week old chicks protrude the tongue far out, and the total volume ingested is sucked up by capillary action between the tongue, the floor, and the roof of the oropharynx. In 2 and 3 week old chicks the relative distance over which water is sucked up by capillarity decreases, whereas the volume of water pushed caudad by the tongue and bills increases. Laryngeal suction also develops in this period. At the age of 4 weeks chickens use the adult mechanism to drink. Most oropharyngeal elements increase two to three times in length and width during post hatching ontogeny. Due to these increases, water transport by capillarity alone does not suffice in the older age groups; therefore additional mechanisms such as pressure development by closing the bills and laryngeal suction must develop. Relative to the oropharyngeal length most elements grow isometrically. The width of the lingual alae and the larynx width, however, increase with positive allometry, which improves both capillary action as well as the transport of water during the tip up phase when the chicks grow older. The need to develop extra water transport mechanisms during growth due to scaling effects is shown to condition the radiation capacity of avian drinking mechanisms. Nidicolous birds are, however, not constrained by the need to have a properly operating drinking mechanism during the early ontogeny and may therefore have a better chance of developing alternativ drinking mechanisms then nidifugous birds.     

Mitochondrial DNA sequence and haplotype variation analysis in the chicken (Gallus gallus)

Although it is known to be useful for certain genotype:phenotype assignments, our knowledge of the nature and extent of variation in the entire chicken (Gallus gallus) mitochondrial genome (mtGenome) is limited. Here, we used experimental and in silico tools to identify nucleotide variants in the mtGenome, including the coding and non-coding (D-loop) regions. The distribution of the experimentally identified mitochondrial DNA variants in meat- (broilers) and egg-type (White Leghorn) chickens was also assessed. A total of 113 single-nucleotide polymorphisms (SNPs) were identified. The in silico analysis revealed a total of 91 SNPs, with 70 in the coding region and 21 in the non-coding region. Of the 41 experimentally identified SNPs, 27 were in the D-loop. Together, the experimentally identified SNPs in the non-coding region formed 11 haplotypes, whereas the 14 SNPs in the coding region formed 6. Though, 9 of the D-loop region haplotypes were observed only in broilers, 3 of the 6 haplotypes from the coding region occurred at a significantly higher frequency in broilers. To our knowledge, this investigation represents the first whole-mtGenome scan for variation and an evaluation, though limited in sample size, of the haplotype distribution in meat- and egg-type populations, using the SNPs and haplotypes identified.     

Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus)

Many years of domestication and breeding have given rise to the wide range of chicken breeds that exist today; however, an increasing number of local chicken breeds are under threat of extinction. A comprehensive characterization of chicken markers (especially type I markers) is needed to monitor and conserve genetic diversity in this species. The explosion of genomics and functional genomics information in recent years has opened new possibilities for the generation of molecular markers. We analyzed a large number of expressed sequence tags (ESTs) to test the possibility of using EST-derived microsatellite markers for investigating the Gallus gallus genome. Chromosomal locations for the majority of these SSRs were predicted. Of the 31,576 unigenes assembled from the 544,150 redundant EST sequences, 1757 SSR markers were discovered on 1544 ESTs, using the SSRLocator software, with an average density of 28.7 kb per SSR. The dimer motifs were the most frequent (46.38%), followed by trimeric (38.58%), tetrameric (10.19%), pentameric (4.5%), and hexameric (<1%) markers. Different from the case for cattle and sheep, AT/TA was the most abundant dimeric repeat, accounting for 41.71% of all dimeric repeats in the chicken ESTs. The EST-SSR distribution was not uniform among the chromosomes; the majority of the EST-SSRs were located on chromosomes GGA2 and GGA10. We found that most of the EST-SSRs are involved in positive regulation of cellular and metabolic processes. This is the first time that EST sequences have been mined to find chicken microsatellites. On average, 3.8% of the G. gallus UniGene sequences could be exploited for development of EST-SSRs, indicating a good source for molecular markers as well as for functional genome analysis.     

Prenatal exposure to testosterone impairs oxidative damage repair efficiency in the domestic chicken (Gallus gallus)

Elevated levels of maternal androgens in avian eggs affect numerous traits, including oxidative stress. However, current studies disagree as to whether prenatal androgen exposure enhances or ameliorates oxidative stress. Here, we tested how prenatal testosterone exposure affects oxidative stress in female domestic chickens (Gallus gallus) during the known oxidative challenge of an acute stressor. Prior to incubation, eggs were either injected with an oil vehicle or 5 ng testosterone. At either 17 or 18 days post-hatch, several oxidative stress markers were assessed from blood taken before and after a 20 min acute stressor, as well as following a 25 min recovery from the stressor. We found that, regardless of yolk treatment, during both stress and recovery all individuals were in a state of oxidative stress, with elevated levels of oxidative damage markers accompanied by a reduced total antioxidant capacity. In addition, testosterone-exposed individuals exhibited poorer DNA damage repair efficiencies in comparison with control individuals. Our work suggests that while yolk androgens do not alter oxidative stress directly, they may impair mechanisms of oxidative damage repair.     

Ontogeny of cholinergic and adrenergic cardiovascular regulation in the domestic chicken (Gallus gallus)

Adrenergic and cholinergic tone on the cardiovascular system of embryonic chickens was determined during days 12, 15, 19, 20, and 21 of development. Administration of the muscarinic antagonist atropine (1 mg/kg) resulted in no significant change in heart rate or arterial pressure at any developmental age. In addition, the general cardiovascular depressive effects of hypoxia were unaltered by pretreatment with atropine. In addition, the ganglionic blocking agent hexamethonium (25 mg/kg) did not induce changes in heart rate. The beta-adrenergic antagonist propranolol (3 mg/kg) induced a bradycardia of similar magnitude on all days studied, with a transient hypertensive action on days 19-20, indicating the existence of an important cardiac and vascular beta-adrenergic tone. Injections of the alpha-adrenergic antagonists prazosin or phentolamine (1 mg/kg) reduced arterial pressure significantly on all days of incubation studied. Collectively, the data indicate that embryonic chickens rely primarily on adrenergic control of cardiovascular function, with no contribution from the parasympathetic nervous system.     

Development of the innervation in the chicken pineal gland (Gallus gallus).

The innervation of the pineal gland has been studied during the embryonic development and the first 10 days after hatching. On day 17 of embryonic development, the first nerve fibers are observed in the pineal capsule. They appear at the stalk level and rise to locate mostly on the anterior side of the capsule. Some nerve fibers leave these nerve bundles to penetrate the gland and they situate in the connective septa (18 days of development). From day 19 of development onwards, nerve fibers locate only in the parafollicular layer. Cells that may be identified as neurons are found in the pineal parenchyma.     

Langerhans cell-like dendritic cells in the cornea,tongue and oesophagus of the chicken (Gallus gallus)

Langerhans cells are dendritic leucocytes which reside mainly within stratified squamous epithelia of skin and mucosa. Their visualization requires the use of ATPase histochemistry, electron microscopy for identifying the unique trilaminar cytoplasmic organelles (the Langerhans cell granules or Birbeck granules), and the expression of major histocompatibility complex class II molecules. Following uptake of antigen, Langerhans cells migrate via the afferent lymphatics to the lymph nodes and undergo differentiation from an antigen-processing cell to an antigen-presenting cell. Using the same approach as that employed in previous studies for the identification of chicken epidermal Langerhans cells, we show here the presence of ATPase-positive and major histocompatibility complex class II-positive Langerhans cell-like dendritic cells at the mucosal surface of the eye, tongue and oesophagus of the chicken. Ultrastructurally, these cells qualified as Langerhans cells except that they lack Langerhans cell granules. Thus, as in mammalian skin and mucosa, chicken mucosa contains mucosal dendritic cells with morphological and phenotypical features for the engagement of incoming antigens within epithelium and lamina propria.     

Sex inversion in domestic chicken (Gallus gallus domesticus) by letrozole and tamoxifen

In multicellular organisms, determination of sex identity is a complex, multistage process. Sex hormones are synthesized in gonads and fulfill the role of inductors in this process. The effect of androgen is currently well studied. However, the participation of estrogen in the formation of female gonads and female sex on the whole is not much known. Here, we present the results of experimental sex inversion by inhibition of aromatase (an enzyme involved in estrogen synthesis) and tamoxifen (a modulator of estrogen receptors) in chick embryos. It was shown that masculinization depended on the dose of the substance and quantity of injections. Inhibition of aromatase did not block the meiotic prophase in oogoniums. It has been suggested that retinoic acid and estrogens have different mechanisms of effect on oogenesis. Proteins and nucleoproteins interacting with estrogen receptor 1 and their gene localization in human and chicken genomes have been shown for the first time.     

Chromosome abnormalities in chicken (Gallus domesticus) embryos: Types,frequencies and phenotypic effects

Cytological screening of 4182 chick embryos from 10 strains and 5 strain crosses was performed to determine the types and frequencies of chromosome abnormalities. Gross phenotypic effects, such as growth retardation and malformation, were noted. Clues to the etiology of such chromosome aberrations were also sought. The following euploid series was observed: Haploid mosaics (A-Z/2A-ZZ, A-Z/2A-ZZ/3A-ZZZ, A-Z/A-W/2A-ZW/2A-ZZ, A-Z/A-W/2A-ZW/ 3A-Z?), diploid (2A-ZZ and 2A-ZW), triploid (3A-ZWW, 3A-ZZW, 3A-ZZZ, 3A-ZZZW) and tetraploid (4A-ZZWW and 4A-ZZZZ). Aneuploidy was observed as follows: Trisomy for chromosome numbers 1, 2, 3, 4 and double trisomy 2/5. Trisomy-4 with deletion of 50% of the long arm of one member of the trisomic triplet was observed. A 3A-ZWW embryo was found with two cell populations: one, disomic for chromosome 2 and 6; the other, tetrasomic for 2 and 6. Of the 4182 embryos sampled 1.4% were haploids, 97.5% diploids, 0.8% triploids, 0.1% tetraploids and 0.2% trisomics. On the average 10.8% of the early dead embryos were euploid (excluding diploid) or aneuploid. However, the range for euploidy and aneuploidy among strains was 2.3–23.7% of early deads. Haploid embryos were consistently underdeveloped at 4 days of incubation (D.I.), and died by 5–7 D.I. About 90% of (36) triploid embryos died at or before 4 D.I. The remaining 10% (normal embryos) died prior to hatching. Trisomic embryos were dead or underdeveloped at 4 D.I. Tetraploidy appeared to be lethal at a very early stage. The various strains examined had different overall rates of chromosome aberrations (0.4–8.9%), and also showed different varieties of such aberrations. The modes and possible causes of meiotic, mitotic and fertilization errors are considered. Genetic control of chromosome abnormalities, particularly haploidy, is postulated.     

Maternal diet influences gene expression in intestine of offspring in chicken (Gallus gallus)

The diet of the mother during pregnancy influences the onset of different diseases and health-related traits in the offspring. We investigated the influence of the mother hen diet on the intestinal gene expression pattern in the offspring. Hens received for 11 weeks either a commercial feed or a commercial feed supplemented with vitamins and minerals. The offspring of the two groups showed no changes in growth rate or feed conversion. Of this offspring, gene expression patterns in the intestine were measured at 3 and 14 days of age with an intestinal cDNA-microarray. Between the two groups, 11 genes were found to be differentially expressed both at 3 and 14 days of age. Thus, these genes were differently regulated when the intestine is developing as well as when the intestine is more mature. Genes that are differentially expressed at day 3 and/or day 14 affect intestinal turnover, proliferation and development, metabolism and feed absorption. To confirm that differences in gene expression are related to intestinal development, we investigated intestinal proliferation. This indeed also showed differences in proliferation between the two groups at day 3 and day 14 of age. The gene expression and proliferation results indicate that feed of the hens influences the functionality of intestine of the offspring at day 3 and 14 of age.     

Identification of a novel mtDNA lineage B3 in chicken (Gallus gallus domesticus)

DEAR EDITOR, In this study,we sequenced the complete mitochondrial DNA genome (mitogenome) of the Zhengyang Yellow chicken (Gallus gallus domesticus) by next-generation sequencing technology.Samples were taken from Zhumadian city,Henan Province,China.The complete mitogenome was 16 785 bp in size,and had a nucleotide composition of 30.3％ (A),23.7％ (T),32.5％ (C),and 13.5％ (G),with a high AT content of 54.0％.The assembled mitogenome exhibited typical mitochondrial DNA (mtDNA) structure,including a non-coding control region,two rRNA genes,13 protein-coding genes,and 22 tRNA genes.Phylogenetic analysis indicated that this mitogenome defined a novel sub-haplogroup B3 within haplogroup B.These results should provide essential information for chicken domestication and insight into the evolution of genomes.     

Crossing over in chicken (Gallus gallus domesticus) oogenesis: Periodic arrangement of chiasmata over chromosomes

The periodic occurrence of chiasmata was studied in lampbrush chromosomes of the chicken (Gallus gallus domesticus). It was shown that the most probable interference distance in chicken macrobivalents 1–3 corresponded to 24.48 Mb. The distance at which absolute interference is observed in chicken macrochromosomes varies from 5.75 to 9.02 Mb.     

Assembly errors cause false tandem duplicate regions in the chicken (Gallus gallus) genome sequence

The complexity of eukaryote genomes makes assembly errors inevitable in the process of constructing reference genomes. Next-generation sequencing (NGS) could provide an efficient way to validate previously assembled genomes. Here, we exploited NGS data to interrogate the chicken reference genome and identified 35 pairs of nearly identical regions with >99.5 % sequence similarity and a median size of 109 kb. Several lines of evidence, including read depth, the composition of junction sequences, and sequence similarity, suggest that these regions present genome assembly errors and should be excluded from forthcoming genomic studies.     

Experimental alteration of limb posture in the chicken (Gallus gallus) and its bearing on the use of birds as analogs for dinosaur locomotion

Extant birds represent the only diverse living bipeds, and can be informative for investigations into the life‐history parameters of their extinct dinosaurian relatives. However, morphological changes that occurred during early avian evolution, including the unique adoption of a nearly horizontal femoral orientation associated with a shift in center of mass (CM), suggest that caution is warranted in the use of birds as analogs for nonavian dinosaur locomotion. In this study, we fitted a group of white leghorn chickens (Gallus gallus) with a weight suspended posterior to the hip in order to examine the effects on loading and morphology. This caused a CM shift that necessitated a change in femoral posture (by 35° towards the horizontal, P < 0.001), and resulted in reorientation of the ground reaction force (GRF) vector relative to the femur (from 41° to 82°, P < 0.001). Despite similar strain magnitudes, an overall increase in torsion relative to bending (from 1.70 to 1.95 times bending, P < 0.001) was observed, which was weakly associated with a tendency for increased femoral cross‐sectional dimensions (P = 0.1). We suggest that a relative increase in torsion is consistent with a change in femoral posture towards the horizontal, since this change increases the degree to which the bone axis and the GRF vector produce mediolateral long‐axis rotation of the bone. These results support the hypothesis that a postural change during early avian evolution could underlie the allometric differences seen between bird and nonavian dinosaur femora by requiring more robust femoral dimensions in birds due to an increase in torsion. J. Morphol. 240:237–249, 1999. © 1999 Wiley‐Liss, Inc.     

Maturation of the angiotensin II cardiovascular response in the embryonic White Leghorn chicken (Gallus gallus)

Angiotensin II (Ang II) is an important regulator of cardiovascular function in adult vertebrates. Although its role in regulating the adult system has been extensively investigated, the cardiovascular response to Ang II in embryonic vertebrates is relatively unknown. We investigated the potential of Ang II as a regulator of cardiovascular function in embryonic chickens, which lack central nervous system control of cardiovascular function throughout the majority of incubation. The cardiovascular response to Ang II in embryonic chickens was investigated over the final 50% of their development. Ang II produced a dose-dependent increase in arterial pressure on each day of development studied, and the response increased in intensity as development progressed. The Ang II type-1 receptor nonspecific competitive peptide antagonist [Sar¹ ile⁸] Ang II blocked the cardiovascular response to subsequent injections of Ang II on day 21 only. The embryonic pressure response to Ang II (hypertension only) differed from that of adult chickens, in which initial hypotension is followed by hypertension. The constant level of gene expression for the Ang II receptor, in conjunction with an increasing pressure response to the peptide, suggests that two Ang II receptor subtypes are present during chicken development. Collectively, the data indicate that Ang II plays an important role in the cardiovascular development of chickens; however, its role in maintaining basal function requires further study.