Comparison of renal ornithine transcarbamylase activities within different chicken breeds

Comparisons were made of the renal ornithine transcarbamylase (OTC) activities within different groups of chickens including Japanese native breeds. OTC activities varied markedly within these groups. The Cochin Bantam breed and White Leghorn B line had an especially high activity, about 400 units/g of kidney, in contrast to two Japanese native breeds, Japanese Game (white variety) and Banshuu Gashiwa, and the California Gray breed, which showed a very low activity, the values being almost undetectable. In crossing experiments using the California Gray breed as a tester strain, Cochin Bantam OTC represents a simple autosomal incompletely dominant trait similar to the White Leghorn B line OTC. Kinetic studies using partially purified OTC preparations from the White Leghorn B line and Cochin Bantam breed revealed that both enzymes were identical for a variety of enzymic characteristics. In light of these results, the physiological significance of chick kidney OTC is discussed.     

Genetic control of ornithine transcarbamylase induction in chick kidney

After ornithine transcarbamylase (OTC) induction by egg-yolk feeding, OTC activity increases rapidly in chicks bearing an Ocb gene. This response to an egg yolk diet does not appear in chicks having no Ocb gene (showing low OTC activity). The chicks showing intermediate OTC activity also respond to the diet, but moderately. Crossing experiments revealed that OTC induction by egg yolk-diet feeding is inherited as a simple autosomal dominant trait. Since a chick develops during embryonic life by utilizing egg yolk from the yolk sac, the variation of OTC activity among chicken breeds and within a breed in 2-day-old chicks seems to depend on a genetically controlled difference of inducibility by egg yolk. The Ocb is an autosomal gene which controls the induction of OTC activity, but it is difficult to explain the consistent difference in OTC activity between sexes by involving this gene or this locus alone.     

Assessing genetic diversity in indigenous Veneto chicken breeds using AFLP markers

Genetic variation in four indigenous chicken breeds from the Veneto region of Italy was assessed using amplified fragment length polymorphism (AFLP) markers. A total of 99 individuals were analysed using three AFLP primer combinations that produced 70 polymorphisms. Four indigenous Veneto chicken breeds (Ermellinata, Padovana, Pépoi and Robusta) and a reference broiler line were included in the analysis. Breed-specific markers were identified in each breed. The expected heterozygosity did not differ significantly among the indigenous Veneto chicken breeds and the broiler line. The coefficient of gene variation (Gst) value across loci indicated that almost half of the total variability was observed among breeds. Nei's standard genetic distance between pairs of breeds showed that the distance between the broiler line and the Pépoi breed was greater than the distances between the broiler line and the other three chicken breeds. Cluster analysis based on standard genetic distances between breeds indicated that the Padovana and Pépoi breeds were closely related. Factorial analysis based on a binary matrix of the AFLP data showed a clear distinction of all breeds.     

Genetic diversity among chicken breeds estimated through randomly amplified polymorphic DNA.

The randomly amplified polymorphic DNA (RAPD) markers were used to detect polymorphism among five breeds of chicken i.e. White Leghorn and Rhodes Island Red (selected for part period egg production and egg mass respectively), Red Cornish and White Plymouth Rock (selected for early body weights) and Kadaknath (native breed). Twelve of the fifty random primers screened yielded distinct polymorphic RAPD profiles. Of the total 96 fragments amplified, about 25% showed polymorphism. Using the RAPD data matrix, the within population and between population genetic similarity was estimated. The selected improved breeds showed higher within population genetic similarity in comparison to the native breed. The two meat type breeds showed a high level of genetic similarity between themselves. The White Leghorn breed showed a low genetic similarity with other breeds. The native breed showed highest similarity with Rhodes Island Red. The dendogram was constructed to show phylogenetic relationship among these breeds. As expected, the genetic distances were lowest within similar type breeds and were highest between dissimilar type breeds. The results indicated the effectiveness of RAPD in detecting polymorphism between chicken populations and their applicability in population studies and establishing genetic relationships among the chicken populations.     

A ∼ 4.1 kb deletion in IRX1 gene upstream is completely associated with rumplessness in Piao chicken

Piao chicken, a Chinese indigenous rumpless chicken breed, lacks pygostyle, caudal vertebra, uropygial gland and tail feathers. The rumplessness in Piao chicken presents an autosomal dominant inheritance pattern. However, the molecular genetic mechanisms underlying the rumplessness in Piao chicken remains unclear. In this study, whole-genome resequencing was performed for 146 individuals from 10 chicken breeds, including 9 tailed chicken breeds and Piao rumpless breed. Tailbone CT scan for Piao chickens and WL chickens, revealed that some Piao chicken tails were normal in number, and for a few Piao chickens tail length and tail bone numbers were between the rumpless and the normal tailed chickens. The results showed that the rumpless phenotype has not been completely fixed in Piao chicken breed. Using selection signature analysis and structural variation detection, we found a 4174 bp deletion located in the upstream region of IRX1 gene on chromosome 2 related to rumpless phenotype. Structural variation genotyping showed that the deletion was present in all 32 rumpless Piao chickens (del/del, wild/del) and absent from all 112 tailed chickens included in the dataset for the other 9 breeds and 2 tailed Piao chickens (wild/wild). In summary, all rumpless Piao chickens tested here carry this deletion mutation, to show a complete linkage association with rumplessness trait. We suggested that the 4174 bp deletion could be causative for rumpless phenotype in Piao chicken since this is the only mutation to show the complete linkage disequilibrium with rumplessness on whole genome level across all of 146 chickens from the 10 breeds. This study could facilitate a better understanding of the genetic characteristics of Piao chicken.     

Genetic Polymorphism of Russian,European, and Asian Chicken Breeds as Revealed with DNA and Protein Markers

The variation in polymorphic DNA (RAPD and minisatellite) and protein markers was compared for nine Russian chicken breeds differing in morphological and productivity types and in origin, three European egg breeds, and three meat breeds of the Asian origin. Genetic diversity indices were calculated for each breed group and each marker type and were used to construct dendrograms of genetic similarity. In all breed groups, minisatellites and RAPD markers revealed higher genetic diversity as compared with protein markers. With any type of markers, genetic diversity of the Russian and Asian meat breeds proved to be significantly higher than that of the European egg breeds. The differentiating potentialities of molecular and genetic biochemical markers at the breed level and the origin of the Russian chicken breeds are discussed.     

Flesh color association with polymorphism of the tyrosinase gene in different Chinese chicken breeds

In order to study genetic variation of tyrosinase gene in four different flesh color chicken breeds selected from special districts including Guyuan, Wenchang, Tibetan and Hisex chicken, five loci of the TYR gene exon-1 and one locus of 5′ flanking region were analyzed in PCR-SSCP and DNA sequencing. The results indicated that there were polymorphisms only at TYR1 and TYR3 locus. At TYR1 locus located in exon-1, there were three genotypes (TT, CC, TC), respectively, in three Chinese chicken breeds, and Genotype CC had not been detected in Hisex chicken. At TYR3 locus located in 5′ flanking region, there were three genotypes (GG, AA and GA) in Chinese local chicken breeds and genotype AA had not been detected in Hisex chicken breed. It was concluded that there were many variations of TYR gene in Chinese local chicken breeds. DNA sequencing of PCR products for different genotypes showed that there were two mutation sites, respectively, C to T at TYR1 locus and G to A at TYR3 locus. Mutation at TYR1 locus did not cause any amino acid variation. The chi-square analysis revealed that there were significant statistical differences generally between flesh color and the two loci among four chicken populations (P < 0.01). Our results suggested that the flesh color was related to genotype of TYR gene in Chinese chicken breeds. This study provided original information for elucidating the possible roles of exon-1 of TYR gene and 5′ flanking region in chickens with different flesh color chicken.     

Genetic polymorphism of Russian,European, and Asian chicken breeds as revealed with DNA and protein markers

The variation in polymorphic DNA (RAPD and minisatellite) and protein markers was compared for nine Russian chicken breeds differing in morphological and productivity types and in origin, three European egg breeds, and three broiler breeds of the Asian origin. Genetic diversity indices were calculated for each breed group and each marker type and were used to construct dendrograms of genetic similarity. In all breed groups, minisatellites and RAPD markers revealed higher genetic diversity as compared with protein markers. With any type of markers, genetic diversity of the Russian and Asian broiler breeds proved to be significantly higher than that of the European egg breeds. The differentiating potentialities of molecular and genetic biochemical markers at the breed level and the origin of the Russian chicken breeds are discussed.     

Genomic and genetic variability of six chicken populations using single nucleotide polymorphism and copy number variants as markers

Genomic and genetic variation among six Italian chicken native breeds (Livornese, Mericanel della Brianza, Milanino, Bionda Piemontese, Bianca di Saluzzo and Siciliana) were studied using single nucleotide polymorphism (SNP) and copy number variants (CNV) as markers. A total of 94 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix) were used in the analyses. The results showed the genetic and genomic variability occurring among the six Italian chicken breeds. The genetic relationship among animals was established with a principal component analysis. The genetic diversity within breeds was calculated using heterozygosity values (expected and observed) and with Wright’s F-statistics. The individual-based CNV calling, based on log R ratio and B-allele frequency values, was done by the Hidden–Markov Model (HMM) of PennCNV software on autosomes. A hierarchical agglomerative clustering was applied in each population according to the absence or presence of definite CNV regions (CNV were grouped by overlapping of at least 1 bp). The CNV map was built on a total of 1003 CNV found in individual samples, after grouping by overlaps, resulting in 564 unique CNV regions (344 gains, 213 losses and 7 complex), for a total of 9.43 Mb of sequence and 1.03% of the chicken assembly autosome. All the approaches using SNP data showed that the Siciliana breed clearly differentiate from other populations, the Livornese breed separates into two distinct groups according to the feather colour (i.e. white and black) and the Bionda Piemontese and Bianca di Saluzzo breeds are closely related. The genetic variability found using SNP is comparable with that found by other authors in the same breeds using microsatellite markers. The CNV markers analysis clearly confirmed the SNP results.     

High malic enzyme activity in tumor cells and its cross-reaction with antipigeon liver malic enzyme serum

Summary Rabbit antibodies against pigeon liver malic enzyme (EC 1.1.1.40) were prepared. The antiserum gave single precipitation line with crude pigeon liver extract. Cross reaction was observed with partially purified malic enzyme or crude extract from chicken liver. Positive cross reaction was also observed with the concentrated cytosolic fraction of two human carcinoma cell lines which were demonstrated to contain high malic enzyme activity. All other proteins examined did not react with the antibodies. When purified pigeon liver malic enzyme was mixed with the antiserumin vitro, a time-dependent inactivation of the enzyme activity was observed. Protection of the enzyme activity against antiserum inactivation was afforded by NADP⁺ orL-malate. Metal Mn²⁺ gave little protection.     

The 24,000 Da subunit is not required for the RNA synthesis activity of chicken leukemia RNA polymerase II

The partially purified RNA polymerase II from chicken leukemia cells (Chuang R. Y., Chuang L. F. & Israel M. (1986) Biochem. Pharmacol. 35, 1293-1297) contained multiple subunits with molecular masses (in Da) ranging from 220,000 to 24,000, as shown by SDS-polyacrylamide gel electrophoresis. The enzyme was further purified through phosphocellulose column and fractions containing the enzyme activity were collected and concentrated 400-fold through a microconcentrator. The microconcentrator contained a membrane with a molecular weight cutoff around 30,000 and, hence, removed the 24,000 Da polypeptide from the enzyme. It was found that the resulting enzyme retained all the catalytic activity as compared to the enzyme preparation before the concentration step, suggesting that the stoichiometric amount of the 24,000 Da polypeptide is not required for RNA synthesis activity with a denatured DNA template.     

Signatures of selection in the genomes of commercial and non-commercial chicken breeds

Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations.     

Patterns of molecular genetic variation among cat breeds

Genetic variation in cat breeds was assessed utilizing a panel of short tandem repeat (STR) loci genotyped in 38 cat breeds and 284 single-nucleotide polymorphisms (SNPs) genotyped in 24 breeds. Population structure in cat breeds generally reflects their recent ancestry and absence of strong breed barriers between some breeds. There is a wide range in the robustness of population definition, from breeds demonstrating high definition to breeds with as little as a third of their genetic variation partitioning into a single population. Utilizing the STRUCTURE algorithm, there was no clear demarcation of the number of population subdivisions; 16 breeds could not be resolved into independent populations, the consequence of outcrossing in established breeds to recently developed breeds with common ancestry. These 16 breeds were divided into 6 populations. Ninety-six percent of cats in a sample set of 1040 were correctly assigned to their classified breed or breed group/population. Average breed STR heterozygosities ranged from moderate (0.53; Havana, Korat) to high (0.85; Norwegian Forest Cat, Manx). Most of the variation in cat breeds was observed within a breed population (83.7%), versus 16.3% of the variation observed between populations. The hierarchical relationships of cat breeds is poorly defined as demonstrated by phylogenetic trees generated from both STR and SNP data, though phylogeographic grouping of breeds derived completely or in part from Southeast Asian ancestors was apparent.     

Domestic chickens defy Rensch's rule: sexual size dimorphism in chicken breeds

Sexual size dimorphism (SSD), i.e. the difference in sizes of males and females, is a key evolutionary feature that is related to ecology, behaviour and life histories of organisms. Although the basic patterns of SSD are well documented for several major taxa, the processes generating SSD are poorly understood. Domesticated animals offer excellent opportunities for testing predictions of functional explanations of SSD theory because domestic stocks were often selected by humans for particular desirable traits. Here, we analyse SSD in 139 breeds of domestic chickens Gallus gallus domesticus and compare them to their wild relatives (pheasants, partridges and grouse; Phasianidae, 53 species). SSD was male-biased in all chicken breeds, because males were 21.5 ± 0.55% (mean ± SE) heavier than females. The extent of SSD did not differ among breed categories (cock fighting, ornamental and breeds selected for egg and meat production). SSD of chicken breeds was not different from wild pheasants and allies (23.5 ± 3.43%), although the wild ancestor of chickens, the red jungle fowl G. gallus, had more extreme SSD (male 68.8% heavier) than any domesticated breed. Male mass and female mass exhibited positive allometry among pheasants and allies, consistently with the Rensch's rule reported from various taxa. However, body mass scaled isometrically across chicken breeds. The latter results suggest that sex-specific selection on males vs. females is necessary to generate positive allometry, i.e. the Rensch's rule, in wild populations.     

Phylogenetic analysis in chicken breeds inferred from complete cytochrome b gene information

Complete cytochrome b (cyt b) gene (1140 bp) nucleotide sequences were used to investigate characteristics of the genetic constitution of Chunky broiler chickens, and these were compared with the Hy-Line and WL-GM (Garber) line of White Leghorn, the GSP line of Fayoumi, the BM-C line of Black Minorca (egg-chickens), and an outgroup of wild-origin Japanese quail. A high genetic difference (five haplotypes) was observed at the cytochrome b region in the Chunky broiler in contrast to the high homologies observed among the other chicken breeds (egg-purpose). Chunky broilers can be distinguished from the other breeds (White Leghorn, Fayoumi, and Black Minorca) at positions 552 and 779. The molecular phylogenetic tree exhibited genetic differences within Chunky broilers, and between Chunky broilers and the other three chicken breeds. As a result, some chicken strains or breeds apparently different from the other egg-chickens may have contributed to the Chunky broiler formation. Artificial selection may be one of the biggest factors causing nucleotide diversity in the chicken breeds.     

Genetic characterization of highly inbred chicken lines by two DNA methods: DNA fingerprinting and polymerase chain reaction using arbitrary primers

Thirteen highly inbred chicken lines were analysed at the DNA level by DNA fingerprinting (DFP) and by polymerase chain reaction (PCR) using random primers. In general, the DFP patterns of individuals within a line were identical. The DFP band-sharing (BS) values among lines from different breeds (Leghorn, Fayoumi, Spanish) ranged from 0.10 to 0.20. The DFP BS values among Leghorn lines from different genetic backgrounds ranged from 0.42 to 0.79. The DFP BS values among lines selected for different major histocompatibility complex serotypes from a common genetic background ranged from 0.70 to 0.95. Some randomly amplified polymorphic DNA (RAPD) PCR products were specific to a single line, some to all lines from the same genetic base, and some to all lines from the same breed. The RAPD-PCR band-sharing values ranged from 0.66 to 0.99 for all between-line comparisons. Thus, the ability to detect biodiversity at the DNA level was greater in this study for DFP than for RAPD-PCR. The possible origin of line-specific bands, relative advantages of detecting biodiversity by using different molecular screening techniques and uses of highly inbred chicken lines in molecular analysis are discussed.     

Genetic Diversity Among Turkish Native Chickens, Denizli and Gerze, Estimated by Microsatellite Markers

The genetic diversity of the Turkish native chicken breeds Denizli and Gerze was evaluated with 10 microsatellite markers. We genotyped a total of 125 individuals from five subpopulations. Among loci, the mean number of alleles was 7.5, expected heterozygosity (H (e)) was 0.665, PIC value was 0.610, and Wright's fixation index was 0.301. H (e) was higher in the Denizli breed (0.656) than in the Gerze breed (0.475). The PIC values were 0.599 and 0.426 for Denizli and Gerze, respectively. A phylogenetic tree was constructed using genetic distance and the neighbor-joining method. Its topology reflects the general pattern of genetic differentiation among the Denizli and Gerze breeds. The present study suggests that Denizli and Gerze subpopulations have a rich genetic diversity. The information about Denizli and Gerze breeds estimated by microsatellite analysis may also be useful as an initial guide in defining objectives for designing future investigations of genetic variation and developing conservation strategies.     

Identification and functional characterization of copy number variations in diverse chicken breeds

Background

The detection and functional characterization of genomic structural variations are important for understanding the landscape of genetic variation in the chicken. A recently recognized aspect of genomic structural variation, called copy number variation (CNV), is gaining interest in chicken genomic studies. The aim of the present study was to investigate the pattern and functional characterization of CNVs in five characteristic chicken breeds, which will be important for future studies associating phenotype with chicken genome architecture.

Results

Using a commercial 385 K array-based comparative genomic hybridization (aCGH) genome array, we performed CNV discovery using 10 chicken samples from four local Chinese breeds and the French breed Houdan chicken. The female Anka broiler was used as a reference. A total of 281 copy number variation regions (CNVR) were identified, covering 12.8 Mb of polymorphic sequences or 1.07% of the entire chicken genome. The functional annotation of CNVRs indicated that these regions completely or partially overlapped with 231 genes and 1032 quantitative traits loci, suggesting these CNVs have important functions and might be promising resources for exploring differences among various breeds. In addition, we employed quantitative PCR (qPCR) to further validate several copy number variable genes, such as prolactin receptor, endothelin 3 (EDN3), suppressor of cytokine signaling 2, CD8a molecule, with important functions, and the results suggested that EDN3 might be a molecular marker for the selection of dark skin color in poultry production. Moreover, we also identified a new CNVR (chr24: 3484617–3512275), encoding the sortilin-related receptor gene, with copy number changes in only black-bone chicken.

Conclusions

Here, we report a genome-wide analysis of the CNVs in five chicken breeds using aCGH. The association between EDN3 and melanoblast proliferation was further confirmed using qPCR. These results provide additional information for understanding genomic variation and related phenotypic characteristics.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-934) contains supplementary material, which is available to authorized users.     

Characterization of the genetic diversity, structure and admixture of British chicken breeds

The characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average F(ST) of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Hardy-Weinberg Equilibrium, as indicated by heterozygote deficiency in the majority of breeds (average F(IS) of 0.20), with an average observed heterozygote frequency of 0.39, ranging from 0.15 in Spanish to 0.49 in Cochin. Individual-based clustering analyses revealed that most individuals clustered to breed origin. However, genetic subdivisions occurred in several breeds, and this was predominantly associated with flock supplier and occasionally by morphological type. The deficit of heterozygotes was likely owing to a Wahlund effect caused by sampling from different flocks, implying structure within breeds. It is proposed that gene flow amongst flocks within breeds should be enhanced to maintain the current levels of genetic diversity. Additionally, certain breeds had low levels of both genetic diversity and uniqueness. Consideration is required for the conservation and preservation of these potentially vulnerable breeds.     

Genetic and environmental variation in the LH response of ovariectomized sheep to LH-RH.

The influence of breed and season on the sensitivity of the pituitary gland of sheep to LH-RH was assessed. Ovariectomized ewes of 3 breeds (Finnish Landrace, Scottish Blackface and Tasmanian Merino) with differing normal breeding seasons and with differing ovulation rates were injected (i.v.) with 3 doses of LH-RH (1.56, 6.25 or 25.0 micrograms) at 3 different times of the year covering the anoestrous and the breeding seasons of intact ewes; 9 ewes of each breed (3 per sub-class) were examined on the first and third occasions, 6 (2 per sub-class) on the second. The response was measured in terms of the concentration of LH in peripheral plasma 20, 40, 60 and 80 min after injection. Time of year, but not the breed of sheep, affected the magnitude of the response; the data indicated that the duration of LH secretion was greater during the breeding season than during anoestrus. It was concluded that changes in the spontaneous activity of the hypothalamus/hypophysis could contribute to seasonal changes in LH secretion independently of the modifying effects of gonadal steroids. Such variation in unmodulated activity apparently does not contribute to the differences in ovulation rate among the 3 breeds.