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Abstract Background Chickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG) chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process. Results A total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69). The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used. Conclusions In contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation.

Abstract Background Previous studies suggested that multiple domestication events in South and South-East Asia (Yunnan and surrounding areas) and India have led to the genesis of modern domestic chickens. Ha Giang province is a northern Vietnamese region, where local chickens, such as the H'mong breed, and wild junglefowl coexist. The assumption was made that hybridisation between wild junglefowl and Ha Giang chickens may have occurred and led to the high genetic diversity previously observed. The objectives of this study were i) to clarify the genetic structure of the chicken population within the Ha Giang province and ii) to give evidence of admixture with G. gallus. A large survey of the molecular polymorphism for 18 microsatellite markers was conducted on 1082 chickens from 30 communes of the Ha Giang province (HG chickens). This dataset was combined with a previous dataset of Asian breeds, commercial lines and samples of Red junglefowl from Thailand and Vietnam (Ha Noï). Measurements of genetic diversity were estimated both within-population and between populations, and a step-by-step Bayesian approach was performed on the global data set. Results The highest value for expected heterozygosity (> 0.60) was found in HG chickens and in the wild junglefowl populations from Thailand. HG chickens exhibited the highest allelic richness (mean A = 2.9). No significant genetic subdivisions of the chicken population within the Ha Giang province were found. As compared to other breeds, HG chickens clustered with wild populations. Furthermore, the neighbornet tree and the Bayesian clustering analysis showed that chickens from 4 communes were closely related to the wild ones and showed an admixture pattern. Conclusion In the absence of any population structuring within the province, the H'mong chicken, identified from its black phenotype, shared a common gene pool with other chickens from the Ha Giang population. The large number of alleles shared exclusively between Ha Giang chickens and junglefowl, as well as the results of a Bayesian clustering analysis, suggest that gene flow has been taking place from junglefowl to Ha Giang chickens.

The 20th Century saw an astonishing advance in our understanding of genetics and the scientific basis of the genetic improvement of farm animals. The application of genetic principles to chickens in the 1950s and 1960s led to a rapid change in the productivity and efficiency of laying hens and broiler chickens, turkeys and ducks. Subsequently, the application of increasingly powerful computers and sophisticated mathematical algorithms has increased the range of traits that could be successfully incorporated into breeding programs. Random sample tests of the performance of laying hens enjoyed a period of popularity and more recently the few remaining tests included husbandry systems in addition to strain evaluation. Characterisation of avian blood groups has led to the identification of the B21 haplotype that confers resistance to Marek's disease and to selection for this locus in commercial lines. The decade following the millennium saw the publication of the genome sequence of the chicken and the identification of millions of single nucleotide polymorphisms that, coupled with technological advances, made the application of whole genome selection practical in poultry. In parallel, the molecular basis for some Mendelian traits described a century ago is now being deciphered. Similar technologies have been applied to study genetic diversity in chickens and have provided insights into the evolution and domestication of chicken breeds. Finally, in this review, the recent development of the European Poultry Genetics Symposia coordinated by Working Group 3 ‘Genetics and Breeding’ that was based on combining the British Poultry Breeders Round Table and AVIAGEN from West and Eastern Europe, is discussed. [ABSTRACT FROM PUBLISHER]

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Background: Chickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG) chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process. Results: A total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69). The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used. Conclusions: In contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation. [ABSTRACT FROM AUTHOR]

Poultry genetic resources encompass all types of populations, from village chickens to commercial and experimental lines. Characterisation includes collection of data on population size and structure, geographical distribution, production systems in which the breed is found, phenotypic attributes (physical features, performance levels and any unique features), historical development of the breed (crossbreeding, selection). Such data can be available for standardised breeds and experimental lines, but are generally confidential for commercial lines and difficult to record for village chickens. In the past, random sample tests provided recurrent data for layer and broiler strains, but these have been discontinued. Available literature on local populations provides information on specific features such as morphological diversity, scavenging behaviour, product quality and disease resistance.Molecular markers provide useful information on genetic variability, either within or between populations, and make it possible to quantify relatedness between populations and to detect introgressions. Molecular markers contribute to define breed identity and may be used to assign individuals to their population of origin. Current results provide a reasonably complete picture of genomic variability and population structure in the domestic chicken. Yet, this does not make it possible to predict performance: phenotypic data are still needed to document molecular data. In the future, the progress of genomics may merge functional data with historical data.Monitoring poultry genetic resources is not always a priority for certain countries. Indicators may be proposed for between- as well as within- population variability. [ABSTRACT FROM PUBLISHER]

A comprehensive linkage map for chicken chromosome Z was constructed as the result of a large-scale screening of single nucleotide polymorphisms (SNPs). A total of 308 SNPs were assigned to Z based on the genotype distribution among 182 birds representing several populations. A linkage map comprising 210 markers and spanning 200.9 cM was established by analyzing a small Red junglefowl/White Leghorn intercross. There was excellent agreement between the linkage map for Z and a recently released assembly of the chicken genome (May 2006). Almost all SNPs assigned to chromosome Z in the present study are on Z in the new genome assembly. The remaining 12 loci are all found on unassigned contigs that can now be assigned to Z. The average recombination rate was estimated at 2.7 cM/Mb but there was a very uneven distribution of recombination events with both cold and hot spots of recombination. The existence of one of the major hot spots of recombination, located around position 39.4 Mb, was supported by the observed pattern of linkage disequilibrium. Thirteen markers from unassigned contigs were shown to be located on chromosome W. Three of these contigs included genes that have homologues on chromosome Z. The preliminary assignment of three more genes to the gene-poor W chromosome may be important for studies on the mechanism of sex determination and dosage compensation in birds. Copyright © 2007 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

1. Relationships between feed conversion ratio, growth curve parameters and carcase composition were investigated on 1061 chickens from a slow-growing line of label-type chickens. The growth curve was modelled with the Gompertz function. Individual feed conversion ratio (FCR) was recorded between 8 and 10 weeks of age and residual feed consumption (RES) was calculated over the same interval. Abdominal fat yield (AFY), breast yield (BRY) and leg yield (LY) were also measured on the birds following slaughter at 75  d of age. 2. The means for FCR and RES were 3·15 and 0·62  g, respectively. Growth curve parameters were 0·141/d for initial specific growth rate ( L ), 0·031/d for maturation rate ( K ) and 48·9  d for age at inflexion (TI). Mean values for BRY, LY and AFY were 166, 306 and 40  g/kg, respectively. 3. Heritability of FCR and RES were moderate to high (0·33 and 0·38 to 0·45). Growth curve parameters and LY were moderately heritable (0·22 to 0·34) and BRY and AFY were highly heritable (0·50 and 0·66). Genetic correlations between growth curve parameters and either FCR or RES were low to moderate (-0·31 to 0·51). LY and AFY were highly correlated with FCR (-0·70 and 0·44) and RES (-0·32 and 0·44) but BRY was not (0·00 and -0·35). These results show that indirect selection for feed conversion ratio is possible by using growth curve parameters and abdominal fatness, which do not require rearing the chickens in cages. [ABSTRACT FROM AUTHOR]

The relationships between phenotype and genotype were first described by Mendelian genetics in the case of genes with a major phenotypic effect. The remarkable improvement of biochemical and molecular tools has now made it possible to identify the molecular nature of major genes, and to understand better their mode of action. From a functional point of view, mutations of a given gene can be classified into three groups: loss of function, interference and dominant negative action, and gain of function. From a structural point of view, a large diversity of molecular polymorphisms can be found, the consequences of which depend rather on their position than on their nature. Genetic abnormalities or mutations with obvious morphological effects provide the most didactic examples to understand the genotype-phenotype relationships. The example of sex-linked dwarfism in chicken is described in detail and the present state of knowledge on the molecular identification of major genes in the chicken is reviewed. Finally, a general discussion, based upon examples taken from human genetics and mouse genetics, draws lessons from the study of major genes in order to approach the study of complex phenotypes or genotype x environment interactions. [ABSTRACT FROM PUBLISHER]

Describes a method to obtain high-resolution chromosome preparations in the chicken, Gallus domesticus. Use of synchronization of embryo fibroblast cells; Characteristics of cultures of chicken embryo fibroblasts; RBG- and GTG-banding patterns.

Residual feed intake (RFI) is an important measure of feed efficiency, which is believed to represent inherent variation in basic metabolic processes in animals. The study was designed by crossing two pedigreed parental lines, the L2 (Taiwan Country chicken) and the R-(experimental line of Rhode Island Red layer) lines to generate the F1 and F2 generations, then the residual feed consumption (RFC) was analyzed. The results showed that the parental lines of the R- was better than the L2 line for RFC (P ≤ 0.01). The F2 generation which were generated by reciprocally crossing between L2R- males and R-L2 females presented the significant differences between sire families (P < 0.01). Our results will be benefit to the selection effect and that could be a reference for the program of genomic selection. [ABSTRACT FROM AUTHOR]

Studies the genetic variability of clutch length in dwarf layers. Egg quality in the selected lines and the control line; Oviposition time in selected lines and the control line.

Reproduction is an economically critical trait in poultry industry. To identify chromosomal regions which associated with reproduction traits, quantitative trait locus (QTL) mapping was conducted in an F2 cross set up between Taiwan Country chicken L2 line and a line of Rhode Island Red layer R-, by using the chicken 60K SNP chip. The results showed that 11 QTL on GGA 2, 3, 5, 9, 10, 11, 19, 23 and Z were identified for chicken reproduction traits. Three of 11 QTL on GGA 3, 5 and 23 had high genome-wide significance (P ≤ 0.01 ). Moreover, the 8 QTL were identified for pause length which were distributed on GGA 2, 3, 5, 9, 10, 11, 13 and Z. Whole-genome QTL mapping led to the identification of specific chromosomal regions that corresponded to reproduction traits and overlapped with published QTL for egg production or quality. The results provided the evidences to the relationship for studied traits, and were useful for the comprehension of the genetic control for chicken reproduction. [ABSTRACT FROM AUTHOR]

Animal genome includes a vatiety of genetic vatiations, these variations contain single point mutation or a wide range of structural change. The most abundant type of mutation is single nucleotide polymorphism (SNP). The different variations of nucleotide may cause changes in protein shape, which influence the regulation of genes. According to the data published by SNP database of NCBI, there are about 3,280,000 positions on chicken genome may be the potential SNPs. Therefore, Illumina iSelect 60K SNP chips were used in the study to detect SNPs which associated with production traits in Taiwan country chickens. The results showed that 732 SNP effects were identified for growth, immune, egg production, egg quality, body composition, meat quality and residual feed consumption traits. The use of SNPs and genome-wide association analysis can identify the SNPs which associated with economically important traits and helpful to the genomic researches and the improvement of animal breeding. [ABSTRACT FROM AUTHOR]

Egg production is an economically critical trait in poultry industry. To identify genetic markers associated with egg production, genome-wide association study was conducted in an F2 cross set up between the Taiwan Country chicken L2 line and an experimental line of Rhode Island Red layer R-, by using chicken 60K single nuclide polymorphism (SNP) chip. A total of 102SNP effects were identified for egg production traits. Seven SNP effects associated with age of first egg, laying rate, maximal clutch length and maximal pause duration which reached 5% genome-wide significance (P < 4.84 X 10-6) and the 95 SNP effects reached suggestive significance (P<9.68 X 10-5). Most of detected SNPs overlapped with published quantitative trait loci for egg production or quality, providing the evidences to the relationship for the studied traits. Our results could be contributed to a better comprehension of the genetic for egg production which is providing substantial benefit for functional studies. [ABSTRACT FROM AUTHOR]