Microsatellite polymorphism between and within broiler populations

Genetic polymorphism of fifteen microsatellite loci in Brazilian (blue-egg Caipira) chickens

The purpose of this study was to investigate the genetic polymorphism of fifteen microsatellites loci in Brazilian (blue-egg Caipira) chickens. Samples were collected from 100 blue eggs of Caipira chickens from rural properties in the city of Dois Lajeados, RS. After DNA extraction, the fragments related to molecular markers LEI0248, LEI0221, LEI0214, LEI0192, LEI0217, LEI0254, LEI0194, LEI0212, MCW0371, ADL0278, LEI0234, MCW0183, MCW0216, MCW0330 and MCW0081 were obtained by polymerase chain reaction (PCR). The statistical analysis were carried out with the softwares ARLEQUIN 3.5 version and CERVUS 3.0.3 version. The allelic and genotypic frequencies, deviations from Hardy-Weinberg equilibrium, estimates of observed (HO) and expected (HE) heterozygosity and polymorphic information content (PIC) were obtained for each marker locus. A total of 186 alleles from 15 loci were obtained, with sizes ranging of 83 to 490 base pairs. The medium number of alleles was 12.4, the HE was 0.76±0.14 and HO was 0.49±0.21 and PIC was 0.706. The first conclusion is that the microsatellites used are polymorphic and can be used to genetic studies in chickens. The second is that the "Caipira" chicken (blue eggs) population investigated has a great genic variability, which makes than an important source of genetic resources for future animal breeding programs.

LEI0258 microsatellite variability in Khorasan, Marandi, and Arian chickens

Microsatellite LEI0258 is a genetic marker for chicken MHC haplotypes and can be used as an indicator of the influence of population genetics on immune responses. LEI0258 microsatellite variability in three Iranian indigenous chicken populations (Khorasan, Marandi, and Arian) was investigated. In total, 142 Khorasan, 42 Marandi, and 58 Arian chickens were examined. Collectively, 25 different alleles and 79 genotypes could be found. The observed levels of heterozygosity were 81% in Khorasan and Marandi and 34% in Arian chickens. Our results indicate that LEI0258 diversity in Marandi chickens is higher than in the other populations. Allelic diversity in Iranian chickens is relatively higher than in the local chicken breeds reported for Brazil and Vietnam.

Genetic variation among native chicken breeds of Iran based on biochemical polymorphisms

(1) Genetic distances and heterozygosity were determined in 5 Iranian native chickens: Dashtyary, Lary, Marandy, Naked neck and Common breed, using three blood group systems (A, B and D) and 4 serum protein loci (albumin, transferrin, alkaline phosphatase and esterase). (2) The highest D(A) and D(S) were obtained between Dashtyary and Lary breeds. (3) The average heterozygosity for each breed in all loci ranged from 0.330 for Dashtyary to 0.370 for Common breed. (4) Dendrograms based on an unweighted pair-group method using an arithmetic average (UPGMA) showed two distinct clusters. One cluster included Dashtyary and the other contained the remaining 4 breeds.

Characteristics of PCR fragments amplified using five microsatellite markers for identifying the Nagoya breed

The Nagoya breed is a native chicken of Aichi Prefecture, Japan, a dual-purpose breed for eggs and meat. A method for distinguishing the Nagoya breed from Aichi Prefecture from other chickens using five microsatellite markers (ABR0015, ABR0257, ABR0417, ABR0495 and ADL0262) has already been utilized in order to check the authenticity of Nagoya breed-labeled chicken on the market. The present study was conducted to investigate nucleotide sequences and sizes of PCR fragments containing the five microsatellite regions for the Nagoya breed and to confirm that the genomic identification could continue to be applied in the future. The DNA sequencing of fragments containing the five markers showed that ABR0015, ABR0417 and ABR0495 had a single haplotype, ABR0257 had three haplotypes, and ADL0262 had two haplotypes, although all the markers exhibited one fixed fragment size each upon sequencing of the fragments and fragment analysis. The results of the fragment analysis of each marker using DNA samples of 28 Nagoya breed males (G0 generation) reared in 2000-2001 and 20 of their offspring males (G8) reared in 2008-2009 showed one fixed fragment size in both populations. Therefore, we confirmed that the five microsatellite markers are useful tools for accurately distinguishing the Nagoya breed from other chickens.

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.

Use of a novel outbred by inbred F1 cross to detect genetic markers for growth

A unique outbred by inbred F1 resource population was established. The population structure facilitated the unique opportunity of examining gene by genetic background interaction through crossing two modern broiler sires with dams from two unrelated inbred lines, with no selection for growth rate, to produce about 600 F1 chicks. Pools of DNA were generated from the phenotypic extremes (20% high and low) for 8-week body weight for each of the four combinations of sire and dam line. For one sire family, pools were also separately generated for each sex. The pools were genoyped with 25 informative (segregating) microsatellites. This unique F1 cross between outbred and inbred populations allowed use of the inbred alleles as an 'internal control' for polymerase chain reaction amplification quality in DNA pools. Ten microsatellites showed marked differences (P < 0.05) in allele frequencies between high and low pools, suggesting an association between marker and quantitative trait loci (QTL). These differences were verified using selective genotyping. For many markers, differences in allele frequencies between the high and the low pools, or marker effect, varied between the two dam lines and the two sexes, suggesting an interaction between some genes and the genetic background as represented by different dam lines or sexes. The suggestive marker-QTL associations identified in this F1 population demonstrate the efficiency of this population design while different QTL effects in different genetic line crosses and sexes highlight the importance of gene by genetic background interaction in QTL detection.

Genetic diversity at the major histocompatibility complex (B) and microsatellite loci in three commercial broiler pure lines

Genetic diversity at the MHC and non-MHC loci was investigated in three commercial broiler chicken pure lines. The MHC class II and IV loci were evaluated in Southern hybridizations and molecular genotypes based on RFLP were interpreted from pedigreed families. Four MHC class II and eight class IV genotypes were identified in the broiler lines, and their frequencies differed among the lines. Line-specific MHC genotypes were identified. The observed heterozygosities (59 to 67%) suggest that the MHC loci are highly polymorphic in the broiler lines. At least 9% of the genetic variation at the MHC was due to line differences; the remainder reflected individual variations. To characterize non-MHC genes, 41 microsatellite loci located throughout the chicken genome were evaluated in the broiler lines. Genetic variation was also observed at the microsatellite loci for the broiler lines; the number of alleles at a single locus ranged from one to eight, and the average number of alleles per locus was 3.5, 2.8, and 3.1 for each of the lines, respectively. The observed heterozygosities for microsatellite loci ranged between 0 and 89% in the lines. Based on the fixation index (Fst), about 19% of the genetic variation at microsatellite loci was attributed to broiler line differences. Deviations from Hardy-Weinberg equilibrium were detected at both MHC and non-MHC loci. Possible explanations for these deviations include genetic selection by the primary broiler breeder or the presence of null alleles that were not identified by the typing procedures described in this report. This study contributes to our knowledge on the molecular characteristics and genetic structure of a commercial broiler chicken population. Analysis of MHC and non-MHC loci suggests that there is still sufficient genetic diversity in the broiler lines to continue the progress toward improved broiler chicken production.

Microsatellites linked to Salmonella enterica Serovar Enteritidis burden in spleen and cecal content of young F1 broiler-cross chicks

Contamination of poultry and poultry products by Salmonella enterica Serovar Enteritidis (SE) continues to be problematic even though biosafety management practices have aided in reduction of the SE burden. Identification of molecular markers linked to disease resistance loci would further reduce SE burden by enabling selection for genetic resistance. The objectives of this study were therefore to evaluate specific genomic regions for resistance to SE burden in young broiler-cross chicks and to evaluate the interaction of allele with dam line and sex. Three hatches of F1 chicks were produced by crossing sires from a broiler breeder male line with hens from three highly inbred lines (Fayoumi 15.2, and MHC-congenic G-B1 and G-B2 Leghorn). At 1 d of age, the chicks were intraesophageally inoculated with SE phage type 13a. Spleen and cecal content samples were harvested at 1 wk, and the levels of SE were quantified by serial plate dilution. Each of the F1 chicks was genotyped with four microsatellites that had previously been shown to be linked to antibody response to SE vaccine. All four microsatellites had a significant (P < or = 0.05) main effect or interaction with dam line or sex on the level of SE in spleen and cecal contents.

Microsatellite markers linked to Salmonella enterica serovar enteritidis vaccine response in young F1 broiler-cross chicks

Reduction in Salmonella enteritidis (SE) contamination is of importance for poultry production as well as for food safety. The objectives of this study were to identify potential genetic markers of antibody response to SE vaccine in young broiler chicks and then to confirm this linkage in broiler-cross offspring, as well as to explore interactions of marker alleles with dam line and sex. The initial identification of suggestive quantitative trait loci (QTL) markers for antibody response to SE vaccine was conducted by using bulked segregant analysis (BSA) with 58 microsatellite markers in a broiler breeder male line. Four unlinked microsatellites that had allele frequency differences between the high and low antibody response DNA pools were selected for subsequent analysis in a linkage study. Antibody response was measured in an F1 population (n = 379) that was derived by crossing each of four males of the broiler line with several dams from four genetically distant, highly inbred lines (Spanish, Fayoumi, and MHC-congenic G-B1 and G-B2 Leghorn). These crosses enabled us to evaluate the broiler sire QTL-marker allele effects and to explore QTL interactions with the dam lines by individual genotyping. Each of the four microsatellites identified by BSA in the broiler population had a significant (P < 0.05) association with F1 population antibody response in one or more sire families. The effect of the interaction of microsatellite allele with dam line or sex on antibody response was frequently significant. Microsatellite markers linked to antibody response QTL were identified, and genetic interactions with dam line and sex were detected.

Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds

We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus genotypes were used to infer genetic clusters. Individuals from each breed were inferred to belong mostly to the same cluster. The clustering success rate, measuring the fraction of individuals that were properly inferred to belong to their correct breeds, was consistently approximately 98%. When markers of highest expected heterozygosity were used, genotypes that included at least 8-10 highly variable markers from among the 27 markers genotyped also achieved >95% clustering success. When 12-15 highly variable markers and only 15-20 of the 30 individuals per breed were used, clustering success was at least 90%. We suggest that in species for which population structure is of interest, databases of multilocus genotypes at highly variable markers should be compiled. These genotypes could then be used as training samples for genetic cluster analysis and to facilitate assignments of individuals of unknown origin to populations. The clustering algorithm has potential applications in defining the within-species genetic units that are useful in problems of conservation.