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

Inhibition of cadmium- induced genotoxicity and histopathological changes in Nile tilapia fish by Egyptian and Tunisian montmorillonite clay

Cadmium (Cd) is an important inorganic toxicant widely distributed in the environment because of its various industrial uses. The aims of the current study were to investigate the efficacy of purified Egyptian and Tunisian montmorillonite clays (EMC and TMC) to inhibit genotoxicity and histological alterations induced by cadmium chloride (CdCl2) utilizing the Nile tilapia fish as an in vivo model. Chromosomal aberrations (CAs), micronucleus (MN) frequencies and DNA fingerprinting profile were genotoxic end points and histopathological changes that were used in this investigation. Six groups of fish were treated for 2 weeks and included control group, CdCl2-treated group and groups treated with EMC or TMC alone or in combination with CdCl2. The present results revealed that, treatment of fish with CdCl2 exhibited significant increased in the number of micronucleated erythrocytes (MnRBCs), frequency of CAs and instability of genomic DNA. Treatment of EMC and TMC in combination with CdCl2 significantly reduced the frequency of MnRBCs by the percentage of 53.28% and 60.77% and the frequency of CAs by 43.91% and 52.17% respectively. As well as, normalized DNA fingerprinting profile and significantly improved histopathological picture induced by Cadmium treatment. It is worth mention that both clays have the ability to tightly bind CdCl2 and decreased its cytotoxicity and genotoxicity; however, Tunisian clay was more efficient in binding with the CdCl2 than Egyptian clay.

Spectroscopic analyses of pollutants in water, sediment and fish

Water ways in Egypt is suffering from continual discharge without adequate treatment especially in the Delta and greater Cairo area. Accordingly water, sediments and catfishes were collected from El Mouheet El Youmna drain in Giza. Cd, Cr, Pb and Zn were determined furthermore the molecular structure of sediment and catfish were conducted with FTIR spectroscopy. Although studied metals were lower in water, higher values are recorded in sediment and catfish samples. FTIR shows possible interaction among metals and organic structures mainly proteins. The bioaccumulation of Pb and Cd proportion was significantly increased in the liver tissues of catfish. A correlation coefficient among sediment and fish liver metals accumulation exist. This infers that the waste assimilation capacity for the drain is high, a phenomena that could be ascribed to dilution, sedimentation and continual water exchange. Furthermore, the genotoxicity affect in catfish genomic corroborates the genus diagnostic markers which attributed to long pollution. This is an indication that agriculture and industrial wastes discharged into the drain has badly a significant effect on the ecological balance.

Genetic differentiation of Indian camel (Camelus dromedarius) breeds using random oligonucleotide primers

The camel population in India is facing a severe decline which demands that immediate steps are taken to ensure its conservation. Characterisation is an integral part of the conservation program. The Polymerase Chain Reaction-Randomly Amplified Polymorphic DNA profile of unrelated camels of the Bikaneri (29), Jaisalmeri (30) and Kachchhi (18) breeds were analyzed. Reproducible polymorphic bands with varying frequencies among the three breeds of camel were obtained with five oligonucleotide primers. A total of 75 bands were amplified, of which 27 (36%) were polymorphic. The probability of obtaining identical fingerprints was observed to be the lowest in primer GC-10 (5.7%) followed by OP-08 (8.7%), GT-10 (11.3%), G-2 (15.5%) and G-1 (80%). Breed informative bands were amplified. The maximum genetic variability was observed in the Bikaneri (0.80±0.05) followed by the Kachchhi (0.84±0.06) and the Jaisalmeri (0.87±0.05) breeds. The inter-breed genetic distance estimates indicated a closer relationship in the Bikaneri-Kachchhi camels, (0.075), followed by the Jaisalmeri-Kachchhi (0.106) and Bikaneri-Jaisalmeri (0.132) breeds. A similar genetic relationship was observed when the degree of population subdivision was measured between the Bikaneri-Kachchhi (0.529), Jaisalmeri-Kachchhi (0.558) and Bikaneri-Jaisalmeri (0.566) breeds.

Evaluation of diversity between different Spanish chicken breeds, a tester line, and a White Leghorn population based on microsatellite markers

The present study was conducted to evaluate the genetic variability and the genetic divergence of 13 Spanish chicken breeds, a tester line, and a White Leghorn population, using 24 microsatellite markers. A total of 150 alleles were detected across all population. The number of alleles by locus ranged from 2 to 13, with the mean value being 6.25. The mean polymorphic information content was 0.591, ranging from 0.847 to 0.172. The combined parentage exclusion probability of excluding 1 parent or 2 parents was 99 and 100%, respectively. The observed heterozygosity was lower than the expected heterozygosity for all loci, the mean values being 0.461 and 0.637. The observed and expected heterozygosity ranged from 0.003 to 0.735 and 0.181 to 0.863, respectively. Mean deficit of heterozygotes within populations (F(IS)) was 0.056 and mean fixation index of each population (F(ST)) was 0.244. The mean global deficit of heterozygotes across populations (F(IT)) was 0.286. A total of 15 private alleles in 10 microsatellites were observed, and in some populations, fixed alleles were found for 7 microsatellites. A total of 300 birds (83%) were properly assigned to the source population. The average observed heterozygosity for each population was 0.461, ranging from 0.328 (Quail Castellana) to 0.538 (Red Villafranquina), and the average expected heterozygosity was 0.488, ranging from 0.320 (Quail Castellana) to 0.550 (White-Faced Spanish). All of the Spanish breeds except the Quail Castellana were more polymorphic than the White Leghorn population. The mean value of the deviation of heterozygote number was 0.052. Nei's genetic distance showed a range from 0.109 (between White-Faced Spanish and Black Menorca) to 0.437 (between Buff Prat and White Leghorn). A phylogenetic tree constructed by the neighbor-joining method, based on Nei's genetic distance, showed a clear separation between the White Leghorn and the remaining breeds. The results indicate that the panel of microsatellite markers was useful in studying the genetic diversity of chicken breeds.

Evaluation of genetic variability and distances among five Iranian native chicken populations using RAPD markers

Genetic variability was studied on five Iranian native chicken populations using Random Amplified Polymorphism DNA (RAPD) markers. The purpose of this study was for the analysis of variation within and between Iranian native chicken populations and for the reconstruction of a phylogenetic tree for these populations using the RAPD marker assay. The populations surveyed were from five provinces including Mazandaran (MZD), Isfahan (ISF), Yazd (YZD), Fars (FRS) and West Azerbaijan (WAZ). On the base of results of this study, the FRS and MZD populations had the highest genetic distance (0.182) and the FRS and ISF populations the lowest one (0.066). The YZD and MZD populations had the highest (0.208) and lowest (0.156) within-population genetic diversity. The phylogenetic tree was reconstructed on UPGMA method and showed two main separated groups. The ISF and FRS populations were first clustered into one group and, then, were clustered into a larger group with YZD and WAZ. Another consists MZD population was clustered separately from this group. This study showed that RAPD technique is an useful tool for evaluation of genetic variation among domesticated animals.

Study the effect of hexavalent chromium on some biochemical, citotoxicological and histopathological aspects of the Orechromis spp. fish

In nature chromium occurs in divalent, trivalent and hexavalent forms. Hexavalent chromium predominates over the trivalent form in natural waters. Knowledge of acute toxicity of a xenobiotic often can be very helpful in predicting and preventing acute damage to aquatic life in receiving waters as well as in regulating toxic waste discharges. The 96 h LC50 tests can be used to obtain toxicity data as rapidly and inexpensively as possible. In the present study, results showed a significant decrease in total glycogen, total lipids and total protein of liver, muscles and gills after 24 and 96 h of exposure to 96 h LC50 of hexavalent chromium (43.7 mg L(-1)). Cytotoxicity of metals is important because some metals are potential mutagens able to induce tumors in humans and experimental animals, the treatment of(Cr VI) at 43.7 mg L(-1) was for 24 and 96 h, respectively. DNA was extracted after treatment from brain and liver of the tested fish. Our results showed appearance of polymorphic bands at the long treatment interval (96 h) ofhexavalent chromium. However, these bands were not appeared when the fish were exposed to the (Cr VI) for the short treatment interval (24 h). Histopathological changes were seen in liver, muscle and gills sections of chromium-exposed fishes. The obtained results were discussed in the study research.

Potential role of cysteine and methionine in the protection against hormonal imbalance and mutagenicity induced by furazolidone in female rats

The use of nitrofurans as veterinary drugs has been banned in the EU since 1993 due to doubts on the safety of the protein-bound residues of these drugs in edible products. Furazolidone (FUZ) is a nitrofuran drug, which has been used for many years as an antibacterial drug in veterinary practice. The aim of the current study is to investigate the role of L-cysteine and L-methionine in the protection against hormonal imbalance and the genotoxicity induced by FUZ using the micronucleus (MN) assay and random amplified polymorphism DNA (RAPD-PCR) analysis in female rats. Forty female Sprague-Dawley rats were divided into four groups included the untreated control group; a group treated with FUZ (300 mg/kg b.w.); a group treated with a mixture of L-cysteine (300 mg/kg b.w.) and L-methionine (42.8 mg/kg b.w.) and a group treated with FUZ plus the mixture of L-cysteine and L-methionine for 10 days. The results indicated that FUZ induced hormonal disturbances involving thyroid, ovarian and adrenal hormones. Moreover, FUZ increased the micronucleus formation and induced changes in polymorphic band patterns. The combined treatment with FUZ and the mixture of L-cysteine and L-methionine succeeded to prevent or diminish the endocrine disturbance and the clastogenic effects of FUZ. The current study is casting new light on the complex mechanisms underlying the ameliorating action of dietary L-cysteine and L-methionine against FUZ toxicity in experimental animals.

Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions

Twenty-five single nucleotide polymorphisms (SNPs) were analyzed in 20 distinct chicken breeds. The SNPs, each located in a different gene and mostly on different chromosomes, were chosen to examine the use of SNPs in or close to genes (g-SNPs), for biodiversity studies. Phylogenetic trees were constructed from these data. When bootstrap values were used as a criterion for the tree repeatability, doubling the number of SNPs from 12 to 25 improved tree repeatability more than doubling the number of individuals per population, from five to ten. Clustering results of these 20 populations, based on the software STRUCTURE, are in agreement with those previously obtained from the analysis of microsatellites. When the number of clusters was similar to the number of populations, affiliation of birds to their original populations was correct (>95%) only when at least the 22 most polymorphic SNP loci (out of 25) were included. When ten populations were clustered into five groups based on STRUCTURE, we used membership coefficient (Q) of the major cluster at each population as an indicator for clustering success level. This value was used to compare between three marker types; microsatellites, SNPs in or close to genes (g-SNPs) and SNPs in random fragments (r-SNPs). In this comparison, the same individuals were used (five to ten birds per population) and the same number of loci (14) used for each of the marker types. The average membership coefficients (Q) of the major cluster for microsatellites, g-SNPs and r-SNPs were 0.85, 0.7, and 0.64, respectively. Analysis based on microsatellites resulted in significantly higher clustering success due to their multi-allelic nature. Nevertheless, SNPs have obvious advantages, and are an efficient and cost-effective genetic tool, providing broader genome coverage and reliable estimates of genetic relatedness.

Natural resistance-associated macrophage protein 1 gene polymorphisms and response to vaccine against or challenge with Salmonella enteritidis in young chicks

Salmonella enteritidis (SE) contamination of poultry products is of global food-safety concern. The natural resistance-associated macrophage protein 1 (NRAMP1) affects host innate immunity to intracellular bacteria because of its ability to transport divalent cations in late endosome/lysosomes. Studying the association of the NRAMP1 gene and chicken innate immune response to SE can, therefore, aid understanding and enhancement of chicken genetic resistance to SE. The chicken NRAMP1 gene was investigated as a candidate gene for SE response in a unique resource population. Outbred broiler sires and three diverse, highly inbred dam lines (two major histocompatibility complex-congenic Leghorn and one Fayoumi line) produced F1 progeny that were evaluated as young chicks for either bacterial load in spleen and cecum after pathogenic SE inoculation or antibody level after SE vaccination. Thirty-seven single nucleotide polymorphisms (SNP) were identified in 3.1 kb of genomic DNA of the NRAMP1 gene. A PCR-RFLP assay was developed to identify a SNP in a conserved transport motif. The sire NRAMP1 gene SNP was associated (P < 0.02) with antibody level to SE vaccine for Sire 8170 offspring in the two Leghorn crosses. In Sire 8296 offspring, NRAMP1 was associated (P < 0.02) with spleen bacterial load in the combined dam-line crosses. This study demonstrated the association of a SNP polymorphism in a highly conserved region of NRAMP1 with SE vaccine and pathogen challenge response in young chicks, indicating that either NRAMP1 or a linked gene controls these SE-response traits.

Genetic diversity of Chinese native chicken breeds based on protein polymorphism, randomly amplified polymorphic DNA, and microsatellite polymorphism

Genetic diversity of Chinese native chicken breeds was investigated using protein polymorphism, randomly amplified polymorphic DNA (RAPD), and microsatellite polymorphism. Imported broiler and layer breeds were also included in the analysis. The results from protein polymorphism did not show distinct differences between Chinese native chicken and imported broilers; however, there were small significant differences between these two types of chickens. The results from RAPD indicated that gene diversity within a population was large in Chinese native chickens, intermediate in broilers, and low in layers and that there were small differences between Chinese native chickens and both broilers and layers. A great difference between broilers and layers was observed. Microsatellite polymorphism data showed that genetic diversity was high in the Chinese native chickens and low in layers and that there was a close relationship between Chinese native chickens and broiler but a remote relationship between Chinese native chickens and layers. The wide genetic diversity of Chinese native breeds can meet different requirements of breeding for chicken quality in China.

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.

Genetic variation among chicken lines and mammalian species in specific genes

Thirteen gene-specific primer sets provided by the U.S. Poultry Genome Coordinators were used to investigate DNA polymorphisms between two highly inbred chicken lines of Leghorn and Fayoumi origin. Nucleotide and predicted amino acid sequences were then compared among these chicken lines and the Genbank sequences of chicken, mouse, and human. The following genes were selected as candidates for immune response or transcription activation: B2M, DAD1, IAP1, IL2, IREB1, LAP18, MAFL, POU1F1, RREB1, TAD, TBP1, TCRG, and ZOV3. Total cDNA was obtained from the spleens of Leghorn and Fayoumi lines by reverse transcriptase-polymerase chain reaction (PCR) and was used as a template to PCR-amplify gene-specific products. All primers except POU1F1 and TCRG generated single PCR products of the predicted 325- to 667-bp size, confirming the efficacy of these gene-specific primers in the chicken. Three and seven of the 11 amplified gene fragments yielded line-specific nucleotide polymorphisms between the Leghorn and Fayoumi sequences and between the Leghorn and Genbank chicken sequences respectively. Similarities between inbred Leghorn and mammalian species were 36 to 86% for nucleotides and 25 to 96% for predicted amino acid sequence. The polymorphisms of some gene fragments between the Leghorn and Fayoumi lines will allow for investigation of associations of these genes with immune response and other biological traits.

Molecular characterization of the Smyth chicken sublines and their parental controls by RFLP and DNA fingerprint analysis

The Smyth line (SL) chicken, a model for autoimmune human vitiligo, is characterized by a spontaneous posthatch epidermal pigment loss (vitiligo). Even though the immunological and morphological changes accompanying the vitiligo process have been well studied, the genetics of this phenomenon remains elusive. The SL lines have been maintained by nonpedigreed matings since their inception, and therefore, the inbreeding status is unknown. The present study was designed to provide an estimate of the inbreeding coefficients and the molecular genetic profiles of the SL sublines, each homozygous for a different MHC haplotype and their MHC-matched parental control (BL) sublines. The DNA fingerprint analysis revealed that there is a moderate level of inbreeding within the SL and BL parental sublines. Of the two SL sublines studied, SL101 had the highest level of inbreeding (0.948). Similarly, its parental control line (BL101) was more inbred than the parental subline of SL102 (BL102). The very high level of similarity between the SL sublines and their respective parental control lines is shown further by the similarity index (SI) estimates (SI between SL101 and BL101 was 0.949 and that between SL102 and BL102 was 0.932). Restriction fragment length polymorphism (RFLP) analysis of the endogenous viral genes (avian leukosis virus subgroup E, ALVE) showed that five ALVE-related BamH1 fragments were present in the SL101 and four in SL102 sublines, whereas the parental BL101 and BL102 sublines had five and six fragments, respectively. SL101 and SL102 shared two fragments, but the frequencies were different. Similarly, BL101 and BL102 shared two fragments. SL101 and BL101 shared three fragments, and SL102 and BL102 also shared three fragments.

Genetic characterization of biodiversity in highly inbred chicken lines by microsatellite markers

Forty-two microsatellite loci were analysed in 23 highly inbred chicken lines derived from Leghorn, Jungle Fowl, Fayoumi and Spanish breeds. Line-specific alleles among breeds and lines were detected. The band-sharing (BS) values were calculated and the proportion of shared alleles distances (Dps) were estimated. The BS values and Dps between sets of MHC-congenic lines ranged from 0.74 to 0.96, and 0.05-0.35, respectively. The BS values between each pair of noncongenic Leghorn lines were 0.32-0.97, and between Leghorn and exotic (Jungle Fowl, Fayoumi and Spanish) breeds were 0.03-0.55. The Dps between Fayoumi lines and other lines were much larger (0.66-1.34) than within Leghorns, and the Jungle Fowl breed had the largest distances with other lines (1.12-5.38). The phylogenetic consensus tree that was constructed grouped these 23 inbred chicken lines into four different clusters. These results are in accordance with the origin and breeding history of these inbred lines, which indicates that the use of microsatellites for the study of genetic biodiversity is accurate and reliable. In addition, the significance and value of inbred chicken lines in molecular genetic research is discussed.

Major histocompatibility complex (MHC) related cDNA probes associated with antibody response in meat-type chickens

The major histocompatibility complex (MHC) region was examined as a set of candidate genes for association between DNA markers and antibody response. Intercross F2 families of chickens were generated from a cross between high (HC) and low (LC) Escherichia coli(i) antibody lines. Restriction fragment length polymorphism (RFLP) analysis was conducted by using three MHC-related cDNA probes: chicken MHC class IV (B-G), chicken MHC class I (B-F), and human MHC-linked Tap2. Association between RFLP bands and three antibody response traits (E. coli, sheep red blood cells and Newcastle disease virus) were determined by two methods: by statistically analyzing each band separately and also by analyzing all bands obtained from the three probes by using multiple regression analysis to account for the multiple comparisons. The MHC class IV probe was the highest in polymorphisms but had the lowest number of bands associated with antibody response. The MHC class I probe yielded 15 polymorphic bands of which four exhibited association with antibody response traits. The Tap2 probe yielded 20 different RFLP bands of which five were associated with antibody production. Some Tap2 bands were associated with multiple antibody response traits. The multiband analysis of the three probes' bands revealed more significant effects than the analysis of each band separately. This study illustrates the efficacy of using multiple MHC region probes as candidate markers for quantitative trait loci (QTLs) controlling antibody response in chickens.

Randomly amplified polymorphic DNA (RAPD) for evaluating genetic relationships among varieties of guinea fowl

The present study investigated the use of randomly amplified polymorphic DNA (RAPD) in estimating the intra and inter varietal genetic variation in three varieties of guinea fowl (Lavender, Pearl and White). The estimates, measured as band sharing were high for within population (0.946-0.971) and between population (0.990-0.999) genetic similarity. The respective estimates were 0.898-0.929 and 0.923-0.928 when estimated as frequency of occurrence of bands. The results indicated a very low level of intra and inter varietal genetic variation in these guinea fowl varieties, which in turn suggested the low level of genetic variation in these populations. The possible reasons for this high genetic similarity has been discussed.

Map-based quantitative trait locus identification

Poultry gene mappers chose microsatellites as the main source of genetic markers for poultry genome mapping, similar to the marker type used for other farm animals, laboratory animals, and humans. Optimal strategies for applying DNA markers in poultry populations are discussed, including the number of markers to be used, genome representation, population structure, choice of markers, population size, statistical stringency for association between markers and quantitative trait loci (QTL), and biological verification of a linkage. It is shown that an efficient strategy should be based on a combination of a low stringent statistical test for the existence of linkage between a marker and QTL and an appropriate genetic test for the discrimination between true and false linkage. The source of the genetic variation to be used is discussed and, as an illustration, three types of resource populations are presented. The informativeness of different matings using various genotypes of the parents are considered and it appears that selection of markers based on the heterozygosity of the sire is the most efficient marker screening approach.

Use of randomly amplified polymorphic DNA markers for the genetic analysis of relatedness and diversity in chickens and turkeys

A study involving the use of random amplified polymorphic DNA (RAPD) was conducted to evaluate genetic polymorphism and relatedness within and among four chicken breeds: Araucona, Rhode Island Red, White Leghorn, and White Plymouth Rock, and two turkey populations, a long-term randombred and a commercial strain. A total of 60 random primers were used in the RAPD analyses. Forty-two of the 60 primers tested amplified patterns with at least one polymorphic fragment in one or more of the populations. Six of these 42 primers amplified polymorphic fragments in each of the six strains with a within- and between-population average band-sharing frequency of less than one but above zero (P < 0.05). Differences among the six primers for genetic distance (D) among populations were significant (P < 0.05). A consensus dendogram was therefore developed to show the phylogenetic relationships among the populations. As expected, estimates of D between populations were lowest within species and highest between species. The results provide evidence of the applicability of RAPD to determining genetic relatedness within and among different poultry populations and in developing reproducible markers useful in evaluating individual variation in chickens and turkeys.