Sequence-tagged microsatellite sites as markers in chicken reference and resource populations

Development of Microsatellite Marker System to Determine the Genetic Diversity of Experimental Chicken, Duck, Goose, and Pigeon Populations

Poultries including chickens, ducks, geese, and pigeons are widely used in the biological and medical research in many aspects. The genetic quality of experimental poultries directly affects the results of the research. In this study, following electrophoresis analysis and short tandem repeat (STR) scanning, we screened out the microsatellite loci for determining the genetic characteristics of Chinese experimental chickens, ducks, geese, and pigeons. The panels of loci selected in our research provide a good choice for genetic monitoring of the population genetic diversity of Chinese native experimental chickens, ducks, geese, and ducks.

The peptide motif of the single dominantly expressed class I molecule of the chicken MHC can explain the response to a molecular defined vaccine of infectious bursal disease virus (IBDV)

In contrast to typical mammals, the chicken MHC (the BF-BL region of the B locus) has strong genetic associations with resistance and susceptibility to infectious pathogens as well as responses to vaccines. We have shown that the chicken MHC encodes a single dominantly expressed class I molecule whose peptide-binding motifs can determine resistance to viral pathogens, such as Rous sarcoma virus and Marek’s disease virus. In this report, we examine the response to a molecular defined vaccine, fp-IBD1, which consists of a fowlpox virus vector carrying the VP2 gene of infectious bursal disease virus (IBDV) fused with β-galactosidase. We vaccinated parental lines and two backcross families with fp-IBD1, challenged with the virulent IBDV strain F52/70, and measured damage to the bursa. We found that the MHC haplotype B15 from line 15I confers no protection, whereas B2 from line 6₁ and B12 from line C determine protection, although another locus from line 6₁ was also important. Using our peptide motifs, we found that many more peptides from VP2 were predicted to bind to the dominantly expressed class I molecule BF2*1201 than BF2*1501. Moreover, most of the peptides predicted to bind BF2*1201 did in fact bind, while none bound BF2*1501. Using peptide vaccination, we identified one B12 peptide that conferred protection to challenge, as assessed by bursal damage and viremia. Thus, we show the strong genetic association of the chicken MHC to a T cell vaccine can be explained by peptide presentation by the single dominantly expressed class I molecule.

Pivotal Advance: Avian colony-stimulating factor 1 (CSF-1), interleukin-34 (IL-34), and CSF-1 receptor genes and gene products

Macrophages are involved in many aspects of development, host defense, pathology, and homeostasis. Their normal differentiation, proliferation, and survival are controlled by CSF-1 via the activation of the CSF1R. A recently discovered cytokine, IL-34, was shown to bind the same receptor in humans. Chicken is a widely used model organism in developmental biology, but the factors that control avian myelopoiesis have not been identified previously. The CSF-1, IL-34, and CSF1R genes in chicken and zebra finch were identified from respective genomic/cDNA sequence resources. Comparative analysis of the avian CSF1R loci revealed likely orthologs of mammalian macrophage-specific promoters and enhancers, and the CSF1R gene is expressed in the developing chick embryo in a pattern consistent with macrophage-specific expression. Chicken CSF-1 and IL-34 were expressed in HEK293 cells and shown to elicit macrophage growth from chicken BM cells in culture. Comparative sequence and co-evolution analysis across all vertebrates suggests that the two ligands interact with distinct regions of the CSF1R. These studies demonstrate that there are two separate ligands for a functional CSF1R across all vertebrates.

Progress from chicken genetics to the chicken genome

The chicken has a proud history, both in genetic research and as a source of food. Here we attempt to provide an overview of past contributions of the chicken in both arenas and to link those contributions to the near future from a genetic perspective. Companion articles will discuss current poultry genetics research in greater detail. The chicken was the first animal species in which Mendelian inheritance was demonstrated. A century later, the chicken was the first among farm animals to have its genome sequenced. Between these firsts, the chicken remained a key organism used in genetic research. Breeding programs, based on sound genetic principles, facilitated the global emergence of the chicken meat and egg industries. Concomitantly, the chicken served as a model whose experimental populations and mutant stocks were used in basic and applied studies with broad application to other species, including humans. In this paper, we review some of these contributions, trace the path from the origin of molecular genetics to the sequence of the chicken genome, and discuss the merits of the chicken as a model organism for furthering our understanding of biology.

Diversity and locus specificity of chicken MHC B class I sequences

The major histocompatibility complex B (MHC B) region in a standard haplotype of Leghorn chickens contains two closely linked class I loci, B-FI and B-FIV. Few sequences of B-FI alleles are available, and therefore alleles of the two loci have not been compared with regard to sequence diversity or locus specificity. Here, we report eight new B-F alpha 1/alpha 2-coding sequences from broiler chicken MHC B haplotypes, and a unique recombinant between the two B-F loci. The new sequences were combined with existing B-F sequences from Leghorn and broiler haplotypes for analysis. On the basis of phylogenetic analysis and conserved sequence motifs, B-F sequences separated into two groups (Groups A and B), corresponding to B-FIV and B-FI locus, respectively. Every broiler haplotype had one B-F sequence in Group A and the second B-F sequence, if it existed, clustered in Group B. Group B (presumptive B-FI locus) sequences identified in broiler haplotypes resembled the human MHC class I HLA-C locus in their distinctive pattern of allelic polymorphism. Compared with B-FIV, B-FI alleles were less polymorphic and possessed a conserved locus-specific motif in the alpha1 helix, but nevertheless demonstrated evidence of diversifying selection. One B-FI alpha 1/alpha 2-coding nucleotide sequence was completely conserved in four different broiler haplotypes, but each allele differed in the exon encoding the alpha 3 domain.

Polymorphic microsatellites developed by cross-species amplifications in common pheasant breeds

Genetic variability was analysed in two common breeds of pheasant (Phasianus colchicus L. 1758) by means of cross-species amplifications of microsatellite loci: 154 chicken, Gallus gallus and 32 turkey, Meleagris gallopavo, primers were tested for amplification of pheasant DNA. Thirty-six primers (25 specific for chicken and 11 for turkey) amplified pheasant DNA. Fifteen markers yielded specific products and were tested for polymorphism. Eight of them (55%) were polymorphic, with an average polymorphism of two alleles per locus. Specific polymerase chain reaction (PCR) products were sequenced; repeats were found in 11 of the 15 markers, although only two loci showed the same repeat and could be homologous to chicken ones.

Chicken microsatellite primers are not efficient markers for Japanese quail

Domestic fowl or chicken (Gallus gallus) and Japanese quail (Coturnix japonica) belong to the family Phasianidae. The exchange of marker information between chicken and quail is an important step towards the construction of a high-resolution comparative genetic map in Phasianidae, which includes several poultry species of agricultural importance. We tested chicken microsatellite markers to see if they would be suitable as genetic linkage markers in Japanese quail. Twenty-six per cent (31/120) of chicken primers amplified individual loci in Japanese quail and 65% (20/31) of the amplified loci were found to be polymorphic. Eleven of the polymorphic loci were excluded as uninformative because of the lack of amplification in some individuals or high frequency of nonspecific amplification. The sequence information of the remaining nine loci revealed six of them to contain microsatellites that were nearly identical with those of the orthologous regions in chicken. For these six loci, allele frequencies were estimated in 50 unrelated quails. Although the very few chicken markers that do work well in quail could be used as anchor points for a comparative mapping, most chicken markers are not useful for studies in quail. Therefore, more effort should be committed to developing quail-specific markers rather than attempting to adapt chicken markers for work in quail.

Microsatellite polymorphism between and within broiler populations

Two independent broiler chicken populations were genotyped with microsatellite markers to determine genetic polymorphisms within and among broiler populations. Birds were genotyped with primers from the US Poultry Genome Mapping Kits 1 and 2. The 59 primer sets selected for this study provided wide genomic coverage. All 59 primer sets amplified a polymerase chain reaction product in Population L, whereas 57 primer sets produced a product in Population C. The average allele number per line per microsatellite was 2.8 and 2.9 for Populations L and C, respectively. Considering the 57 primer pairs generating product in both lines, 72.3% of the total alleles were unique to one or the other population. This study illustrates the high polymorphism level in broiler populations of microsatellites amplified from primers developed from Red Jungle Fowl or White Leghorn sequences.

Research notes: Fresh and frozen pools of chicken red blood cells as substrates for direct polymerase chain reaction

A method is presented for reliable use of pooled chicken blood samples for estimation of microsatellite frequencies by direct polymerase chain reaction (PCR) amplification of DNA. This method overcomes the variability of hematocrit values in individual chickens and eliminates the step of DNA preparation. The estimated frequencies of polymorphic alleles in fresh and frozen pooled blood samples were similar to those obtained by calculating these frequencies from the individual genotyping. When frozen pooled blood samples are used, pools should be prepared prior to their freezing.

Evaluation of genetic variability and genetic distances between eight chicken lines using microsatellite markers

The genetic variability and divergence of eight chicken lines were evaluated using nine microsatellite markers. The chicken lines included three White Leghorn hybrids, three Finnish Landrace lines, a Rhode Island Red line, and a broiler hybrid line. All the microsatellite loci were found to be polymorphic, the number of alleles varying from 4 to 13 per locus and 1 to 10 per line, respectively. Observed heterozygosities ranged from 0.00 to 0.91. The highest (0.67) and lowest (0.29) mean heterozygosity per line was observed in the broiler and in White Leghorn of Mäkelä, respectively. Three of the microsatellite loci deviated from the Hardy-Weinberg equilibrium in some populations. F statistics indicated clearly the subdivision of the total population into different lines. The genetic distances confirmed the classification of Finnish Landraces into different lines. A phylogenetic consensus tree was constructed from resampled data (1,000 times) using the neighbor-joining method. According to the phylogenetic tree, the lines were grouped into three clusters, in which the White Leghorns formed one group, two Landraces a second group, and a Landrace, the Rhode Island Red, and the broiler lines a third group. Allele distribution at the loci does not support either the stepwise or the infinite alleles mutation model, but the distribution pattern was quite irregular at different loci.

A comprehensive microsatellite linkage map of the chicken genome

A comprehensive linkage map of the chicken genome has been developed by segregation analysis of 430 microsatellite markers within a cross between two extreme broiler lines. The population used to construct the linkage map consists of 10 families with a total of 458 F2 individuals. The number of informative meioses per marker varied from 100 to 900 with an average of 400. The markers were placed into 27 autosomal linkage groups and a Z-chromosome-specific linkage group. In addition, 6 markers were unlinked, 1 of which was Z chromosome specific. The coverage within linkage groups is 3062 cM. Although, as in other species, the genetic map of the heterogametic sex (female) is shorter than the genetic map of the homogametic sex (male), the overall difference in length is small (1.15%). Forty-five of the markers represent identified genes or ESTs. Database homology searches with the anonymous markers resulted in the identification of a further 9 genes, bringing the total number of genes/ESTs on the current map to 54. The mapping of these genes led to the identification of two new regions of conserved synteny between human and chicken and confirmed other previously identified regions of conserved synteny between human and chicken. The linkage map has 210 markers in common with the linkage maps based on the East Lansing and Compton reference populations, and most of the corresponding linkage groups in the different maps can be readily aligned.

DNA marker technology: a revolution in animal genetics

The development of DNA-based markers has had a revolutionary impact on gene mapping and, more generally, on all of animal and plant genetics. With DNA-based markers, it is theoretically possible to exploit the entire diversity in DNA sequence that exists in any cross. For this reason, high resolution genetic maps are being developed at an unprecedented speed. The most commonly used DNA-based markers include those based on a cloned and (usually) sequenced DNA fragment and other, more random, assays for genetic polymorphism that can be grouped under the heading of fingerprint markers. The advantages and disadvantages of the various marker types are discussed, along with their application to the reference chicken genetic linkage maps and to the search for quantitative trait loci (QTL). The prospects for the use of DNA-based markers in marker-assisted selection are considered, along with likely future trends in poultry gene mapping. Further development of both physical and linkage genome maps of the chicken will allow animal scientists to more efficiently detect and characterize QTL and will provide them access to the wealth of genetic information that is being generated about the human genome and the genomes of model species, such as the mouse and Drosophila.

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.

Microsatellite polymorphism in commercial broiler and layer lines estimated using pooled blood samples

For 17 microsatellite markers, allele frequencies were determined in nine highly selected commercial broiler and six highly selected commercial layer lines using pooled blood samples from 60 animals. The average number of marker alleles was 5.8 over all lines, 5.2 over broiler lines, and 3.0 over layer lines. The average number of marker alleles within a line was 2.9, 3.6, and 2.0 for all, broiler, and layer lines, respectively. Over all 15 lines, the average percentage of heterozygosity was 42, whereas the heterozygosity in the broiler lines was 53% and in the layer lines only 27%. In broiler lines, 50% of the marker-line combinations showed a heterozygosity above 60%, whereas this was only 5% in layer lines. Estimation of allele frequencies with microsatellite markers was first assessed in pooled and individual samples before usage in the commercial lines. Allele frequencies for 19 microsatellite markers were estimated in chicken pooled blood samples and compared with allele frequencies from individual typed animals. Similar results were obtained when pooled blood samples (heterozygosity of 35.3%) or individual typed animals (heterozygosity of 34.2%) were used. The method to determine allele frequencies using pooled blood samples is faster, cheaper, and as reliable and repeatable as determining allele frequencies using individual typings.

Preliminary linkage map of the chicken (Gallus domesticus) genome based on microsatellite markers: 77 new markers mapped

Microsatellite polymorphisms are finding increasing use in genetics. The objectives of this study were 1) to enlarge the number of markers to contribute to a well-defined linkage map of the chicken genome; and 2) to create a preliminary linkage map only based on microsatellite markers. The need for microsatellite markers is high for performing a whole genome scan for the identification of quantitative trait loci. Seventy-seven newly developed microsatellite markers that were polymorphic on either one or both of the reference populations were mapped and in combination with all previously described markers, used to construct a preliminary linkage map of the chicken genome. The 128 microsatellite markers mapped thus far cover 23 of the 38 linkage groups of the East Lansing reference population. In the case of the Compton reference population, 20 linkage groups out of 40 are covered with microsatellite markers. No linkage was found in the East Lansing population with five markers, and in the case of the Compton population four markers were unlinked. About 42 and 32% of the East Lansing and Compton maps, respectively, were covered by the 128 microsatellite markers. The microsatellite markers are well dispersed among the various linkage groups and there was no evidence for clustering of the markers within the map. With the 38 markers that were mapped on both reference populations, 10 of the East Lansing linkage groups could be associated with 13 of the Compton linkage groups.

Mapping functional chicken genes: an alternative approach

Functional genes were selected for linkage analysis mapping using the East Lansing (EL) reference population ¿[Jungle Fowl (JF) x White Leghorn (WL)] x WL¿. The approach used was based on the identification of DNA sequence polymorphisms in the introns of those genes found in JF and WL. Deoxyribonucleic acid sequence analysis revealed single base substitutions in introns of six Type I marker genes: adenylate kinase 1 (AK1), aldolase B (ALDOB), a lysosomal membrane protein gene (LAMP1), vitellogenin 2 (VTG2), apolipoprotein A1 (APOA1), and creatine kinase B (CKB). Transitions or transversions were found in introns of AK1, ALDOB, LAMP1, VTG2, APOA1, and CKB. A transversion in the intron of the JF allele of AK1 generated a unique BspHI cleavage site. The design of polymerase chain reaction (PCR) primers based on the site of base substitution led to the specific amplification of the JF allele in the remaining five genes. A size polymorphism in the PCR production derived from iron response element binding protein (IREBP) distinguished the JF from the WL allele. Linkage analysis of the EL reference population revealed that these candidate genes were located in the following EL linkage groups (E) or chromosomes (Chrom) of the chicken genome: AK1 (E41), VTG2 (E43), APOA1 (E49), CKB (E07), LAMP1 (E01), ALDOB (Chrom Z), and IREBP (Chrom Z). Provided that a base substitution can be found in the parents of the reference population, this PCR-based approach can be used to map any cloned candidate gene. This approach will lead to further information on synteny of the chicken genome with cognate genes of mammalian species.

Development of a genetic map of the chicken with markers of high utility

Microsatellites are tandem duplications with a simple motif of one to six bases as the repeat unit. Microsatellites provide an excellent opportunity for developing genetic markers of high utility because the number of repeats is highly polymorphic, and the assay to score microsatellite polymorphisms is quick and reliable because the procedure is based on the polymerase chain reaction (PCR). We have identified 404 microsatellite-containing clones of which 219 were suitable as microsatellite markers. Primers for 151 of these microsatellites were developed and used to detect polymorphisms in DNA samples extracted from the parents of two reference populations and three resource populations. Sixty, 39, 46, 49, and 61% of the microsatellites exhibited length polymorphisms in the East Lansing reference population, the Compton reference population, resource population No. 1 (developed to identify resistance genes to Marek's disease), resource population No. 2 (developed to identify genes involved in abdominal fat), and resource population No. 3 (developed to identify genes involved in production traits), respectively. The 91 microsatellites that were polymorphic in the East Lansing reference population were genotyped and 86 genetic markers were eventually mapped. In addition, 11 new random amplified polymorphic DNA (RAPD) markers and 24 new markers based on the chicken CR1 element were mapped. The addition of these markers increases the total number of markers on the East Lansing genetic map to 273, of which 243 markers are resolved into 32 linkage groups. The map coverage within linkage groups is 1,402 cM with an average spacing of 6.7 cM between loci. The utility of the genetic map is greatly enhanced by adding 86 microsatellite markers. Based on our current map, approximately 2,550 cM of the chicken genome is within 20 cM of at least one microsatellite marker.

Functional genes mapped on the chicken genome

Microsatellite polymorphisms are finding increasing use in genetics. In addition to the random isolation of microsatellite markers, such markers can also be developed from sequences already present in public domain databases. An advantage of public domain databases is that these microsatellites are known to be located within or close to identified functional genes. In this study the GenBank and EMBL databases were screened for microsatellite markers and primers were defined for amplification. Subsequently, these markers were tested on a panel of five different birds from layer and broiler stocks and on the international reference families: the East Lansing reference family and the Compton reference family. Of the 33 loci tested, 25 were polymorphic on the test panel and from these 25, 14 were polymorphic in one or both reference families. Twelve of the 14 loci that could be mapped fell into previously defined linkage groups. The other two markers were not linked. Because three of the loci had previously been mapped to specific chromosomes by in situ hybridization, linkage groups E6 and C3 could be assigned to chromosome 6, E5 and C17 to chromosome 4 and E21 to one of the microchromosomes.

The chicken transforming growth factor-beta 3 gene: genomic structure, transcriptional analysis, and chromosomal location

In this paper, we report the isolation, characterization, and mapping of the chicken transforming growth factor-beta 3 (TGF-beta 3) gene. The gene contains seven exons and six introns spanning 16-kb of the chicken genome. A comparison of the 5'-flanking regions of human and chicken TGF-beta 3 genes reveals two regions of sequence conservation. The first contains ATF/CRE and TBP/TATA sequence motifs within an 87-bp region. The second is a 162-bp region with no known sequence motifs. Identification of transcription start sites using chicken RNA isolated from various embryonic and adult tissues reveals two sites of initiation, P1 and P2, which map to these two conserved regions. Comparison of 3'-flanking regions of chicken and mammalian TGF-beta 3 genes also revealed conserved sequences. The most significant homologies were found in the 3'-most end of the transcribed region. DNA sequence analysis of chicken TGF-beta 3 cDNAs isolated by 3'-RACE revealed multiple polyadenylation sites unusually distant from a poly(A) signal motif. A Msc I restriction fragment length polymorphism (RFLP) marker was used to map the TGFB3 locus to linkage group E7 on the East Lansing reference backcross. Linkage to the TH locus showed that the TGFB3 locus was physically located on chicken chromosome 5.

Microsatellite markers for genetic mapping in the chicken

Microsatellite markers have been found to be abundant, evenly distributed, and highly polymorphic in a number of eukaryotic genomes. The objective of this study was to determine the utility of (TG)n microsatellites in the chicken. A chicken library enriched for (TG)n repeats was generated and 42 unique clones containing (TG)n microsatellites were identified and sequenced. The number of uninterrupted TG repeats ranged from 4 to 14 with an average of 7.8, which was considerably less than the number of repeats found in mammalian species. When primers designed to amplify across the (TG)n microsatellites were used in polymerase chain reactions (PCR) containing genomic chicken DNA, 19 of the 33 primer sets examined yielded polymorphisms in at least one of the three sets of chicken families: 15, 11, and 11 primer sets detected polymorphisms in the East Lansing (EL) reference population, the Compton (C) reference family, and between Line 63 and Line 72 chickens, respectively. The polymorphic microsatellite markers in the EL and C reference families were genetically mapped. Nine and seven mapped markers in the EL and C reference families, respectively, are polymorphic between Line 63 and Line 72, indicating that microsatellite markers will greatly enhance the ability to genotype specific loci of any chicken population.