Genetic diversity of Hungarian indigenous chicken breeds based on microsatellite markers

Six local chicken breeds are registered in Hungary and are regarded as Hungarian national treasures: Hungarian White, Yellow and Speckled, and Transylvanian Naked Neck White, Black and Speckled. Three Hungarian academic institutes have maintained these genetic resources for more than 30 years. The Hungarian Yellow, the Hungarian Speckled and the Transylvanian Naked Neck Speckled breeds were kept as duplicates in two separate subpopulations since time of formation of conservation flocks at different institutes. In this study, we investigated genetic diversity of these nine Hungarian chicken populations using 29 microsatellite markers. We assessed degree of polymorphism and relationships within and between Hungarian breeds on the basis of molecular markers, and compared the Hungarian chicken populations with commercial lines and European local breeds. In total, 168 alleles were observed in the nine Hungarian populations. The F _ST estimate indicated that about 22% of the total variation originated from variation between the Hungarian breeds. Clustering using structure software showed clear separation between the Hungarian populations. The most frequent solutions were found at K  = 5 and K  = 6, respectively, classifying the Transylvanian Naked Neck breeds as a separate group of populations. To identify genetic resources unique to Hungary, marker estimated kinships were estimated and a safe set analysis was performed. We show that the contribution of all Hungarian breeds together to the total diversity of a given set of populations was lower when added to the commercial lines than when added to the European set of breeds.     

Genetic diversity of ten Egyptian chicken strains using 29 microsatellite markers

In this study, we assessed the genetic diversity of three Egyptian local chicken strains (Fayoumi, Dandarawi and Sinai) and six synthetic breeds derived from Fayoumi and Sinai by intercrossing with Barren Plymouth Rock, Rhode Island Red or White Cornish. Diversity measures were based on interrogation of 29 microsatellites. We identified three main clusters of chicken populations encompassing selected Fayoumi lines and Doki-4 (cluster-1), native Dandarawi (cluster-2) and Sinai, and all six synthetic breeds (cluster-3). Dandarawi and Fayoumi lines exhibited lower intra-population genetic diversity and allelic privacy than Sinai and synthetic breeds. The global inbreeding (F(IT) ) was 0.11, among-population differentiation (F(ST) ) was 0.07, and within-population differentiation (F(IS) ) was 0.04. The between-population marker-estimated kinship was lower than within-population estimates. The cluster analysis classified the Fayoumi lines, Dandarawi and Gimmizah as clearly separated populations. The other strains were configured in mosaic admixed groups.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F _ST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.     

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.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is regarded as one of the domestication cen-ters for chickens and archaeological studies provided evidence of chicken domestication in northern Chinaas early as 6000 BC[1]. At present, China has the larg-est chicken population in the world, represen…     

Multicolour fluorescent detection and mapping of AFLP markers in chicken (Gallus domesticus)

We describe the mapping of amplified restriction fragment polymorphism (AFLP) markers in chicken (Gallus domesticus) using a multi-colour fluorescent detection system. DNA was used from a population consisting of four families with a total of 183 F2 individuals. The enzyme combination EcoRI/TaqI was used for double digestion, and fluorescently labelled fragments were analysed on an ABI PRISM 377 DNA sequencer. Polymorphic signals in the range of 50-500 bp were genotyped with the ABI PRISM Genotyper 2.0 software, which enabled the analysis of both dominant and incomplete dominant markers (with respect to AFLP, often referred to as codominant). In 19 sets consisting of 3 EcoRI/TaqI primer pair combinations each, a total of 475 polymorphic markers was detected. From these polymorphisms 344 markers could be mapped on the Wageningen linkage map. Fourteen markers were length polymorphisms of the same fragment and 28 markers Z-linked and uniformative; 64 AFLP markers appeared to be unlinked and 25 AFLP markers could not be accurately mapped on the basis of the genotyping results. The resulting AFLP/microsatellite linkage map is comprised of 33 linkage groups with a total of 835 loci.     

The isolation and mapping of 19 tetranucleotide microsatellite markers in the chicken

Microsatellites consisting of tetranucleotide repeats are more easily, and consequently efficiently, scored than loci consisting of dinucleotides. However, they are much less frequent in the genome. A hybridisation selection protocol was therefore employed to generate a chicken genomic library enriched for inserts containing the tetranucleotide repeat motif (TTTC)n. Forty-five new microsatellite sequences were isolated that mainly consisted of perfect repeats of the tetranucleotide (TTTC) motif. Nineteen markers were mapped in one or both of the East Lansing and Compton international chicken reference populations.     

Toward fully automated genotyping: genotyping microsatellite markers by deconvolution.

Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA)n repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements.     

Developing microsatellite markers from cDNA: a tool for adding expressed sequence tags to the genetic linkage map of the chicken

A chicken embryonic cDNA library was screened with a (TG)₁₃ probe in order to develop polymorphic microsatellite markers. The redundancy of the embryonic cDNA library with a chicken brain cDNA library, which was used for microsatellite development in a previous study, was extremely high. Of the 300 (TG)₁₃ positive clones, only 80 were unique for the embryonic cDNA library. Still, nine expressed sequences derived from the embryonic cDNA library were mapped in the Wageningen (WAU) resource population. In addition seven microsatellite markers from the chicken brain cDNA library, which were monomorphic or unlinked in the two international reference families in the previous study, were also mapped in the WAU population. Three of the 16 mapped chicken expressed sequence tags (ESTs) showed relatively high percentages of sequence similarity to sequences found in other species. As two of these genes, RAB6 and ZFX/ZFY, have been mapped in humans, they contribute to the comparative map of the chicken.     

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.     

黄羽肉鸡微卫星多态性与体重的相关分析

利用选自家禽基因组中的13个微卫星标记,对黄羽肉鸡A系、B系回交F2代群体100个个体的基因组DNA进行PCR扩增,经分析后,计算出各标记的基因频率、多态信息含量、杂合度,通过与性状初生重、8周龄体重的相关分析,得出与体重相关的标记,并进行了同一标记不同基因型间的多重比较。     

Chicken microsatellite markers isolated from libraries enriched for simple tandem repeats

The total number of microsatellite loci is considered to be at least 10-fold lower in avian species than in mammalian species. Therefore, efficient large-scale cloning of chicken microsatellites, as required for the construction of a high-resolution linkage map, is facilitated by the construction of libraries using an enrichment strategy. In this study, a plasmid library enriched for tandem repeats was constructed from chicken genomic DNA by hybridization selection. Using this technique the proportion of recombinant clones that cross-hybridized to probes containing simple tandem repeats was raised to 16%, compared with < 0·1% in a non-enriched library. Primers were designed from 121 different sequences. Polymerase chain reaction (PCR) analysis of two chicken reference pedigrees enabled 72 loci to be localized within the collaborative chicken genetic map, and at least 30 of the remaining loci have been shown to be informative in these or other crosses.     

Exclusion probabilities of 22 bovine microsatellite markers in fluorescent multiplexes for semiautomated parentage testing

Six multiplexes developed for semiautomated fluorescence genotyping were evaluated for parentage testing. These multiplexes contained primer pairs for the amplification of 22 microsatellites on 17 bovine autosomes. Exclusion probabilities were determined from genotypes of 1022 Holstein cattle and 311 beef cattle belonging to five breeds. Two cases were considered: case 1, genotypes are known for an alleged parent and an offspring but genotypes of a confirmed parent are unknown; and case 2, genotypes are known for an alleged parent, a confirmed parent and an offspring. If the alleged parent is not the true parent, then the 22 markers will exclude the alleged parent with a probability of >0·9986 for case 1 and with a probability of >0·99999 for case 2. On the basis of these exclusion probabilities, the probability that an alleged parent will be falsely included as a parent is in the range of 1/716 to 1/2845 for case 1 and 1/1·2 million to 1/159753 for case 2. In addition to these results, a rapid and efficient non-organic method for extraction of DNA from semen is described.     

Use of chicken microsatellite markers in turkey: a pessimistic view

Eighty-eight chicken microsatellite markers, previously developed in our laboratory, were tested for their ability to amplify polymorphic fragments using turkey genomic DNA. Amplification products were obtained for 61 chicken microsatellite markers (69.1%) whereas 27 (30.9%) did not give rise to any products, even when different polymerase chain reaction conditions were employed. From the 61 markers that gave a product, only eight showed a length polymorphism while 37 were monomorphic on the three divergent commercial turkey lines used. The remaining 16 markers yielded many unspecific bands and no specific amplification product could be obtained. Five polymorphic and eleven monomorphic products contained a detectable microsatellite repeat. Furthermore, of the markers that detected a polymorphism in turkey, the observed heterozygosity (15–50%) and allelic variation (only 2 in most cases) was very low. Therefore, on the basis of our results, we think that chicken microsatellite markers are not very useful for mapping purposes in turkey.     

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

Two chicken genomic libraries were screened for the presence of poly(TG/AC) microsatellite tracts. The number of positive clones was low, confirming the low frequency of such micro-satellites in the chicken genome relative to mammalian genomes. Polymorphism of 29 microsatellite tracts, comprising 11 from the library screening and 18 obtained from GenBank, was examined in the East Lansing and Compton reference families, in a resource population formed by a cross between a single White Rock broiler and inbred Leghorn females, and in a panel of birds from five layer stocks. Twenty microsatellites, primarily of the poly(TG/AC) type, were polymorphic in at least one of the populations. Thirteen of the microsatellites were polymorphic in the East Lansing reference family and 13 were also polymorphic in the resource population, confirming that the genetic distance between White Rock and White Leghorn is about as great as between Jungle fowl and White Leghorn. Only six microsatellites were polymorphic in the Compton reference family, formed by a cross between two White Leghorn strains. Twelve of the microsatellites were mapped in the East Lansing and/or Compton reference families. These were well dispersed among the various linkage groups and did not show any indications of terminal clustering.     

应用微卫星标记分析中国地方鸡种的遗传变异

利用 8个微卫星位点对中国 9个地方鸡种和 1个引进品种进行了遗传检测。计算出了各品种的平均杂合度、平均多态信息含量 (PIC)及品种间的遗传距离 ,并进行了系统聚类。结果表明 :8个微卫星位点上共检测到了5 4个等位基因 ,每个位点上平均为 6 .75个。各位点平均多态信息含量为 0 .5 0 71～ 0 .74 34,均表现出了高度多态性。各群体平均杂合度较高 ,为 0 .5 5 6 4～ 0 .7135 ,说明我国地方鸡种有着较丰富的遗传多样性。地方鸡种间的遗传距离相对较远 ,10个鸡种共分为三大类。研究结果对我国鸡种资源的评估、保存和预测杂种优势具有一定的指导意义     

Six polymorphic microsatellite markers for Plantago maritima

Plantago maritima displays an extraordinary variation in breeding system. In northern Europe, the species occurs as either self‐incompatible or self‐compatible, and as unisexual females or co‐sexual hermaphrodites. The isolation of polymorphic codominant markers will provide the necessary tools to investigate the proportion of self‐fertilized seeds and levels of inbreeding depression in natural populations of this species. Isolation of microsatellite loci was achieved using a membrane‐enrichment method for four loci, and a streptavidin‐coated‐beads method for two loci. Primers were designed in microsatellite flanking sequences and were analysed using fluorescent labels.     

Isolation and multiplex genotyping of polymorphic microsatellite DNA markers in the snakehead murrel, Channa striata

Seven polymorphic microsatellite loci were isolated and characterized for the snakehead murrel, Channa striata (Channidae), a valuable tropical freshwater fish species. Among 25 specimens collected from Kedah state in Malaysia, the number of alleles per locus ranged from 2 to 7. Observed and expected heterozygosities ranged from 0.120 to 0.880 and 0.117 to 0.698, respectively. A single locus (CS1-C07) was significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction. These novel markers would be useful for population genetic studies of the C. striata.     

Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds

French and Asian subsets of chicken breeds were first analysed using 22 microsatellites and then compared to the AVIANDIV European set using 14 loci. Positive correlations were observed between F _IT or F _ST and typological values or variance of markers using the multivariate analysis mcoa . The first axis of the multivariate representation separated Asian from European breeds, revealing breeds with Asian ancestor. Using all or 14 loci, correct assignation rate was always higher than 93%. The Weitzman index and the aggregate diversity D were calculated using 22 loci within French and Asian breeds. The French breed Coucou de Rennes and the Hua-Tung breed seemed to contribute the most to the global diversity of each subset. This approach on French-only breeds and then on French with AVIANDIV domestic breeds (14 loci) showed that the Marans breed contributed the most. The AVIANDIV framework could be useful to evaluate the genetic diversity of local breeds and to help in connecting national and regional conservation policies.