Genetic structure of a wide-spectrum chicken gene pool

The genetic structure of 65 chicken populations was studied using 29 simple sequence repeat loci. Six main clusters which corresponded to geographical origins and histories were identified: Brown Egg Layers; predominantly Broilers; native Chinese breeds or breeds with recent Asian origin; predominantly breeds of European derivation; a small cluster containing populations with no common history and populations that had breeding history with White Leghorn. Another group of populations that shared their genome with several clusters was defined as 'Multi-clusters'. Gallus gallus gallus (Multi-clusters), one of the subspecies of the Red Jungle Fowl, which was previously suggested to be one of the ancestors of the domesticated chicken, has almost no shared loci with European and White Egg layer populations. In a further sub-clustering of the populations, discrimination between all the 65 populations was possible, and relationships between each were suggested. The genetic variation between populations was found to account for about 34% of the total genetic variation, 11% of the variation being between clusters and 23% being between populations within clusters. The suggested clusters may assist in future studies of genetic aspects of the chicken gene pool.     

Global diversity and genetic contributions of chicken populations from African,Asian and European regions

Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (F_ST) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour‐Net genetic clustering and structure analysis revealed two main groups of Asian and north‐west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north‐west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds.     

Molecular Characterization of Mx1 Gene in Native Indian Breeds of Chicken

The genetic polymorphism of Mx1 gene was explored in Indian chicken breeds. PCR-RFLP analysis in 102?bp fragment of partial intron 13 and partial exon 14 of Mx1 gene revealed two genotypes viz. RS and SS with two alleles viz. R and S both in Naked Neck and Tellicherry breeds of chicken. The homozygous genotype RR was not identified. When deduced amino acid sequences were compared, the asparagine amino acid was found to be substituted in “R” allele for serine in “S” allele. PCR-SSCP analysis of 284?bp fragment in 5′-UTR and partial promoter region revealed three genotypes viz. CC, CG, and CH with three different alleles viz. C, G, and H in Naked Neck breed of chicken and five genotypes viz. DI, JK, KK, KL, and KM with six different alleles viz. D, I, J, K, L, and M in Tellicherry breed of chicken. The homozygous genotypes viz. GG and HH in Naked Neck and DD, II, JJ, LL, and MM in Tellicherry chicken was not identified. The nucleotide substitution rate estimated to be in the range of 0.004–0.011. The identified genetic variation can be helpful for better insight to disease resistance property of the Mx1 gene.     

Origin of Hungarian indigenous chicken breeds inferred from mitochondrial DNA D-loop sequences

In this study, we assessed the maternal origin of six Hungarian indigenous chicken breeds using mitochondrial DNA information. Sequences of Hungarian chickens were compared with the D-loop chicken sequences annotated in the GenBank and to nine previously described reference haplotypes representing the main haplogroups of chicken. The first 530 bases of the D-loop region were sequenced in 74 chickens of nine populations. Eleven haplotypes (HIC1-HIC11) were observed from 17 variable sites. Three sequences (HIC3, HIC8 and HIC9) of our chickens were found as unique to Hungary when searched against the NCBI GenBank database. Hungarian domestic chicken mtDNA sequences could be assigned into three clades and probably two maternal lineages. Results indicated that 86% of the Hungarian haplotypes are related to the reference sequence that likely originated from the Indian subcontinent, while the minor part of our sequences presumably derive from South East Asia, China and Japan.     

Polymorphism of microsatellite markers in Russian common carp (<Emphasis Type="Italic">Cyprinus carpio</Emphasis> L.) breeds

Using five microsatellite loci, genotyping and genetic diversity estimates were obtained for nine samples representing seven common carp breeds most widespread in Russia. For comparison, the samples of Amur wild common carp (Cyprinus carpio haematopterus) and a sample of European Hungarian carp were used. In the samples examined (n = 148) a total of 78 alleles were revealed. The highest mean allele number per locus (7.3) was identified in Amur wild common carp, while the lowest number was found in Cherepets carps (4.0). In different breeds, the observed heterozygosities varied from 0.819 (Altai carp) to 0.651 (Cherepets scaly carp). Three out of five microsatellite loci (MFW-24, MFW-28, and MFW-19) revealed a high level of population differentiation. In the dendrogram of genetic differences, all breeds clustered into two groups. One of these groups was composed of the two strains of Ropsha carp, Stavropol carp, Amur wild common carp, and the two samples of Cherepets carp. The second cluster included Altai carp (Priobskii and Chumysh populations), two Angelinskii carp breeds (mirror and scaly), and Hungarian carp. The pairs of breeds/populations/strains, having common origin, were differentiated. Specifically, these were two populations of Altai carp, two strains of Ropsha carp, as well as the breeds of Angelinskii and Cherepets carps. The reasons for genetic differentiation of Russian common carp breeds, as well as the concordance of the evolutionary histories of these breeds, some of which originated from the European breeds, while the others contain substantial admixture of the Amur wild common carp, are discussed.     

Genetic diversity among chicken breeds estimated through randomly amplified polymorphic DNA.

The randomly amplified polymorphic DNA (RAPD) markers were used to detect polymorphism among five breeds of chicken i.e. White Leghorn and Rhodes Island Red (selected for part period egg production and egg mass respectively), Red Cornish and White Plymouth Rock (selected for early body weights) and Kadaknath (native breed). Twelve of the fifty random primers screened yielded distinct polymorphic RAPD profiles. Of the total 96 fragments amplified, about 25% showed polymorphism. Using the RAPD data matrix, the within population and between population genetic similarity was estimated. The selected improved breeds showed higher within population genetic similarity in comparison to the native breed. The two meat type breeds showed a high level of genetic similarity between themselves. The White Leghorn breed showed a low genetic similarity with other breeds. The native breed showed highest similarity with Rhodes Island Red. The dendogram was constructed to show phylogenetic relationship among these breeds. As expected, the genetic distances were lowest within similar type breeds and were highest between dissimilar type breeds. The results indicated the effectiveness of RAPD in detecting polymorphism between chicken populations and their applicability in population studies and establishing genetic relationships among the chicken populations.     

The footprint of recent and strong demographic decline in the genomes of Mangalitza pigs

The Mangalitza pig breed has suffered strong population reductions due to competition with more productive cosmopolitan breeds. In the current work, we aimed to investigate the effects of this sustained demographic recession on the genomic diversity of Mangalitza pigs. By using the Porcine Single Nucleotid Polymorphism BeadChip, we have characterized the genome-wide diversity of 350 individuals including 45 Red Mangalitza (number of samples; n=20 from Hungary and n=25 from Romania), 37 Blond Mangalitza, 26 Swallow-belly Mangalitza, 48 Blond Mangalitza × Duroc crossbreds, 5 Bazna swine, 143 pigs from the Hampshire, Duroc, Landrace, Large White and Pietrain breeds and 46 wild boars from Romania (n=18) and Hungary (n=28). Performance of a multidimensional scaling plot showed that Landrace, Large White and Pietrain pigs clustered independently from Mangalitza pigs and Romanian and Hungarian wild boars. The number and total length of ROH (runs of homozygosity), as well as F_ROH coefficients (proportion of the autosomal genome covered ROH) did not show major differences between Mangalitza pigs and other wild and domestic pig populations. However, Romanian and Hungarian Red Mangalitza pigs displayed an increased frequency of very long ROH (>30 Mb) when compared with other porcine breeds. These results indicate that Red Mangalitza pigs underwent recent and strong inbreeding probably as a consequence of severe reductions in census size.     

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     

A mitochondrial DNA phylogeny of the endangered vipers of the Vipera ursinii complex

The last two populations of the Hungarian meadow viper Vipera ursinii rakosiensis were thought to persist in the steppe fragments of Hungary until meadow vipers were discovered in central Romania (Transylvania), suggesting a possible existence of remnant populations elsewhere. We assessed the phylogenetic position of the Transylvanian vipers using 2030 bp of mitochondrial DNA sequence. We showed that they were closely related to the Hungarian vipers, while those from northeastern Romania (Moldavia) and Danube Delta belonged to the subspecies Vipera ursinii moldavica. Montane subspecies from Europe (Vipera ursinii ursinii and Vipera ursinii macrops) formed a sister clade to the two lowland subspecies. Vipera renardi formed a sister clade to V. ursinii, with populations from the Greater Caucasus (Vipera renardi lotievi) and Tien Shan (Vipera renardi tienshanica) as the sister group to Vipera renardi renardi, and Vipera renardi eriwanensis from the Lesser Caucasus as the most basal taxon in the species. Our results illustrate that the divergence between the lowland and montane populations occurred separately in each species and several times in V. renardi. We demonstrated that the recently discovered Transylvanian population is the third surviving population of V. u. rakosiensis and the only known population outside of Hungary.     

Genetic Polymorphism of Russian,European, and Asian Chicken Breeds as Revealed with DNA and Protein Markers

The variation in polymorphic DNA (RAPD and minisatellite) and protein markers was compared for nine Russian chicken breeds differing in morphological and productivity types and in origin, three European egg breeds, and three meat breeds of the Asian origin. Genetic diversity indices were calculated for each breed group and each marker type and were used to construct dendrograms of genetic similarity. In all breed groups, minisatellites and RAPD markers revealed higher genetic diversity as compared with protein markers. With any type of markers, genetic diversity of the Russian and Asian meat breeds proved to be significantly higher than that of the European egg breeds. The differentiating potentialities of molecular and genetic biochemical markers at the breed level and the origin of the Russian chicken breeds are discussed.     

Genetic polymorphism of Russian,European, and Asian chicken breeds as revealed with DNA and protein markers

The variation in polymorphic DNA (RAPD and minisatellite) and protein markers was compared for nine Russian chicken breeds differing in morphological and productivity types and in origin, three European egg breeds, and three broiler breeds of the Asian origin. Genetic diversity indices were calculated for each breed group and each marker type and were used to construct dendrograms of genetic similarity. In all breed groups, minisatellites and RAPD markers revealed higher genetic diversity as compared with protein markers. With any type of markers, genetic diversity of the Russian and Asian broiler breeds proved to be significantly higher than that of the European egg breeds. The differentiating potentialities of molecular and genetic biochemical markers at the breed level and the origin of the Russian chicken breeds are discussed.     

Comparison on DNA patterns of different ecotypes of European corn borer (Ostrinia nubilalis Hübner) in Hungary

For a molecular genetic study on Hungarian populations of European corn borer L5 stage larvae were collected from 14 places of three different regions of the country (uni- and bivoltine ecotypes). Additionally, the study included larvae from Egypt, too (multivoltine ecotype). Molecular examinations of European corn borer larvae using the study of mitochondrial cytochrome b (cyt b) revealed that by single strand conformation polimorphism (SSCP) the populations found in Hungary represented the same haplotype. Even the Egyptian sample showed no genetic divergence. Some minor deviatons were found in the case of a sample from Székkutas, but that did not prove the genetic divergence of the bivoltine ecotype either, since the other samples of South-East Hungary did not display this kind of genetic variation. On the basis of our investigations it can be said that the univoltine and bivoltine generations, have uniform genetic complements.     

Marker-assisted conservation of European cattle breeds: An evaluation

Two methods have been developed for the assessment of conservation priorities on the basis of molecular markers. According to the Weitzman approach, contributions to genetic diversity are derived from genetic distances between populations. Alternatively, diversity within and across populations is optimized by minimizing marker-estimated kinships. We have applied, for the first time, both methods to a comprehensive data set of 69 European cattle breeds, including all cosmopolitan breeds and several local breeds, for which genotypes of 30 microsatellite markers in 25–50 animals per breed have been obtained. Both methods were used to calculate the gain in diversity if a breed was added to a set of nine non-endangered breeds. Weitzman-derived diversities were confounded by genetic drift in isolated populations, which dominates the genetic distances but does not necessarily increase the conservation value of a breed. Marker-estimated kinships across populations were less disturbed by genetic drift than the Weitzman diversities and assigned high conservation values to Mediterranean breeds, which indeed have genetic histories that differ from the non-endangered breeds. Prospects and limitations of marker-assisted decisions on conservation priorities are discussed.     

The genetic impact of demographic decline and reintroduction in the wild boar (Sus scrofa): a microsatellite analysis

The reintroduction of wild boar from central Europe after World War II has contributed substantially to the range expansion of this species in Italy, where indiscriminate hunting in earlier times resulted in extreme demographic reduction. However, the genetic impact of such processes is not well-understood. In this study, 105 individuals from Italian and Hungarian wild boar populations were characterized for nine autosomal microsatellite loci. The Hungarian samples, and two central Italian samples from protected areas (parks) where reintroduction is not documented, were assumed to be representative of the genetic composition of the source and the target populations in the reintroduction process, respectively. Animals hunted in the wild in the Florence area of Tuscany (Italy) were then studied to identify the effects of reintroduction. The results we obtained can be summarized as follows: (i) none of the populations analysed shows genetic evidence of demographic decline; (ii) the three parental populations from Italy and Hungary are genetically distinct; however, the low level of divergence appears in conflict with the naming of the Italian and the European subspecies (Sus scrofa majori and Sus scrofa scrofa, respectively); in addition, the Italian groups appear to be as divergent from each other as they are from the Hungarian population; (iii) most of the individuals hunted near Florence are genetically intermediate between the parental groups, suggesting that hybridization has occurred in this area, the average introgression of Hungarian genotypes is 13%, but approximately 45% of the genetic pool of these individuals can not be directly attributed to any of the parental populations we analysed; (iv) analysis of microsatellite loci, though in a limited number, is an important tool for estimating the genetic effect of reintroduction in the wild boar, and therefore for the development of conservation and management strategies for this species.     

Mapping of quantitative trait loci on porcine chromosome 4

A F₂ population derived from a cross between European Large White and Chinese Meishan pigs was established in order to study the genetic basis of breed differences for growth and fat traits. Chromosome 4 was chosen for initial study as previous work had revealed quantitative trait loci (QTLs) on this chromosome affected growth and fat traits in a Wild Boar × Large White cross. Individuals in the F₂ population were typed for nine markers spanning a region of approximately 124 c m . We found evidence for QTLs affecting growth between weaning and the end of test (additive effect: 43·4 g/day) and fat depth measured in the mid-back position (additive effect: 1·82 mm). There was no evidence of interactions between the QTLs and sex, grandparents or F₁ sires, suggesting that the detected QTLs were fixed for alternative alleles in the Meishan and Large White breeds. Comparison of locations suggests that these QTLs could be the same as those found in the Wild Boar × Large White cross.     

Analysis of genetic structure and relationship among nine indigenous Chinese chicken populations by the <Emphasis Type="Italic">Structure</Emphasis> program

The multi-locus model-based clustering method Structure program was used to infer the genetic structure of nine indigenous Chinese chicken (Gallus gallus) populations based on 16 microsatellite markers. Twenty runs were carried out at each chosen value of predefined cluster numbers (K) under admixture model. The Structure program properly inferred the presence of genetic structure with 0.999 probabilities. The genetic structure not only indicated that the nine kinds of chicken populations were defined actually by their locations, phenotypes or culture, but also reflected the underlying genetic variations. At K = 2, nine chicken populations were divided into two main clusters, one light-body type, including Chahua chicken (CHA), Tibet chicken (TIB), Xianju chicken (XIA), Gushi chicken (GUS) and Baier chicken (BAI); and the other heavy-body type, including Beijing You chicken (YOU), Xiaoshan chicken (XIA), Luyuan chicken (LUY) and Dagu chicken (DAG). GUS and DAG were divided into independent clusters respectively when K equaled 4, 5, or 6. XIA and BIA chicken, XIA and LUY chicken, TIB and CHA chicken still clustered together when K equaled 6, 7, and 8, respectively. These clustering results were consistent with the breeding directions of the nine chicken populations. The Structure program also identified migrants or admixed individuals. The admixed individuals were distributed in all the nine chicken populations, while migrants were only distributed in TIB, XIA and LUY populations. These results indicated that the clustering analysis using the Structure program might provide an accurate representation of the genetic relationship among the breeds.     

江西省主要地方鸡种的RAPD分析及其群体遗传关系的研究

采用RAPD技术分析了南城黑鸡、余干五黑鸡、泰和乌骨鸡、东乡绿壳蛋鸡、崇仁麻鸡、宁都三黄鸡、广丰白耳黄鸡和万载康乐黄鸡等8个江西地方鸡种、1个培育鸡种--景德黄鸡以及1个外来鸡种--以色列隐性白羽鸡基因组池DNA的多态性,经OPERONA,B,C,D,G5组100种随机引物扩增筛选,14种引物获得了33个多态标记.各品种间的遗传距离指数的计算结果和UPGMA聚类关系图表明:在10个鸡种间,南城黑鸡和余干五黑鸡的遗传距离最近,两者有着极密切的亲缘关系.据此认为这两个鸡群可视为同一品种的两个地方系.此外,广丰白耳黄鸡和景德黄鸡也表现出较密切的亲缘关系,这与景德黄鸡在培育过程中曾掺有白耳黄鸡血缘的选育历史相吻合。 Abstract:Random amphfied polymorphic DNAs (RAPD) analysis was explored to investigate genetic polymorphisms of pooled genomic DNA from 8 native and 1 cultivated chicken breeds in Jiangxi province as well as 1 exotic chicken breed,which include Guangfeng baier huang,Jingde huang,Yugan wuhei,Nancheng hei,Congren ma,Taihe Silky Fowl,Ningdu san huang,Dongxiang green-shell,Wanzai kangle huang and Israel Recessive White Feather Fowl.of 100 OPERON random primers screened,14 primers produced 34 polymorphic RAPD markers.The genetic distance index and UPGMA dendrogram indicated that Nancheng hei and Yugan wuhei chickens had very closely genetic relationship,the genetic distance between the two populations was closer than any other pair of breeds.Therefore,the two chicken populations were suggested to be classified into one breed.In addition,Guangfeng baier huang and Jingde huang shown intimately relationship,it was consistent with the cultivation history of Jingde huang chicken breed,in which Guangfeng baier huang was introduced as one of parental breed.     

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…