Assessing genetic diversity in Italian goat populations using AFLP® markers (original) (raw)
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Assessing genetic diversity in Italian goat populations using AFLPR markers
Animal Genetics, 2001
Ampli®ed fragment length polymorphism (AFLP Ò ) markers were used to investigate the genetic variation in a sample of seven goat (Capra hircus) populations. A total of 210 individuals (30 per population) were analysed using seven selected AFLP primer combinations that produced 219 clear polymorphisms. Four autochthonous goat breeds (Bionda dell'Adamello, Frisa, Orobica and Verzaschese), two primary populations, one from the Lombardy Alps (Val di Livo) and the other from Sardinia island (Sarda) and a reference cosmopolitan breed (Saanen) were included in the analysis. The expected heterozygosity (Het) did not differ signi®cantly among breeds (range 0.21±0.24). No breed speci®c markers were identi®ed. The variability at AFLP loci was largely maintained within breeds, as indicated by the coef®cient of genetic differentiation (Gst) value (0.11). Dice similarities calculated between pairs of individuals belonging to the same or to different breeds largely overlapped. Bootstrapping on markers indicated that the coef®cient of variation (CV) of the genetic indexes tested decreases only marginally by adding markers over 100 AFLPs. Cluster analysis based on standard genetic distance between breeds indicates that Sarda is the most distant population, while Bionda, Frisa, Verzaschese and Val di Livo seem to be highly related populations. Interestingly, Saanen is closer than Orobica to the other four goat populations of the Lombardy Alps. Principal co-ordinates analysis based on Dice similarities con®rms these observations. Genetic diversity of the goat populations investigated con®rms what is expected on the basis of their geographical location. Results from Orobica are not correlated with geographical distances and may re¯ect undocumented migrations and gene¯ows and identify an original genetic resource.
BMC Ecology, 2009
Background SNP data of goats of three Mediterranean countries were used for population studies and reconstruction of geographical patterning. 496 individuals belonging to Italian, Albanian and Greek breeds were genotyped to assess the basic population parameters. Results A total of 26 SNPs were used, for a total of 12,896 genotypes assayed. Statistical analysis revealed that breeds are not so similar in terms of genetic variability, as reported in studies performed using different markers. The Mantel test showed a strongly significant correlation between genetic and geographic distance. Also, PCA analysis revealed that breeds are grouped according to geographical origin, with the exception of the Greek Skopelos breed. Conclusion Our data point out that the use of SNP markers to analyze a wider breed sample could help in understanding the recent evolutionary history of domestic goats. We found correlation between genetic diversity and geographic distance. Also PCA analysis shows that the breeds are well differentiated, with good correspondence to geographical locations, thus confirming the correlation between geographical and genetic distances. This suggests that migration history of the species played a pivotal role in the present-day structure of the breeds and a scenario in which coastal routes were easier for migrating in comparison with inland routes. A westward coastal route to Italy through Greece could have led to gene flow along the Northern Mediterranean.
Identifying native animals in crossbred populations: the case of the Sardinian goat population
Animal Genetics, 2007
The aim of this work was to develop a strategy for using a genetic analysis for identifying native animals in regions where local breeds have been crossed with improved breeds and then compare that strategy to the overall morphology and breeding histories of the herds for identifying these animals. The experiment included the Sardinian goat population, which is a crossbred of native animals with the Maltese breed. Whole herds were assigned to Maltese (five herds; 49 animals), crossbred (18 herds; 117 animals) or Sardinian (12 herds; 164 animals) groups. For the genetic analysis, genotypes of 22 microsatellites were determined on 330 animals, and basic measurements of genetic diversity were calculated. Genetic variability in the microsatellites was different in the three groups. High positive F IS showed that inbreeding existed in the subpopulations. The index of genetic differentiation, Nei's standard genetic distance and ReynoldsÕ genetic distance were calculated and found to be significantly different between the three groups. The Sardinian and Maltese groups were the most distant whereas the crossbred group was closer to the Sardinian group. The proportion of the genome derived from two ancestral populations (native Sardinian and Maltese) was assessed using the STRUCTURE software. Animals were assigned to three clusters on the basis of native Sardinian thresholds. A good correspondence between the empirical (morphology and breeding histories) and the objective genetic analysis was found. Both approaches indicate the presence of three different subpopulations in the Sardinian goat population.
Patterns of homozygosity in insular and continental goat breeds
Genetics Selection Evolution
Background: Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diversity patterns by genotyping 480 individuals from 25 European and African breeds with the Goat SNP50 BeadChip and comparing patterns of homozygosity of insular and nearby continental breeds. Results: Among the breeds analysed, number and total length of ROH varied considerably and depending on breeds, ROH could cover a substantial fraction of the genome (up to 1.6 Gb in Icelandic goats). When compared with their continental counterparts, goats from Iceland, Madagascar, La Palma and Ireland (Bilberry and Arran) displayed a significant increase in ROH coverage, ROH number and F ROH values (P value < 0.05). Goats from Mediterranean islands represent a more complex case because certain populations displayed a significantly increased level of homozygosity (e.g. Girgentana) and others did not (e.g. Corse and Sarda). Correlations of number and total length of ROH for insular goat populations with the distance between islands and the nearest continental locations revealed an effect of extremely long distances on the patterns of homozygosity. Conclusions: These results indicate that the effects of insularization on the patterns of homozygosity are variable. Goats raised in Madagascar, Iceland, Ireland (Bilberry and Arran) and La Palma, show high levels of homozygosity, whereas those bred in Mediterranean islands display patterns of homozygosity that are similar to those found in continental populations. These results indicate that the diversity of insular goat populations is modulated by multiple factors such as geographic distribution, population size, demographic history, trading and breed management.
Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip
Genetics Selection Evolution, 2015
Background: Among the European countries, Italy counts the largest number of local goat breeds. Thanks to the recent availability of a medium-density SNP (single nucleotide polymorphism) chip for goat, the genetic diversity of Italian goat populations was characterized by genotyping samples from 14 Italian goat breeds that originate from different geographical areas with more than 50 000 SNPs evenly distributed on the genome. Results: Analysis of the genotyping data revealed high levels of genetic polymorphism and an underlying North-south geographic pattern of genetic diversity that was highlighted by both the first dimension of the multi-dimensional scaling plot and the Neighbour network reconstruction. We observed a moderate and weak population structure in Northern and Central-Southern breeds, respectively, with pairwise F ST values between breeds ranging from 0.013 to 0.164 and 7.49 % of the total variance assigned to the between-breed level. Only 2.11 % of the variance explained the clustering of breeds into geographical groups (Northern, Central and Southern Italy and Islands). Conclusions: Our results indicate that the present-day genetic diversity of Italian goat populations was shaped by the combined effects of drift, presence or lack of gene flow and, to some extent, by the consequences of traditional management systems and recent demographic history. Our findings may constitute the starting point for the development of marker-assisted approaches, to better address future breeding and management policies in a species that is particularly relevant for the medium-and long-term sustainability of marginal regions.
Genetics and Molecular Biology, 2000
Goats of an undefined breed (called UDB) from the State of Ceará, northeastern Brazil (N = 447), European Mediterranean goats (N =3,847) and African Mediterranean goats (N = 325) were compared to establish genetic distances and taxonomic trees. Allelic frequencies in each population for presence or absence of the following traits were used: horns, reduced ears, long hair, wattles, beard, roan color, brown eumelanin and eumelanic standard pigmentation. The genetic distance, applying the method developed by Nei (1972), was: least between goats from different meso-regions of the State of Ceará (0.0008 to 0.0120); small between all UDB of Ceará and French goats of Rove and Haute Roya (0.0236 and 0.0459); greater between all UDB of Ceará and northern Spanish goats (0.1166), and greatest between all UDB of Ceará and northern African goats (Moroccan of Drâa, Rhâali and Zagora), Balkan goats (Sakhar from Bulgaria and Macedonia from Greece) and some insular Mediterranean populations (Corsica, Sicily and Sardinia), which ranged from 0.1237 to 0.2714. Brazilian UDB goats are more closely related to Continental and Western European populations than to North African, Balkan or Insular Mediterranean populations.
Genetic diversity revealed by AFLP markers in Albanian goat breeds
Archives of Biological Sciences, 2012
The amplified fragment length polymorphism (AFLP) technique with three EcoRI/TaqI primer combinations was used in 185 unrelated individuals, representative of 6 local goat breeds of Albania, and 107 markers were generated. The mean Nei?s expected heterozygosity value for the whole population was 0.199 and the mean Shannon index was 0.249, indicating a high level of within-breed diversity. Wright?s FST index, Nei?s unbiased genetic distance and Reynolds? genetic distance were calculated. Pairwise Fst values among the populations ranged from 0.019 to 0.047. A highly significant average FST of 0.031 was estimated, showing a low level of breed subdivision. Most of the variation is accounted for by differences among individuals. Cluster analysis based on Reynolds? genetic distance between breeds and PCA were performed. An individual UPGMA tree based on Jaccard?s similarity index showed clusters with individuals from all goat breeds. Analysis of population structure points to a high level...
Genetic diversity and population structure in Portuguese goat breeds
Genetic diversity was assessed in the Portuguese native breeds of goats Algarvia (AL), Bravia (BR), Charnequeira (CH), Preta de Montesinho (PM), Serpentina (SP) and Serrana (SR), by analyzing 25 microsatellite markers in 193 animals. Genetic variability was high, with means for expected heterozygosity of 0.70 across loci, and nearly 7.0 and 4.4 for total and effective number of alleles per locus, respectively. The six breeds analyzed had similar levels of genetic variability, and the estimated F ST was 0.031, indicating that, with the neutral genetic markers used, the proportion of genetic variability accounted for by differences among breeds is small. Depending on the breed considered, between 0.16 and 0.28 of the loci presented significant departures from Hardy-Weinberg proportions, mostly because of a deficit in heterozygosity, with a significant positive F IS in most breeds, particularly in PM. The dendrogram based on Nei's standard genetic distance and the analysis by principal components indicate a separation of AL and BR from the remaining breeds, with some clustering of PM with SR, and of SP with CH, in agreement with their geographical distribution. Individual distances based on allele sharing indicate that only AL and BR animals tended to cluster together, while overlapping was common for the other breeds. The analysis with STRUCTURE confirmed the separation of AL and BR, which were more closely identified with independent clusters of potential ancestral populations. For the other breeds, there was clear evidence of admixture, with various ancestral populations contributing differently to the current breeds. Evidence was found of a geographical cline, with a given ancestral population contributing more to breeds located nearby, and with a declining contribution as the geographical distribution of breeds became more distant. Our results indicate that native breeds of goats in Portugal present high levels of genetic diversity, but the differentiation among closely located breeds is weak. Some of the breeds show signs of genetic erosion, which imply the need for urgent measures of conservation and sustainable management of their gene pool.
Geographical partitioning of goat diversity in Europe and the Middle East
Animal genetics, 2006
Thirty microsatellite markers were analysed in 1426 goats from 45 traditional or rare breeds in 15 European and Middle Eastern countries. In all populations inbreeding was indicated by heterozygosity deficiency (mean FIS = 0.10). Genetic differentiation between breeds was moderate with a mean FST value of 0.07, but for most (c. 71%) northern and central European breeds, individuals could be assigned to their breeds with a success rate of more than 80%. Bayesian-based clustering analysis of allele frequencies and multivariate analysis revealed at least four discrete clusters: eastern Mediterranean (Middle East), central Mediterranean, western Mediterranean and central/northern Europe. About 41% of the genetic variability among the breeds could be explained by their geographical origin. A decrease in genetic diversity from the south-east to the north-west was accompanied by an increase in the level of differentiation at the breed level. These observations support the hypothesis that domestic livestock migrated from the Middle East towards western and northern Europe and indicate that breed formation was more systematic in north-central Europe than in the Middle East. We propose that breed differentiation and molecular diversity are independent criteria for conservation.
Genetic structure and phylogeny of three goat populations in the Middle East
Abstract Text: ABSTRACT: This study aimed to analyze genetic structure and differentiation of Ardi, Black Bedouin and Damascus goats from Saudi Arabia, Jordan and Syria respectively. Therefore, four Microsatellite markers were genotyped onto a total of 98 individuals. The heterozygosity, intra-population differentiation and admixture coefficients were analyzed. All populations exhibit high average allele number and expected heterozygosity. The F-statistics coefficients indicating 6.0% of total genetic variation corresponded to differences between populations, whereas 94.0% was explained by difference between individuals. Damascus goat was more differentiated from Black Bedouin goat. Strong evidence of admixture between Ardi and Black Bedouin goat was found. The Genetic distances between Ardi and Black Bedouin goat was the shortest. Phylogeny relationship also revealed the expected degree of differentiation in all populations. Overall, the present study sheds new light on genetic dif...