Analysis of the genetic structure of the canary goat populations using microsatellites (original) (raw)
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Small Ruminant Research, 2018
Nineteen microsatellite markers were used to tag 668 goats from Spanish breeds from the Iberian Peninsula and Canary Islands and a population from north Morocco. The mean value of the allelic number per locus for the whole population studied was 12.7. The Moroccan population showed the highest values in allelic richness (8.043), with a mean number of alleles per locus of 10.7 and 17 private alleles. The levels of breed differentiation were relatively low (F ST = 0.05). The AMOVA analysis revealed a significant genetic differentiation among populations, but only 4.96% of the variance could be explained by differences between the 13 populations. Most of the variation (93.42%) was due to variation within individuals. The dispersion of the breeds, according to the Correspondence Analysis, was consistent with the geographical locations of the different populations studied. We used microsatellite markers to carry out the first genetic study, which included a population from northern Morocco and 12 Spanish goat breeds which were mainly bred in southern Spain and the Canary Islands. All the approaches used showed that the Spanish and, in particular, the Moroccan population, presented an important level of genetic diversity. We reported that the Agrupacion de las Mesetas, Payoya and Malagueña breeds differ little and have a closer relationship with the Moroccan population. As for the Payoya and Malagueña breeds, this indicated that geographical proximity favoured the gene flow between them. Our results showed that the population studied had a robust structure, with a clear differentiation between the Moroccan population and the Spanish goat breed. The cluster of three Canary Island breeds was completely separate. Coincidences in geographical location and the genetic structures suggested that common ancestries and/or genetic flow between the Iberian Peninsula and North Africa may have occurred over a long period of time or more recently.
BMC Genetics, 2009
Background: Assessing genetic biodiversity and population structure of minor breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. Analysis of microsatellite loci is known to be highly informative in the reconstruction of the historical processes underlying the evolution and differentiation of animal populations. Guadarrama goat is a threatened Spanish breed which actual census (2008) consists of 3057 females and 203 males distributed in 22 populations more or less isolated. The aim of this work is to study the genetic status of this breed through the analysis of molecular data from 10 microsatellites typed in historic and actual live animals.
Strong phylogeographic relationships among three goat breeds from the Canary Islands
Journal of Dairy Research, 2004
We partially sequenced the mitochondrial D-loop region in 47 individuals from eleven Spanish and foreign goat breeds. Phylogenetic analysis of these sequences allowed us to identify a particular D-loop haplotype shared by individuals from the Palmera, Majorera and Tinerfeñ a Canarian breeds. Genotyping of 281 goats from 17 different breeds by PCR-HpaII RFLP evidenced that the geographical distribution of this haplotype is restricted to the Canary Islands. This ancestral mitochondrial haplotype might originate in the domestic goat herds brought by the native Canarian inhabitants approximately 3000 years ago. Although we observed other miscellaneous D-loop haplotypes in the Palmera, Majorera and Tinerfeñ a breeds, any of them allowed us to group individuals from these three populations in a single cluster, a feature that suggests that these haplotypes might have diverse origins. The remarkable degree of phylogeographic structure of the Canary goat breeds with regard to other Spanish and foreign populations might be attributed to the isolation of these breeds in the Canary Islands for approximately 2500 years, without exposure to the migratory movements and commercial trading events that probably affected the genesis of most domestic goat breeds worldwide. The Canarian D-loop haplotype can be efficiently genotyped by using DNA isolated from milk and cheese samples, which paves the way for the future establishment of a Canary breed identity test for these dairy products.
Genetics and Molecular Research, 2017
The aim of this study was to access the genetic diversity and relatedness between Canindé and British Alpine goat breeds in the States of Piauí and Ceará using microsatellite markers. Genomic DNA was isolated from hair samples of 99 goats belonging to six different flocks. A panel of polymorphic heterologous microsatellite loci was used to genotype individuals. The microsatellite markers resulted in a total number of 145 alleles, with an average of 8.5 alleles per locus. The observed and expected heterozygosities were ≥0.687 and ≥0.627, respectively, for all loci. The polymorphic information content showed that all loci were highly informative with an overall mean of 0.757. Overall F ST across all populations and loci was 18%, which was consistent with the coefficient of gene differentiation (G ST = 0.104). AMOVA revealed that 12.8% of the variation was captured between breeds. The Bayesian STRUCTURE clustering detected the maximum likelihood for a model of two genetically distinct groups, in agreement with the number of predefined studied breeds and the two-dimensional plot from the PCoA analysis. The exotic British Alpine breed and the naturalized Brazilian Canindé breed were clearly differentiated by the microsatellite markers, indicating that these two breeds have distant genetic identities, despite the phenotypic similarity.
Indian Journal of Animal Research, 2020
Background: Teressa goat is an indigenous goat breed of Andaman and Nicobar Islands. These goats are mainly distributed in the Nicobar group of islands, however, sparse population is also available in the Andaman Islands. In order to understand the genetic diversity and variation among the population of Teressa goat, the studies on the molecular characterization was done by using microsatellite molecular markers. Methods: Randomly a total of 48 blood samples were collected different areas of the Nicobar Islands representing the breeding tract of the Teressa goat. Based on the guidelines of ISAG and FAO, a total of 15 recommended microsatellite markers were selected for the microsatellite analysis study. The data were analysed to study the diversity analysis at each locus by using GENETIX software package. Bottleneck hypothesis was also studied by using BOTTLENECK 1.2.01 and FIS, FIT and FIT values were calculated and heterozygosity deficiency at each locus using FSTAT software. Resu...
Genetic diversity of Sardinian goat population based on microsatellites
Italian Journal of Animal Science, 2010
RIASSUNTO -Diversità genetica della popolazione caprina sarda basata sull'analisi di microsatelliti. Sono stati analizzati 331 caprini, provenienti da 35 allevamenti di diverse aree della Sardegna, con 17 microsatelliti. Gli allevamenti sono stati suddivisi in tre gruppi, maltese (M), meticcio (C) e tipo Sardo autoctono (S), sulla base dei profili fenotipici degli animali e delle informazioni fornite dall'allevatore riguardo l'origine dei riproduttori utilizzati. Le statistiche calcolate (eterozigosità, alleli privati, distanza genetica standard e di Reynolds, Gst) hanno messo in evidenza una ridotta variabilità genetica del gruppo M rispetto agli altri due, nonché, la presenza di un gruppo di allevamenti i cui individui sono assimilabili al tipo Sardo autoctono. Il gruppo meticcio ha mostrato un'elevata variabilità e distanze significative con gli altri 2 gruppi. I risultati hanno consentito di identificare il nucleo di allevamenti da cui partire per la conservazione del tipo genetico autoctono. Resta ancora da definire il ruolo del gruppo meticcio nel preservare la variabilità genetica complessiva.
The genetic relationships and structure of fourteen goat (Capra hircus) populations were estimated based on genotyping data from 14 goat populations (n = 410 goats) at 13 microsatellite loci. We used analysis of molecular variance (AMOVA), principal component analysis (PCA) and F statistics (FIS, FIT and FST) to evaluate the genetic diversity (Ho, He and ad) of the goats. Genetic distances between the 14 goat populations were calculated from allelic frequency data for the 13 microsatellite markers. Moderate differentiation was observed for the populations of the undefined breeds (including the Anglo-Nubian-M breed), the naturalized Brazilian breeds (Moxotó, Canindé), the exotic purebred breeds (Alpine, Saanen, Toggenbourg and Anglo-Nubian) and the naturalized Brazilian Graúna group. Our AMOVA showed that a major portion (88.51%) of the total genetic variation resulted from differences between individual goats within populations, while between-populations variation accounted for the remaining 11.49% of genetic variation. We used a Reynolds genetic distance matrix and PCA to produce a phenogram based on the 14 goat populations and found three clusters, or groups, consisting of the goats belonging to the undefined breed, the naturalized breeds and the exotic purebred breeds. The closer proximity of the Canindé breed from the Brazilian state of Paraíba to the Graúna breed from the same state than to the genetically conserved Canindé breed from the Brazilian state of Ceará, as well as the heterozygosity values and significant deviations from Hardy-Weinberg equilibrium suggests that there was a high number of homozygotes in the populations studied, and indicates the importance of the State for the conservation of the local breeds. Cataloguing the genetic profile of Brazilian goat populations provides essential information for conservation and genetic improvements programs.
AFRICAN JOURNAL OF BIOTECHNOLOGY
The aim of this work was to characterize a Sicilian autochthonous goat population using microsatellite markers and genetic polymorphisms at the casein genes. In order to investigate the genetic structure of the Mascaruna goat, a total of 60 (20 Girgentana, 20 mixed populations, and 20 Mascaruna) individuals were analyzed, using a panel of 18 microsatellite markers. Moreover, the Mascaruna goats were genotyped at casein loci using several molecular techniques. Based on the genetic structure at casein genes, the Mascaruna goat was similar to most goat breeds from the Mediterranean area, which are characterized by the predominance of strong alleles. The low value of genetic differentiation among populations (Fst=0.027) could indicate that these populations were differentiated little probably due to gene flow and breeding practices. The analysis of genetic distances between groups indicated that the Mascaruna goat was the most distanced group, and this result was confirmed by the unroot...
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.
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.