Comparative analysis of intra- and interpopulation genetic diversity in Bufo bufo, using allozyme, single-locus microsatellite, minisatellite, and multilocus minisatellite data

Genetic characterization of Gaddi goat breed of Western Himalayas using microsatellite markers

Aim:

In the present study, genetic characterization of Gaddi goat breed, a native to north temperate western Himalayan region of India, was carried out for the purpose of breed characterization and assessing existing intra-population genetic diversity.

Materials and Methods:

Totally, 75 blood samples procured at random from genetically unrelated animals of two sexes and different age groups and true to breed type were collected from different locations in the breeding tract of these goats in Himachal Pradesh, of which only 51 samples with desired quantity and quality were subjected to further processing for DNA isolation. The multi-locus genotype data were generated on 51 Gaddi goats sampled across different regions of the breeding tract in Himachal Pradesh using 15 FAO recommended goat specific microsatellite markers, which gave amplification and observed and effective number of alleles, gene frequency, observed and expected heterozygosity were estimated through PopGene software (1.3.1).

Results:

A total of 135 distinct alleles were observed with mean observed and effective number of alleles as 9.0000±0.82 and 6.5874±0.56 respectively across all 15 studied loci. The maximum (15) alleles were contributed by loci DRBP1 and P19/DYA and the least (5) by SRCRSP5. The mean heterozygosity was observed to be 0.8347±0.01 ranging from 0.7584 (SRCRSP5) to 0.9156 (P19-DYA) across all loci. The mean observed (H_O) and expected (H_E) heterozygosities across all loci were 0.7484±0.02 and 0.8431±0.01 respectively. The polymorphism information content (PIC) value ranged from 0.7148 (SRCPS5) to 0.909 (P19-DYA) with mean PIC of 0.8105±0.01 in the present study. The average heterozygosity was observed to be 0.8347±0.01 ranging from 0.7584 (SRCRSP5) to 0.9156 P19 (DYA) across all loci.

Conclusion:

Microsatellite analysis revealed high level of polymorphism across studied microsatellite markers and informativeness of the markers for genetic diversity analysis studies in Gaddi goats. This high level of polymorphism can be utilized to plan future association studies to exploit the uniqueness and adaptability of indigenous Gaddi goat breed of Western Himalayas. Most studied microsatellite markers had desired neutrality, thus proving to be good candidates for genetic characterization and diversity analysis in Gaddi breed of goats also.

Genetic diversity and molecular differentiation of Chinese toad based on microsatellite markers

Genetic diversity and population structure of 9 populations of Bufo gargarizans with total 111 samples in China were assessed using seven microsatellite loci. The analysed microsatellite markers produced 161 alleles, varied from 9 to 38 alleles each locus. The number of alleles per population per locus ranged from 4.43 to 10.29. Polymorphic information content showed that all seven loci were highly informative (mean = 0.810 + or - 0.071). The average observed heterozygosity was less than the expected (0.353 + or - 0.051 and 0.828 + or - 0.067, respectively). All tested populations gave significant departures from Hardy-Weinberg equilibrium. Genetic differentiation among the populations was considerably high with the overall and pairwise F (ST) values (mean = 0.160 + or - 0.039), and showed fairly high level of inbreeding (indicated by a mean F (IS) value of 0.504 + or - 0.051) and global heterozygote deficit. In comparison to other amphibian studies; however, our results suggested that the level of genetic structuring in B. gargarizans was relatively low in the geographical scale of the study area. Interestingly, the speculated population bottleneck was found to be absent and the analyses provide only weak evidence for a recent contraction in size even though there was severe inbreeding (indicated by the F (IS) value) in the Chinese toad populations.

Variability of canine microsatellites within and between different dog breeds

Polymorphic animal microsatellites have proved valuable genetic markers. For this project, the variability of 19 canine microsatellite loci was examined within and between three pure breeds of dog: Greyhounds, Labradors, and German Shepherds. The number of alleles, absolute and relative frequencies, and the statistics that express polymorphism within a breed were determined. The evolutionary relationships among these closely related dog breeds were estimated by genetic distance measures developed for use with microsatellite loci. According to the pairwise genetic distances, Greyhounds and German Shepherds had longer diverse evolutionary histories than Greyhounds and Labradors or Labradors and German Shepherds. Although a few breed-specific alleles were observed, the significant differences between breeds are in their relative frequencies and distribution of the alleles across a locus. None of the three pure dog breeds corresponds to Hardy-Weinberg equilibrium. A considerable reduction in intrapopulation variation was observed within three pure breeds, compared with the population of individuals belonging to 15 dog breeds. This reduction was especially pronounced in the Greyhound breed, which expressed the lowest degree of variation. Intrapopulation variations of Labradors and German Shepherds did not differ significantly, that of Labradors being only slightly higher. The intra-species variation of dogs is lower than in humans, mouse, or rat, but similar to that in domestic animals, probably reflecting similarly high inbreeding coefficients. However, some highly informative loci were common to all dog breeds tested so far. Such population data are necessary for mapping studies and linkage analysis in dogs.

Molecular characterization and cytogenetic analysis of highly repeated DNAs of lake trout, Salvelinus namaycush

The chromosomes of lake trout (Salvelinus namaycush) contain a considerable amount of heterochromatin located at the centromeres and/or telomeres of several chromosomes, including a sex-specific block located distally on the X chromosome. In order to investigate further the repetitive DNAs of lake trout, genomic DNA from a female was size fractionated (<600 bp) with the restriction endonuclease AluI and fragments were cloned into the bacteriophage M13. A total of 42 clones were isolated. Relative copy number of individual inserts within the lake trout genome was estimated by Southern analysis. Twelve clones were determined to be highly repetitive and were chosen for further investigation. Inserts of these clones contained sequences similar to the AluI/RsaI, EcoRI/DraI, DraI/BstEII, and MboI/BglII families reported from Arctic char (Salvelinus alpinus). The chromosomal location of several of these fragments was determined in lake trout by fluorescence in situ hybridization (FISH). Two related AluI/RsaI sequences (Type A, approximately 140 bp, and Type B,approximately 120 bp) showed differential hybridization. Type A hybridized to the centromeres of all metacentric as well as several acrocentric chromosomes. Type B hybridized to the centromeres of most acrocentric chromosomes. A sequence with homology to the EcoRI/DraI family hybridized to the centromeres of several acrocentric chromosomes. Sequences with partial similarity to the DraI/BstEII family hybridized to the major rDNA sites (nucleolar organizer regions, NORs) and several minor telomeric sites. The interstitial and telomeric heterochromatin of lake trout, including that of the X chromosome, appears to comprise sequences belonging to the MboI/BglII family.