Development of novel microsatellite markers for dogs and testing of microsatellite markers for cats in Taiwan populations
Date Issued
2014
Date
2014
Author(s)
Lin, Yu-Chen
Abstract
Along with the rise of animal protection consciousness in Taiwan, the public pays more attention on dog and cat genetic deficiencies due to inbreeding in the pet market. The goal of this study was to isolate novel microsatellite markers and develop a set of microsatellite markers for monitoring their genetic structure of the domestic dog and cat populations in Taiwan.
The microsatellite-enriched genomic library was constructed from one male and one female dog DNA samples by selective hybridization with mixed probes containing different repeat units. There were 230 positive clones selected, and only 65 clones could be desiged primers for single repeats by the Primer 3 Plus software. A total of 113 DNA samples of three dog breeds, including 74 Beagles from Taiwan, 8 Beagles from Japan, 17 Bichon, and 14 Schnauzer, were used in the following polymorphic tests. The results showed that only 14 sets of novel microsatellite markers were polymorphic in the three breeds; among those markers, the majority of repeat unit was dinucleotide. The average number of alleles (Na) and the average number of effective alleles (Ne) were 6.3±3.4 and 3.6±1.6, respectively. The average expected heterozygosity (HE) and average observed heterozygosity (HO) were 0.662±0.162 and 0.567±0.136, respectively. The estimated of average polymorphic information content (PIC) was 0.612±0.179. The FIS was 0.002±0.128; the FST was 0.212±0.103 and the FIT was 0.209±0.173. The high level of genetic diversity observed in these novel microsatellite markers provided a high discriminating power. The estimated probability of identity (P(ID)) and the probability of identity among sibs (P(ID)sib) of the 14 sets of novel microsatellite markers amounted to 1.7×10-12 and 1.6×10-5, respectively. Furthermore, power of exclusion (PE) of the 14 sets of novel microsatellite markers in this study is 99.98%。The neighbor-joining trees were constructed among the three breeds on the basis of the genetic distance estimated from the 14 sets of novel microsatellite markers. The configuration indicated that the 14 sets of novel microsatellite markers were sufficient to correctly cluster the three dog breeds — Beagle, Bichon, and Schnauzer. Still, the subgroups of Japanese Beagle within the Beagle cluster were clearly separated from Taiwanese Beagle. Principal coordinate analysis (PCoA) based on the allele frequency of 14 loci was used to visualize the dissimilarities among these experiment populations. The 3D plot showed that the dogs could be accurately separated by these 14 loci baled on different breeds; moreover, the Beagles from different sources were also distinguished. The first, the second, and the third principal coordinates could be used to explain 44.15, 26.35 and 19.97% of the genetic variation.
In the second part of this study, genomic DNA samples were extracted from blood samples of 25 Bengal cats. Twenty-two sets of highly polymorphic microsatellite markers containing tetranucleotide repeat unit were chosen from a previous study. The results showed that there were only 17 sets of microsatellite markers amplified and 14 sets of them showed polymorphism in the Bengal cat population tested. The average Na and the average Ne were 5.8±1.8 and 3.7±1.3, respectively. Also, the average HE and HO per locus were 0.726±0.095 and 0.660±0.157, respectively. Average PIC was 0.669±0.104, and FIS was 0.097±0.167. P(ID) and P(ID)sib of all 14 sets of markers were 9.7×10-14 and 1.1×10-4, respectively. PE of all 14 sets of microsatellite markers is 99.99%。These parameters showed that the 14 loci could sufficiently monitor the genetic structure and individual identity of Bengal population in Taiwan.
The results of this study could be used as powerful examination methods for genetic background structure of the domestic dog and cat populations in Taiwan.
Subjects
貓隻
犬隻
微衛星標幟
族群遺傳分析
Type
thesis
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