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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.19.0175    [Accepted] Published online August 26, 2019.
Monitoring of genetic closed Tsaiya duck populations using novel microsatellite markers with high polymorphism
Fang-Yu Lai1  , Yi-Ying Chang2  , Yi-Chen Chen3  , En-Chung Lin1  , Hsiu-Chou Liu2  , Jeng-Fang Huang4  , Shih-Torng Ding1,*  , Pei-Hwa Wang1,* 
1Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10672, Taiwan
2Ilan Branch, Livestock Research Institute, Council of Agriculture, Executive Yuan, Ilan County 26846, Taiwan
3Department of Animal Science and Biotechnology, Tunghai University, Taichung 40704, Taiwan
4Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan
Correspondence:  Shih-Torng Ding,Email: sding@ntu.edu.tw
Pei-Hwa Wang, Tel: +886-02-33664164, Fax: +886-02-27324070, Email: demonwang@ntu.edu.tw
Received: 4 March 2019   • Revised: 6 June 2019   • Accepted: 14 August 2019
A set of microsatellite markers with high polymorphism from Tsaiya duck were used for the genetic monitoring and genetic structure analysis of Brown and White Tsaiya duck populations in Taiwan.
The synthetic short tandem repeated probes were used to isolate new microsatellite markers from the genomic DNA of Tsaiya ducks. Eight populations, a total of 566 samples, sourced from Ilan Branch, Livestock Research Institute were genotyped through novel and known markers. The population genetic variables were calculated using optional programs in order to describe and monitor the genetic variability and the genetic structures of these Tsaiya duck populations.
In total 24 primer pairs, including 17 novel microsatellite loci from this study and seven previously known loci, were constructed for the detection of genetic variations in duck populations. The average values for the allele number (Na), the effective number of alleles (Ne), the observed heterozygosity (Ho), the expected heterozygosity (HE), and the polymorphism information content (PIC) were 11.29, 5.370, 0.591, 0.746, and 0.708, respectively. The results of AMOVA and principal component analysis (PCA) indicated a contracting Brown Tsaiya duck cluster and a spreading White Tsaiya duck cluster. The Brown Tsaiya ducks and the White Tsaiya ducks with Pekin ducks were just split to six clusters and three clusters when K was set equal to 6 and 3 in the Bayesian cluster analysis. The individual phylogenetic tree revealed eight taxa, and each individual was assigned to its own population.
According to our study, the 24 novel microsatellite markers exhibited a high capacity to analyze relationships of inter- and intra-population in those populations with a relatively limited degree of genetic diversity. We suggest that duck farms in Taiwan could use the new (novel) microsatellite set to monitor the genetic characteristics and structures of their Tsaiya duck populations at various intervals in order to ensure quality breeding and conservation strategies.
Keywords: Breeding and Conservation Strategies; Genetic Structure; Novel Microsatellite Markers; Tsaiya Ducks

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