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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.19.0958    [Accepted] Published online April 13, 2020.
Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers
Hee-Jong Roh1,*  , Seung-Chang Kim1  , Chang-Yeon Cho1  , Jinwook Lee1  , Dayeon Jeon1  , Dong-kyo Kim1  , Kwan-Woo Kim1  , Fahmida Afrin1  , Yeoung-Gyu Ko1  , Jun-Heon Lee2  , Solongo Batsaikhan3  , Triana Susanti4  , Sergey Hegay5  , Siton Kongvongxay6  , Neena Amatya Gorkhali7  , Lan Anh Nguyen Thi8  , Trinh Thi Thu Thao8  , Lakmalie Manikku9 
1Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
2Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
3Production and technology, National Centre for Livestock Genebank, Ulaanbaatar, 210349, Mongolia
4Indonesia Research Institute for Animal Production, Bogor, 16720, Indonesia
5Institute of Biochemistry & Physiology, National Academy of Science of Kyrgyzstan, Bishkek, 720071, Kyrgyzstan
6Livestock Research Centre, Vientiane, 7170, Lao People’s Democratic Republic
7Animal Breeding Division, Nepal Agricultural Research Council, Kathmandu, 44600, Nepal
8Department of Animal Breeding and Genetics, Institute of Animal Sciences for Southern Vietnam, Binh Duong, 75000, Vietnam
9Department of Animal Production and Health, Veterinary Research Institute, Colombo, 20400, Sri Lanka
Correspondence:  Hee-Jong Roh, Tel: +821083107819, Fax: +82559603590, Email: nhj1513@korea.kr
Received: 16 December 2019   • Revised: 5 February 2020   • Accepted: 3 April 2020
Abstract
Objective
Estimating the genetic diversity and structures, both within and among chicken breeds, is critical for the identification and conservation of valuable genetic resources. In chickens, microsatellite (MS) marker polymorphisms have previously been widely used to evaluate these distinctions. Our objective was to analyze the genetic diversity and relationships among 22 chicken breeds in Asia based on allelic frequencies.
Methods
We used 469 genomic DNA samples from 22 chicken breeds from eight Asian countries (South Korea: KNG, KNB, KNR, KNW, KNY, KNO, Laos: LYO, LCH, LBB, LOU, Indonesia: INK, INS, ING, Vietnam: VTN, VNH, Mongolia: MGN, Kyrgyzstan: KGPS, Nepal: NPS, Sri Lanka: SBC) and three imported breeds (RIR: Rhode Island Red, WLG: White Leghorn, CON: Cornish). Their genetic diversity and phylogenetic relationships were analyzed using 20 MS markers.
Results
In total, 193 alleles were observed across all 20 MS markers, and the number of alleles ranged from 3 (MCW0103) to 20 (LEI0192) with a mean of 9.7 overall. The NPS breed had the highest expected heterozygosity (Hexp, 0.718 ± 0.027) and polymorphism information content (PIC, 0.663 ± 0.030). Additionally, the observed heterozygosity (Hobs) was highest in LCH (0.690 ± 0.039), whereas WLG showed the lowest Hexp (0.372 ± 0.055), Hobs (0.384 ± 0.019), and PIC (0.325 ± 0.049). Nei’s DA genetic distance was the closest between VTN and VNH (0.086), and farthest between KNG and MGN (0.503). Principal coordinate analysis showed similar results to the phylogenetic analysis, and three axes explained 56.2 % of the variance (axis 1: 19.17 %; 2: 18.92 %; 3: 18.11 %). STRUCTURE analysis revealed that the 22 chicken breeds should be divided into 20 clusters, based on the highest △K value (46.92).
Conclusion
This study provides a basis for future genetic variation studies and the development of conservation strategies for 22 chicken breeds in Asia.
Keywords: Asian Chicken Breeds; Genetic Diversity; Genetic Relationship; Microsatellite Markers; Heterozygosity; Polymorphism Information Content


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