Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers

Hee-Jong Roh; Seung-Chang Kim; Chang-Yeon Cho; Jinwook Lee; Dayeon Jeon; Dong-Kyo Kim; Kwan-Woo Kim; Fahmida Afrin; Yeoung-Gyu Ko; Jun-Heon Lee; Solongo Batsaikhan; Triana Susanti; Sergey Hegay; Siton Kongvongxay; Neena Amatya Gorkhali; Lan Anh Nguyen Thi; Trinh Thi Thu Thao; Lakmalie Manikku

doi:10.5713/ajas.19.0958

Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers

Asian-Australas J Anim Sci. 2020 Dec;33(12):1896-1904. doi: 10.5713/ajas.19.0958. Epub 2020 Apr 13.

Authors

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

Affiliations

¹ Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea.
² Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea.
³ Production and technology, National Centre for Livestock Genebank, Ulaanbaatar, 210349, Mongolia.
⁴ Indonesia Research Institute for Animal Production, Bogor, 16720, Indonesia.
⁵ Institute of Biochemistry & Physiology, National Academy of Science of Kyrgyzstan, Bishkek, 720071, Kyrgyzstan.
⁶ Livestock Research Centre, Vientiane, 7170, Lao People's Democratic Republic.
⁷ Animal Breeding Division, Nepal Agricultural Research Council, Kathmandu, 44600, Nepal.
⁸ Department of Animal Breeding and Genetics, Institute of Animal Sciences for Southern Vietnam, Binh Duong 75000, Vietnam.
⁹ Department of Animal Production and Health, Veterinary Research Institute, Colombo, 20400, Sri Lanka.

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 ΔK 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; Heterozygosity; Microsatellite Markers; Polymorphism Information Content.

Abstract

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