Asian-Australasian Journal of Animal Sciences (Dec 2020)

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
https://doi.org/10.5713/ajas.19.0958
Journal volume & issue
Vol. 33, no. 12
pp. 1896 – 1904

Abstract

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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.

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