Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers
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. O...
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| Language: | English |
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Asian-Australasian Association of Animal Production Societies
2020-12-01
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| Series: | Asian-Australasian Journal of Animal Sciences |
| Subjects: | |
| Online Access: | http://www.ajas.info/upload/pdf/ajas-19-0958.pdf |
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| author | 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 |
| author_facet | 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 |
| author_sort | Hee-Jong Roh |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T04:50:18Z |
| format | Article |
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| issn | 1011-2367 1976-5517 |
| language | English |
| last_indexed | 2024-04-13T04:50:18Z |
| publishDate | 2020-12-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
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| series | Asian-Australasian Journal of Animal Sciences |
| spelling | doaj.art-0484f6a76e8a4211bf36d5dac3ad048a2022-12-22T03:01:42ZengAsian-Australasian Association of Animal Production SocietiesAsian-Australasian Journal of Animal Sciences1011-23671976-55172020-12-0133121896190410.5713/ajas.19.095824511Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markersHee-Jong Roh0Seung-Chang Kim1Chang-Yeon Cho2Jinwook Lee3Dayeon Jeon4Dong-kyo Kim5Kwan-Woo Kim6Fahmida Afrin7Yeoung-Gyu Ko8Jun-Heon Lee9Solongo Batsaikhan10Triana Susanti11Sergey Hegay12Siton Kongvongxay13Neena Amatya Gorkhali14Lan Anh Nguyen Thi15Trinh Thi Thu Thao16Lakmalie Manikku17 Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea Production and technology, National Centre for Livestock Genebank, Ulaanbaatar, 210349, Mongolia Indonesia Research Institute for Animal Production, Bogor, 16720, Indonesia Institute of Biochemistry & Physiology, National Academy of Science of Kyrgyzstan, Bishkek, 720071, Kyrgyzstan Livestock Research Centre, Vientiane, 7170, Lao People’s Democratic Republic Animal Breeding Division, Nepal Agricultural Research Council, Kathmandu, 44600, Nepal Department of Animal Breeding and Genetics, Institute of Animal Sciences for Southern Vietnam, Binh Duong 75000, Vietnam Department of Animal Breeding and Genetics, Institute of Animal Sciences for Southern Vietnam, Binh Duong 75000, Vietnam Department of Animal Production and Health, Veterinary Research Institute, Colombo, 20400, Sri LankaObjective 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.http://www.ajas.info/upload/pdf/ajas-19-0958.pdfasian chicken breedsgenetic diversitygenetic relationshipmicrosatellite markersheterozygositypolymorphism information content |
| spellingShingle | 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 Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers Asian-Australasian Journal of Animal Sciences asian chicken breeds genetic diversity genetic relationship microsatellite markers heterozygosity polymorphism information content |
| title | Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers |
| title_full | Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers |
| title_fullStr | Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers |
| title_full_unstemmed | Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers |
| title_short | Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers |
| title_sort | estimating genetic diversity and population structure of 22 chicken breeds in asia using microsatellite markers |
| topic | asian chicken breeds genetic diversity genetic relationship microsatellite markers heterozygosity polymorphism information content |
| url | http://www.ajas.info/upload/pdf/ajas-19-0958.pdf |
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