Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens
Genetic diversity analysis is crucial for maintaining and managing genetic resources. Several studies have examined the genetic diversity of Korean domestic chicken (KDC) populations using microsatellite markers, but it is difficult to capture the characteristics of the whole genome in this manner....
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| Format: | Article |
| Language: | English |
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Korean Society of Animal Sciences and Technology
2023-09-01
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| Series: | Journal of Animal Science and Technology |
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| Online Access: | http://www.ejast.org/archive/view_article?doi=10.5187/jast.2023.e8 |
| _version_ | 1797666068091633664 |
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| author | Eunjin Cho Minjun Kim Jae-Hwan Kim Hee-Jong Roh Seung Chang Kim Dae-Hyeok Jin Dae Cheol Kim Jun Heon Lee |
| author_facet | Eunjin Cho Minjun Kim Jae-Hwan Kim Hee-Jong Roh Seung Chang Kim Dae-Hyeok Jin Dae Cheol Kim Jun Heon Lee |
| author_sort | Eunjin Cho |
| collection | DOAJ |
| description | Genetic diversity analysis is crucial for maintaining and managing genetic resources. Several studies have examined the genetic diversity of Korean domestic chicken (KDC) populations using microsatellite markers, but it is difficult to capture the characteristics of the whole genome in this manner. Hence, this study analyzed the genetic diversity of several KDC populations using high-density single nucleotide polymorphism (SNP) genotype data. We examined 935 birds from 21 KDC populations, including indigenous and adapted Korean native chicken (KNC), Hyunin and Jeju KDC, and Hanhyup commercial KDC populations. A total of 212,420 SNPs of 21 KDC populations were used for calculating genetic distances and fixation index, and for ADMIXTURE analysis. As a result of the analysis, the indigenous KNC groups were genetically closer and more fixed than the other groups. Furthermore, Hyunin and Jeju KDC were similar to the indigenous KNC. In comparison, adapted KNC and Hanhyup KDC populations derived from the same original species were genetically close to each other, but had different genetic structures from the others. In conclusion, this study suggests that continuous evaluation and management are required to prevent a loss of genetic diversity in each group. Basic genetic information is provided that can be used to improve breeds quickly by utilizing the various characteristics of native chickens. |
| first_indexed | 2024-03-11T19:53:54Z |
| format | Article |
| id | doaj.art-fe018314794d47d3ba2642d2897346f6 |
| institution | Directory Open Access Journal |
| issn | 2672-0191 2055-0391 |
| language | English |
| last_indexed | 2024-03-11T19:53:54Z |
| publishDate | 2023-09-01 |
| publisher | Korean Society of Animal Sciences and Technology |
| record_format | Article |
| series | Journal of Animal Science and Technology |
| spelling | doaj.art-fe018314794d47d3ba2642d2897346f62023-10-05T01:39:24ZengKorean Society of Animal Sciences and TechnologyJournal of Animal Science and Technology2672-01912055-03912023-09-0165591292110.5187/jast.2023.e8Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickensEunjin Cho0Minjun Kim1Jae-Hwan Kim2Hee-Jong Roh3Seung Chang Kim4Dae-Hyeok Jin5Dae Cheol Kim6Jun Heon Lee7Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, KoreaDivision of Animal & Dairy Science, Chungnam National University, Daejeon 34134, KoreaAnimal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, KoreaAnimal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, KoreaAnimal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, KoreaAnimal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, KoreaJeju Special Self-Governing Province Livestock Promotion Agency, Jeju 63078, KoreaDepartment of Bio-AI Convergence, Chungnam National University, Daejeon 34134, KoreaGenetic diversity analysis is crucial for maintaining and managing genetic resources. Several studies have examined the genetic diversity of Korean domestic chicken (KDC) populations using microsatellite markers, but it is difficult to capture the characteristics of the whole genome in this manner. Hence, this study analyzed the genetic diversity of several KDC populations using high-density single nucleotide polymorphism (SNP) genotype data. We examined 935 birds from 21 KDC populations, including indigenous and adapted Korean native chicken (KNC), Hyunin and Jeju KDC, and Hanhyup commercial KDC populations. A total of 212,420 SNPs of 21 KDC populations were used for calculating genetic distances and fixation index, and for ADMIXTURE analysis. As a result of the analysis, the indigenous KNC groups were genetically closer and more fixed than the other groups. Furthermore, Hyunin and Jeju KDC were similar to the indigenous KNC. In comparison, adapted KNC and Hanhyup KDC populations derived from the same original species were genetically close to each other, but had different genetic structures from the others. In conclusion, this study suggests that continuous evaluation and management are required to prevent a loss of genetic diversity in each group. Basic genetic information is provided that can be used to improve breeds quickly by utilizing the various characteristics of native chickens. http://www.ejast.org/archive/view_article?doi=10.5187/jast.2023.e8Genetic diversityPopulation structureKorean domestic chickenSingle nucleotide polymorphism |
| spellingShingle | Eunjin Cho Minjun Kim Jae-Hwan Kim Hee-Jong Roh Seung Chang Kim Dae-Hyeok Jin Dae Cheol Kim Jun Heon Lee Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens Journal of Animal Science and Technology Genetic diversity Population structure Korean domestic chicken Single nucleotide polymorphism |
| title | Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens |
| title_full | Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens |
| title_fullStr | Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens |
| title_full_unstemmed | Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens |
| title_short | Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens |
| title_sort | application of genomic big data to analyze the genetic diversity and population structure of korean domestic chickens |
| topic | Genetic diversity Population structure Korean domestic chicken Single nucleotide polymorphism |
| url | http://www.ejast.org/archive/view_article?doi=10.5187/jast.2023.e8 |
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