Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens
2
조회
0
다운로드
2
인용
0
참고문헌
키워드
초록
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.
Abstract
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.
참고문헌 (25)
- Ellegren H, "Determinants of genetic diversity", Nat Rev Genet, 17, pp.422~433 (2016)[DOI]
- Nxumalo N, "Genetic diversity, population structure and ancestral origin of KwaZulu-Natal native chicken ecotypes using microsatellite and mitochondrial DNA markers", Ital J Anim Sci, 19, pp.1275~1288 (2020)[DOI]
- Serrano M, "Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed", BMC Genet, 10, pp.61~ (2009)[DOI]
- 오재돈, "Genetic Traceability of Black Pig Meats Using Microsatellite Markers", Animal Bioscience, 27(7), pp.926~931 (2014), 아세아·태평양축산학회[DOI]
- 최누리, "Discrimination of the commercial Korean native chicken population using microsatellite markers", 한국축산학회지, 57(2), pp.1~8 (2015), 한국축산학회[DOI]
- Fischer MC, "Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri", BMC Genomics, 18, pp.69~ (2017)[DOI]
- Karniol B, "Development of a 25-plex SNP assay for traceability in cattle", Anim Genet, 40, pp.353~356 (2009)[DOI]
- Duran C, "Molecular genetic markers : discovery, applications, data storage and visualisation", Curr Bioinform, 4, pp.16~27 (2009)[DOI]
- H.S. Kong, "Genetic Variation and Relationships of Korean Native Chickens and Foreign Breeds Using 15 Microsatellite Markers", Animal Bioscience, 19(11), pp.1546~1550 (2006), 아세아·태평양축산학회
- 이학교, "Microsatellite Marker를 활용한 토종닭 브랜드 집단 간의 유전적 다양성 분석", 한국가금학회지, 37(4), pp.355~360 (2010), 한국가금학회
- 최누리, "ISAG-recommended Microsatellite Marker Analysis Among Five Korean Native Chicken Lines", 한국축산학회지, 54(6), pp.401~409 (2012), 한국축산학회
- 서주희, "Assessment of genetic diversity and phylogenetic relationships of Korean native chicken breeds using microsatellite markers", Animal Bioscience, 30(10), pp.1365~1371 (2017), 아세아·태평양축산학회[DOI]
- 노희종, "초위성체 마커를 활용한 가축다양성정보시스템(DAD-IS) 등재 재래닭 집단의 유전적 다양성 분석", 한국가금학회지, 46(2), pp.65~75 (2019), 한국가금학회[DOI]
- Kranis A, "Development of a high density 600K SNP genotyping array for chicken", BMC Genomics, 14, pp.59~ (2013)[DOI]
- Das S, "Next-generation genotype imputation service and methods", Nat Genet, 48, pp.1284~1287 (2016)[DOI]
- Purcell S, "PLINK : a tool set for whole-genome association and population-based linkage analyses", Am J Hum Genet, 81, pp.559~575 (2007)[DOI]
- Reynolds J, "Estimation of the coancestry coefficient : basis for a short-term genetic distance", Genetics, 105, pp.767~779 (1983)[DOI]
- Kamvar ZN, "Poppr : an R package for genetic analysis of populations with clonal, partially clonal, and", or sexual reproduction, 2014, pp.2, e281~
- Weir BS, "Estimating F-statistics for the analysis of population structure", Evolution, 38, pp.1358~1370 (1984)[DOI]
- Zheng X, "A high-performance computing toolset for relatedness and principal component analysis of SNP data", Bioinformatics, 28, pp.3326~3328 (2012)[DOI]
- "Pheatmap: pretty heatmaps: R package version" (2012)[URL]
- Jombart T, "adegenet : a R package for the multivariate analysis of genetic markers", Bioinformatics, 24, pp.1403~1405 (2008)[DOI]
- Alexander DH, "Enhancements to the ADMIXTURE algorithm for individual ancestry estimation", BMC Bioinformatics, 12, pp.246~ (2011)[DOI]
- Petit RJ, "Identifying populations for conservation on the basis of genetic markers", Conserv Biol, 12, pp.844~855 (1998)[DOI]
- 서주희, "Microsatellite Marker를 활용한 한국 토종닭 품종의 유전적 다양성 및 유연관계 분석", 한국가금학회지, 42(1), pp.15~26 (2015), 한국가금학회