Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds
Indigenous breeds develop their own genomic characteristics by adapting to local environments or cultures over long periods of time. Most of them are not particularly productive in commercial terms, but they have abilities to survive in harsh environments or tolerate to specific diseases. Their adap...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-08-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00699/full |
| _version_ | 1819104193984593920 |
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| author | Jae-Yoon Kim Jae-Yoon Kim Seongmun Jeong Kyoung Hyoun Kim Kyoung Hyoun Kim Won-Jun Lim Won-Jun Lim Ho-Yeon Lee Ho-Yeon Lee Namshin Kim Namshin Kim |
| author_facet | Jae-Yoon Kim Jae-Yoon Kim Seongmun Jeong Kyoung Hyoun Kim Kyoung Hyoun Kim Won-Jun Lim Won-Jun Lim Ho-Yeon Lee Ho-Yeon Lee Namshin Kim Namshin Kim |
| author_sort | Jae-Yoon Kim |
| collection | DOAJ |
| description | Indigenous breeds develop their own genomic characteristics by adapting to local environments or cultures over long periods of time. Most of them are not particularly productive in commercial terms, but they have abilities to survive in harsh environments or tolerate to specific diseases. Their adaptive characteristics play an important role as genetic materials for improving commercial breeds. As a step toward this goal, we analyzed the genome of Korean indigenous goats within 10 goat breeds. We collected 136 goat individuals by sequencing 46 new goats and employing 90 publicly available goats. Our whole-genome data was comprised of three indigenous breeds (Korean indigenous goat, Iranian indigenous goat, and Moroccan indigenous goat; n = 29, 18, 20), six commercial breeds (Saanen, Boer, Anglo-Nubian, British Alpine, Alpine, and Korean crossbred; n = 16, 11, 5, 5, 2, 13), and their ancestral species (Capra aegagrus; n = 17). We identified that the Iranian indigenous goat and the Moroccan indigenous goat have relatively similar genomic characteristics within a large category of genomic diversity but found that the Korean indigenous goat has unique genomic characteristics distinguished from the other nine breeds. Through population analysis, we confirmed that these characteristics have resulted from a near-isolated environment with strong genetic drift. The Korean indigenous goat experienced a severe genetic bottleneck upon entering the Korean Peninsula about 2,000 years ago, and has subsequently rarely experienced genetic interactions with other goat breeds. From selection analysis and gene-set enrichment analysis, we revealed selection signals for Salmonella infection and cardiomyopathy in the genome of the Korean indigenous goat. These adaptive characteristics were further identified with genomic-based evidence. We uncovered genomic regions of selective sweeps in the LBP and BPI genes (Salmonella infection) and the TTN and ITGB6 genes (cardiomyopathy), among several candidate genes. Our research presents unique genomic characteristics and distinctive selection signals of the Korean indigenous goat based on the extensive comparison. Although the adaptive traits require further validation through biological experiments, our findings are expected to provide a direction for future biodiversity conservation strategies and to contribute another option to genomic-based breeding programmes for improving the viability of Capra hircus. |
| first_indexed | 2024-12-22T02:02:28Z |
| format | Article |
| id | doaj.art-b00696b563af4af48a16c4ef0d0243b1 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-22T02:02:28Z |
| publishDate | 2019-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-b00696b563af4af48a16c4ef0d0243b12022-12-21T18:42:37ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-08-011010.3389/fgene.2019.00699438454Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat BreedsJae-Yoon Kim0Jae-Yoon Kim1Seongmun Jeong2Kyoung Hyoun Kim3Kyoung Hyoun Kim4Won-Jun Lim5Won-Jun Lim6Ho-Yeon Lee7Ho-Yeon Lee8Namshin Kim9Namshin Kim10Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South KoreaDepartment of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South KoreaGenome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South KoreaGenome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South KoreaDepartment of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South KoreaGenome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South KoreaDepartment of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South KoreaGenome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South KoreaDepartment of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South KoreaGenome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South KoreaDepartment of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South KoreaIndigenous breeds develop their own genomic characteristics by adapting to local environments or cultures over long periods of time. Most of them are not particularly productive in commercial terms, but they have abilities to survive in harsh environments or tolerate to specific diseases. Their adaptive characteristics play an important role as genetic materials for improving commercial breeds. As a step toward this goal, we analyzed the genome of Korean indigenous goats within 10 goat breeds. We collected 136 goat individuals by sequencing 46 new goats and employing 90 publicly available goats. Our whole-genome data was comprised of three indigenous breeds (Korean indigenous goat, Iranian indigenous goat, and Moroccan indigenous goat; n = 29, 18, 20), six commercial breeds (Saanen, Boer, Anglo-Nubian, British Alpine, Alpine, and Korean crossbred; n = 16, 11, 5, 5, 2, 13), and their ancestral species (Capra aegagrus; n = 17). We identified that the Iranian indigenous goat and the Moroccan indigenous goat have relatively similar genomic characteristics within a large category of genomic diversity but found that the Korean indigenous goat has unique genomic characteristics distinguished from the other nine breeds. Through population analysis, we confirmed that these characteristics have resulted from a near-isolated environment with strong genetic drift. The Korean indigenous goat experienced a severe genetic bottleneck upon entering the Korean Peninsula about 2,000 years ago, and has subsequently rarely experienced genetic interactions with other goat breeds. From selection analysis and gene-set enrichment analysis, we revealed selection signals for Salmonella infection and cardiomyopathy in the genome of the Korean indigenous goat. These adaptive characteristics were further identified with genomic-based evidence. We uncovered genomic regions of selective sweeps in the LBP and BPI genes (Salmonella infection) and the TTN and ITGB6 genes (cardiomyopathy), among several candidate genes. Our research presents unique genomic characteristics and distinctive selection signals of the Korean indigenous goat based on the extensive comparison. Although the adaptive traits require further validation through biological experiments, our findings are expected to provide a direction for future biodiversity conservation strategies and to contribute another option to genomic-based breeding programmes for improving the viability of Capra hircus.https://www.frontiersin.org/article/10.3389/fgene.2019.00699/fullKorean indigenous goatsselection signaturegenomic characteristicspopulation geneticsCapra hircus (goat) |
| spellingShingle | Jae-Yoon Kim Jae-Yoon Kim Seongmun Jeong Kyoung Hyoun Kim Kyoung Hyoun Kim Won-Jun Lim Won-Jun Lim Ho-Yeon Lee Ho-Yeon Lee Namshin Kim Namshin Kim Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds Frontiers in Genetics Korean indigenous goats selection signature genomic characteristics population genetics Capra hircus (goat) |
| title | Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds |
| title_full | Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds |
| title_fullStr | Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds |
| title_full_unstemmed | Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds |
| title_short | Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds |
| title_sort | discovery of genomic characteristics and selection signatures in korean indigenous goats through comparison of 10 goat breeds |
| topic | Korean indigenous goats selection signature genomic characteristics population genetics Capra hircus (goat) |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00699/full |
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