Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide
Genetic diversity, population structure, and population expansion of goats worldwide (4 165 individuals from 196 breeds) were analyzed using published mitochondrial DNA (mtDNA) D_loop hypervariable region sequences. Results showed that 2 409 haplotypes and 301 polymorphic sites were present within t...
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| Format: | Article |
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KeAi Communications Co., Ltd.
2022-06-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311921638820 |
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| author | Yi GUO Ying GONG Yong-meng HE Bai-gao YANG Wei-yi ZHANG Bo-er CHEN Yong-fu HUANG Yong-ju ZHAO Dan-ping ZHANG Yue-hui MA Ming-xing CHU Guang-xin E |
| author_facet | Yi GUO Ying GONG Yong-meng HE Bai-gao YANG Wei-yi ZHANG Bo-er CHEN Yong-fu HUANG Yong-ju ZHAO Dan-ping ZHANG Yue-hui MA Ming-xing CHU Guang-xin E |
| author_sort | Yi GUO |
| collection | DOAJ |
| description | Genetic diversity, population structure, and population expansion of goats worldwide (4 165 individuals from 196 breeds) were analyzed using published mitochondrial DNA (mtDNA) D_loop hypervariable region sequences. Results showed that 2 409 haplotypes and 301 polymorphic sites were present within the 401-bp length D_loop region, the nucleotide diversity (Pi) was 0.03471, and the haplotype diversity (Hd) was 0.9983. Phylogenetic analysis revealed that 98.92% of haplotypes were divided into six obvious clusters, consistent with the classification of the known mitochondrial haplogroups of goats. Haplogroup A accounted for the largest proportion (86%). Interestingly, two unknown divisions (Unknown I and Unknown II) were discovered from goats in Southwest China, suggesting that Southwest China has unique maternal haplogroups. Analysis of molecular variance (AMOVA) and the average number of pairwise differences between populations (PiXY) indicated that geographical variation was small but significant. Neutrality tests (Tajima's D and Fu's FS tests) and mismatch distribution showed that haplogroups B, C, and G had expansion histories. In addition, the phylogenetic relationship between domestic and wild goats suggested that Capra aegagrus is the most likely wild ancestor and may have participated in the domestication of ancestral populations of A, B, C, and F haplogroups. A meta-analysis on the mtDNA sequences of goats from international databases was conducted to analyze goats’ genetic diversity, population structure, and matrilineal system evolution worldwide. The results may help further understand the domestication history and gene flow of goats worldwide. |
| format | Article |
| id | doaj-art-6d08dea1a20f4a3d96d5929e05e05a98 |
| institution | Matheson Library |
| issn | 2095-3119 |
| language | English |
| publishDate | 2022-06-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj-art-6d08dea1a20f4a3d96d5929e05e05a982025-08-02T10:27:35ZengKeAi Communications Co., Ltd.Journal of Integrative Agriculture2095-31192022-06-0121618301837Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwideYi GUO0Ying GONG1Yong-meng HE2Bai-gao YANG3Wei-yi ZHANG4Bo-er CHEN5Yong-fu HUANG6Yong-ju ZHAO7Dan-ping ZHANG8Yue-hui MA9Ming-xing CHU10Guang-xin E11College of Animal Science and Technology, Southwest University, Chongqing 400715, P.R.ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, P.R.ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, P.R.ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, P.R.ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, P.R.ChinaChongqing Agriculture and Rural Affairs Committee of Tongnan, Chongqing 402660, P.R.ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, P.R.ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, P.R.ChinaDazhou Animal Husbandry Technology Extension Station, Dazhou 635299, P.R.ChinaInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.ChinaInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, P.R.China; Correspondence E Guang-xin, Tel: +86-23-68250205, Fax: +86-23-68251192Genetic diversity, population structure, and population expansion of goats worldwide (4 165 individuals from 196 breeds) were analyzed using published mitochondrial DNA (mtDNA) D_loop hypervariable region sequences. Results showed that 2 409 haplotypes and 301 polymorphic sites were present within the 401-bp length D_loop region, the nucleotide diversity (Pi) was 0.03471, and the haplotype diversity (Hd) was 0.9983. Phylogenetic analysis revealed that 98.92% of haplotypes were divided into six obvious clusters, consistent with the classification of the known mitochondrial haplogroups of goats. Haplogroup A accounted for the largest proportion (86%). Interestingly, two unknown divisions (Unknown I and Unknown II) were discovered from goats in Southwest China, suggesting that Southwest China has unique maternal haplogroups. Analysis of molecular variance (AMOVA) and the average number of pairwise differences between populations (PiXY) indicated that geographical variation was small but significant. Neutrality tests (Tajima's D and Fu's FS tests) and mismatch distribution showed that haplogroups B, C, and G had expansion histories. In addition, the phylogenetic relationship between domestic and wild goats suggested that Capra aegagrus is the most likely wild ancestor and may have participated in the domestication of ancestral populations of A, B, C, and F haplogroups. A meta-analysis on the mtDNA sequences of goats from international databases was conducted to analyze goats’ genetic diversity, population structure, and matrilineal system evolution worldwide. The results may help further understand the domestication history and gene flow of goats worldwide.http://www.sciencedirect.com/science/article/pii/S2095311921638820mitochondrial DNAgenetic diversitypopulation structurepopulation expansionphylogeny |
| spellingShingle | Yi GUO Ying GONG Yong-meng HE Bai-gao YANG Wei-yi ZHANG Bo-er CHEN Yong-fu HUANG Yong-ju ZHAO Dan-ping ZHANG Yue-hui MA Ming-xing CHU Guang-xin E Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide Journal of Integrative Agriculture mitochondrial DNA genetic diversity population structure population expansion phylogeny |
| title | Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide |
| title_full | Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide |
| title_fullStr | Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide |
| title_full_unstemmed | Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide |
| title_short | Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide |
| title_sort | investigation of mitochondrial dna genetic diversity and phylogeny of goats worldwide |
| topic | mitochondrial DNA genetic diversity population structure population expansion phylogeny |
| url | http://www.sciencedirect.com/science/article/pii/S2095311921638820 |
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