Table_4_Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs.xlsx
There are dozens of recognized indigenous dog breeds in China. However, these breeds have not had extensive studies to describe their population structure, genomic linkage disequilibrium (LD) patterns, and selection signatures. Here, we systematically surveyed the genomes of 157 unrelated dogs that...
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ftfrontimediafig:oai:figshare.com:article/10309022 2023-05-15T16:30:33+02:00 Table_4_Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs.xlsx Qianyong Yang Hao Chen Junhua Ye Chenlong Liu Rongxing Wei Congying Chen Lusheng Huang 2019-11-15T04:35:01Z https://doi.org/10.3389/fgene.2019.01174.s016 https://figshare.com/articles/Table_4_Genetic_Diversity_and_Signatures_of_Selection_in_15_Chinese_Indigenous_Dog_Breeds_Revealed_by_Genome-Wide_SNPs_xlsx/10309022 unknown doi:10.3389/fgene.2019.01174.s016 https://figshare.com/articles/Table_4_Genetic_Diversity_and_Signatures_of_Selection_in_15_Chinese_Indigenous_Dog_Breeds_Revealed_by_Genome-Wide_SNPs_xlsx/10309022 CC BY 4.0 CC-BY Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy population structure linkage disequilibrium selection signatures 170K SNP chip Chinese indigenous dogs Dataset 2019 ftfrontimediafig https://doi.org/10.3389/fgene.2019.01174.s016 2019-11-20T23:50:44Z There are dozens of recognized indigenous dog breeds in China. However, these breeds have not had extensive studies to describe their population structure, genomic linkage disequilibrium (LD) patterns, and selection signatures. Here, we systematically surveyed the genomes of 157 unrelated dogs that were from 15 diverse Chinese dog breeds. Canine 170K SNP chips were used to compare the genomic structures of Chinese and Western dogs. The genotyping data of 170K SNP chips in Western dogs were downloaded from the LUPA (a European initiative of canine genome project) database. Chinese indigenous dogs had lower LD and shorter accumulative runs of homozygosity (ROH) in the genome. The genetic distances between individuals within each Chinese breed were larger than those within Western breeds. Chinese indigenous and Western dog breeds were clearly differentiated into two separate clades revealed by the PCA and NJ-tree. We found evidence for historical introgression of Western dogs into Chinese Kazakhstan shepherd and Mongolia Xi dogs. We suggested that Greenland sledge dog, Papillon, and European Eurasier have Chinese dog lineages. Selection sweep analysis identified genome-wide selection signatures of each Chinese breed and three breed groups. We highlighted several genes including EPAS1 and DNAH9 that show signatures of natural selection in Qinghai-Tibetan plateau dogs and are likely important for genetic adaptation to high altitude. Comparison of our findings with previous reports suggested RBP7, NMNAT1, SLC2A5, and H6PD that exhibit signatures of natural selection in Chinese mountain hounds as promising candidate genes for the traits of endurance and night vision, and NOL8, KRT9, RORB, and CAMTA1 that show signals of selection in Xi dogs might be candidate genes influencing dog running speed. The results about genomic and population structures, and selection signatures of Chinese dog breeds reinforce the conclusion that Chinese indigenous dogs with great variations of phenotypes are important resources for ... Dataset Greenland Frontiers: Figshare Greenland Lupa ENVELOPE(-66.734,-66.734,-68.432,-68.432) |
institution |
Open Polar |
collection |
Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy population structure linkage disequilibrium selection signatures 170K SNP chip Chinese indigenous dogs |
spellingShingle |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy population structure linkage disequilibrium selection signatures 170K SNP chip Chinese indigenous dogs Qianyong Yang Hao Chen Junhua Ye Chenlong Liu Rongxing Wei Congying Chen Lusheng Huang Table_4_Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs.xlsx |
topic_facet |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy population structure linkage disequilibrium selection signatures 170K SNP chip Chinese indigenous dogs |
description |
There are dozens of recognized indigenous dog breeds in China. However, these breeds have not had extensive studies to describe their population structure, genomic linkage disequilibrium (LD) patterns, and selection signatures. Here, we systematically surveyed the genomes of 157 unrelated dogs that were from 15 diverse Chinese dog breeds. Canine 170K SNP chips were used to compare the genomic structures of Chinese and Western dogs. The genotyping data of 170K SNP chips in Western dogs were downloaded from the LUPA (a European initiative of canine genome project) database. Chinese indigenous dogs had lower LD and shorter accumulative runs of homozygosity (ROH) in the genome. The genetic distances between individuals within each Chinese breed were larger than those within Western breeds. Chinese indigenous and Western dog breeds were clearly differentiated into two separate clades revealed by the PCA and NJ-tree. We found evidence for historical introgression of Western dogs into Chinese Kazakhstan shepherd and Mongolia Xi dogs. We suggested that Greenland sledge dog, Papillon, and European Eurasier have Chinese dog lineages. Selection sweep analysis identified genome-wide selection signatures of each Chinese breed and three breed groups. We highlighted several genes including EPAS1 and DNAH9 that show signatures of natural selection in Qinghai-Tibetan plateau dogs and are likely important for genetic adaptation to high altitude. Comparison of our findings with previous reports suggested RBP7, NMNAT1, SLC2A5, and H6PD that exhibit signatures of natural selection in Chinese mountain hounds as promising candidate genes for the traits of endurance and night vision, and NOL8, KRT9, RORB, and CAMTA1 that show signals of selection in Xi dogs might be candidate genes influencing dog running speed. The results about genomic and population structures, and selection signatures of Chinese dog breeds reinforce the conclusion that Chinese indigenous dogs with great variations of phenotypes are important resources for ... |
format |
Dataset |
author |
Qianyong Yang Hao Chen Junhua Ye Chenlong Liu Rongxing Wei Congying Chen Lusheng Huang |
author_facet |
Qianyong Yang Hao Chen Junhua Ye Chenlong Liu Rongxing Wei Congying Chen Lusheng Huang |
author_sort |
Qianyong Yang |
title |
Table_4_Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs.xlsx |
title_short |
Table_4_Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs.xlsx |
title_full |
Table_4_Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs.xlsx |
title_fullStr |
Table_4_Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs.xlsx |
title_full_unstemmed |
Table_4_Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs.xlsx |
title_sort |
table_4_genetic diversity and signatures of selection in 15 chinese indigenous dog breeds revealed by genome-wide snps.xlsx |
publishDate |
2019 |
url |
https://doi.org/10.3389/fgene.2019.01174.s016 https://figshare.com/articles/Table_4_Genetic_Diversity_and_Signatures_of_Selection_in_15_Chinese_Indigenous_Dog_Breeds_Revealed_by_Genome-Wide_SNPs_xlsx/10309022 |
long_lat |
ENVELOPE(-66.734,-66.734,-68.432,-68.432) |
geographic |
Greenland Lupa |
geographic_facet |
Greenland Lupa |
genre |
Greenland |
genre_facet |
Greenland |
op_relation |
doi:10.3389/fgene.2019.01174.s016 https://figshare.com/articles/Table_4_Genetic_Diversity_and_Signatures_of_Selection_in_15_Chinese_Indigenous_Dog_Breeds_Revealed_by_Genome-Wide_SNPs_xlsx/10309022 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fgene.2019.01174.s016 |
_version_ |
1766020276236058624 |