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A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies #
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Structured data

SNP array
Date Published
PLOS Genetics

Summary #

Introduction #

말(Horse)은 5000년 이상 인류의 문명화에 함께 해 왔다. 400 이상의 품종이 구분되어 있다.

Horse genome has 2.67 Gb, and 96% assembled.

EquineSNP50 BeadChip으로 타이핑.

Results #

SNP array properties, polymorphism, and genome coverage in the domestic horse (Equus caballus) #

14개의 서로 다른 품종에서 354 개체 genotyping, 3 개체는 실패. 8 쌍의 동일 시료를 포함하여, 각 시료가 완전 매치함을 확인. 18 trio에서 15의 멘델 유전 확인.

54,602 SNPs에서 53,524개 validated. 53,066 were polymorphic (MAF>0.001).

Average spacing between functional SNPs was 43.1 kb.

Utility of the EquineSNP50 BeadChip in extant Perissodactyla #

진화적으로 관련된 18개 생물종 (기제목, Perissodactyla, 코뿔소, 말 등)으로 부터 53 개체 genotyping. 그 가운데 zebra는 완전 실패함.

Minor allele frequency and genetic diversity within and across domestic horse breeds #

Genome-wide linkage disequilibrium analysis within and across domestic horse breeds #

Inbreeding, genetic distance, and relationships between domestic horse breeds #

Relationships between the domestic horse and extant Hippomorpha #

Application to genome-wide association studies (GWAS) #

Discussion #

Properties of the EquineSNP50 BeadChip #

Genetic diversity, inbreeding, and LD in the domestic horse #

Relationships between domestic horse breeds #

Relationship between the domestic horse and other Hippomorpha #

Concluding statement #

Meterials and Methods #

Design of the EquineSNP50 BeadChip #

Horses #

Samples from other Perissodactyla #

SNP summary statistics #

Additional data filtering in extant Perissodactyla #

Genome-wide linkage disequilibrium #

Relationship between breeds and genetic structure in the domestic horse #

Estimation of inbreeding #

Relationship among the domestic horse breeds and the Prezwalski’s horse #

Relationship among the extant equids and the domestic horse #

Mapping of coat color loci #

Haplotypes at coat color loci #

Suggested Pages #