title: Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds.
abstract: Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69,903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.
authors.affiliation: 1Department of Animal Science,Chungbuk National University,Cheongju 361-763,Korea.
authors.forename: Z
authors.initials: Z
authors.lastname: Edea
authors.affiliation: 3Department of Animal Breeding and Genetics,Bangladesh Agricultural University,Mymensingh-2202,Bangladesh.
authors.forename: M S A
authors.initials: MS
authors.lastname: Bhuiyan
authors.affiliation: 2International Livestock Research Institute (ILRI),PO Box 5689,Addis Ababa,Ethiopia.
authors.forename: T
authors.initials: T
authors.lastname: Dessie
authors.affiliation: 4Department of Animal Science,Iowa State University,Ames,IA 50011,USA.
authors.forename: M F
authors.initials: MF
authors.lastname: Rothschild
authors.affiliation: 5Department of Animal Biotechnology,College of Animal Bioscience and Technology,Konkuk University,Seoul 143-701,Korea.
authors.forename: H
authors.initials: H
authors.lastname: Dadi
authors.affiliation: 1Department of Animal Science,Chungbuk National University,Cheongju 361-763,Korea.
authors.forename: K S
authors.initials: KS
authors.lastname: Kim
mesh_terms: D000483:Alleles; D000818:Animals; D000829:Animals, Domestic; D001459:Bangladesh; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D016000:Cluster Analysis; D003710:Demography; D005002:Ethiopia; D014644:Genetic Variation; D016678:Genome / Q000235:genetics*; D055106:Genome-Wide Association Study; D005838:Genotype; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D056910:Republic of Korea
keywords: Bos indicus; Bos taurus; Ethiopia; genetic diversity; population structure