Document Detail

Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle.
MedLine Citation:
PMID:  22529356     Owner:  NLM     Status:  MEDLINE    
Using a combination of whole-genome resequencing and high-density genotyping arrays, genome-wide haplotypes were reconstructed for two of the most important bulls in the history of the dairy cattle industry, Pawnee Farm Arlinda Chief ("Chief") and his son Walkway Chief Mark ("Mark"), each accounting for ∼7% of all current genomes. We aligned 20.5 Gbp (∼7.3× coverage) and 37.9 Gbp (∼13.5× coverage) of the Chief and Mark genomic sequences, respectively. More than 1.3 million high-quality SNPs were detected in Chief and Mark sequences. The genome-wide haplotypes inherited by Mark from Chief were reconstructed using ∼1 million informative SNPs. Comparison of a set of 15,826 SNPs that overlapped in the sequence-based and BovineSNP50 SNPs showed the accuracy of the sequence-based haplotype reconstruction to be as high as 97%. By using the BovineSNP50 genotypes, the frequencies of Chief alleles on his two haplotypes then were determined in 1,149 of his descendants, and the distribution was compared with the frequencies that would be expected assuming no selection. We identified 49 chromosomal segments in which Chief alleles showed strong evidence of selection. Candidate polymorphisms for traits that have been under selection in the dairy cattle population then were identified by referencing Chief's DNA sequence within these selected chromosome blocks. Eleven candidate genes were identified with functions related to milk-production, fertility, and disease-resistance traits. These data demonstrate that haplotype reconstruction of an ancestral proband by whole-genome resequencing in combination with high-density SNP genotyping of descendants can be used for rapid, genome-wide identification of the ancestor's alleles that have been subjected to artificial selection.
Denis M Larkin; Hans D Daetwyler; Alvaro G Hernandez; Chris L Wright; Lorie A Hetrick; Lisa Boucek; Sharon L Bachman; Mark R Band; Tatsiana V Akraiko; Miri Cohen-Zinder; Jyothi Thimmapuram; Iona M Macleod; Timothy T Harkins; Jennifer E McCague; Michael E Goddard; Ben J Hayes; Harris A Lewin
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Publication Detail:
Type:  Journal Article; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2012-04-23
Journal Detail:
Title:  Proceedings of the National Academy of Sciences of the United States of America     Volume:  109     ISSN:  1091-6490     ISO Abbreviation:  Proc. Natl. Acad. Sci. U.S.A.     Publication Date:  2012 May 
Date Detail:
Created Date:  2012-05-16     Completed Date:  2012-07-27     Revised Date:  2013-06-25    
Medline Journal Info:
Nlm Unique ID:  7505876     Medline TA:  Proc Natl Acad Sci U S A     Country:  United States    
Other Details:
Languages:  eng     Pagination:  7693-8     Citation Subset:  IM    
Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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MeSH Terms
Base Sequence
Breeding / methods*
Cattle / genetics*
Genetic Association Studies / veterinary
Genome / genetics*
Haplotypes / genetics*
Molecular Sequence Data
Polymorphism, Single Nucleotide / genetics
Selection, Genetic*
Sequence Analysis, DNA

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