Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle

Larkin, Denis M., Daetwyler, Hans D., Hernandez, Alvaro G., Wright, Chris L., Hetrick, Lorie A., Boucek, Lisa, Bachman, Sharon L., Band, Mark R., Akraiko, Tatsiana V., Cohen-Zinder, Miri, Thimmapuram, Jyothi, Macleod, Iona M., Harkins, Timothy T., McCague, Jennifer E., Goddard, Michael E., Hayes, Ben J. and Lewin, Harris A. (2012) Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. Proceedings of the National Academy of Sciences of the United States of America, 109 20: 7693-7698. doi:10.1073/pnas.1114546109

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Author Larkin, Denis M.
Daetwyler, Hans D.
Hernandez, Alvaro G.
Wright, Chris L.
Hetrick, Lorie A.
Boucek, Lisa
Bachman, Sharon L.
Band, Mark R.
Akraiko, Tatsiana V.
Cohen-Zinder, Miri
Thimmapuram, Jyothi
Macleod, Iona M.
Harkins, Timothy T.
McCague, Jennifer E.
Goddard, Michael E.
Hayes, Ben J.
Lewin, Harris A.
Title Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle
Journal name Proceedings of the National Academy of Sciences of the United States of America   Check publisher's open access policy
ISSN 0027-8424
1091-6490
Publication date 2012-05-15
Sub-type Article (original research)
DOI 10.1073/pnas.1114546109
Open Access Status File (Publisher version)
Volume 109
Issue 20
Start page 7693
End page 7698
Total pages 6
Place of publication Washington, DC, United States
Publisher National Academy of Sciences
Language eng
Abstract 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.
Keyword Next generation sequencing
Quantitative trait locus
Single nucleotide polymorphism
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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