אסיף מאגר המחקר החקלאי

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

Year:

2012

Source of publication :

Authors :

Volume :

109

Co-Authors:

Larkin, D.M., Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
Daetwyler, H.D., Biosciences Research Division, Department of Primary Industries, Bundoora, VIC 3083, Australia
Hernandez, A.G., W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
Wright, C.L., W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
Hetrick, L.A., W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
Boucek, L., W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
Bachman, S.L., W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
Band, M.R., W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
Akraiko, T.V., W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
Cohen-Zinder, M., Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
Thimmapuram, J., W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
Macleod, I.M., Department of Food and Agricultural Systems, University of Melbourne, Parkville, VIC 3011, Australia
Harkins, T.T., Roche, Indianapolis, IN 46250, United States
McCague, J.E., 454 Life Sciences, Branford, CT 06405, United States
Goddard, M.E., Biosciences Research Division, Department of Primary Industries, Bundoora, VIC 3083, Australia, Department of Food and Agricultural Systems, University of Melbourne, Parkville, VIC 3011, Australia
Hayes, B.J., Biosciences Research Division, Department of Primary Industries, Bundoora, VIC 3083, Australia, Biosciences Research Centre, La Trobe University, Bundoorax, VIC 3011, Australia
Lewin, H.A., Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States, Department of Evolution and Ecology, UC Davis Genome Center, University of California, Davis, CA 95616, United States

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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 (∼7.3x coverage) and 37.9 Gbp (∼13.5x 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 diseaseresistance 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.

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