ArticleProceedings of the National Academy of Sciences of the United States of America2012
Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
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44 citing papers in PubMed, 1 synthesis or guideline pooled it, 79 citations in OpenAlex.
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- Climate-Resilient Dairy Cattle Production: Applications of Genomic Tools and Statistical Models.Frontiers in veterinary science · 2021Review
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- Genome changes due to artificial selection in U.S. Holstein cattle.BMC genomics · 2019Article
- A large-scale pedigree resource of wheat reveals evidence for adaptation and selection by breeders.PLoS biology · 2019Article
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- Impact of rare and low-frequency sequence variants on reliability of genomic prediction in dairy cattle.Genetics, selection, evolution : GSE · 2018Article
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- De novo assembly of haplotype-resolved genomes with trio binning.Nature biotechnology · 2018Article
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- Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.Genome research · 2017Article
- Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance.Mammalian genome : official journal of the International Mammalian Genome Society · 2017Article
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Authors and funding
17 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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