ArticleMammalian genome : official journal of the International Mammalian Genome Society2015
The assessment of inter-individual variation of whole-genome DNA sequence in 32 cows.
Article in Mammalian genome : official journal of the International Mammalian Genome Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 13 citations in OpenAlex.
- An Explainable Deep Learning Classifier of Bovine Mastitis Based on Whole-Genome Sequence Data-Circumventing the p >> n Problem.International journal of molecular sciences · 2024Article
- Single Nucleotide Polymorphisms, Gene Expression and Economic Evaluation of Parameters Associated with Mastitis Susceptibility in European Cattle Breeds.Veterinary sciences · 2022Article
- Landscape of copy number variations in Bos taurus: individual - and inter-breed variability.BMC genomics · 2018Article
- Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions.Frontiers in genetics · 2018Article
- Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer (G3 (Bethesda, Md.) · 2017Article
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the growing number of sequenced bovine genomes, the knowledge of the population-wide variation of sequences remains limited. In many studies, statistical methodology was not applied in order to relate findings in the sequenced samples to a population-wide level. Our goal was to assess the population-wide variation in DNA sequence based on whole-genome sequences of 32 Holstein-Friesian cows. The number of SNPs significantly varied across individuals. The number of identified SNPs increased with coverage, following a logarithmic curve. A total of 15,272,427 SNPs were identified, 99.16 % of them being bi-allelic. Missense SNPs were classified into three categories based on their genomic location: housekeeping genes, genes undergoing strong selection, and genes neutral to selection. The number of missense SNPs was significantly higher within genes neutral to selection than in the other two categories. The number of variants located within 3'UTR and 5'UTR regions was also significantly different across gene families. Moreover, the number of insertions and deletions differed significantly among cows varying between 261,712 and 330,103 insertions and from 271,398 to 343,649 deletions. Results not only demonstrate inter-individual variation in the number of SNPs and indels but also show that the number of missense SNPs differs across genes representing different functional backgrounds.
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Registered trials
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