title: The assessment of inter-individual variation of whole-genome DNA sequence in 32 cows.
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.
authors.affiliation: Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland. joanna.szyda@up.wroc.pl.
authors.forename: Joanna
authors.initials: J
authors.lastname: Szyda
authors.affiliation: Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Frąszczak
authors.affiliation: Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland.
authors.forename: Magda
authors.initials: M
authors.lastname: Mielczarek
authors.affiliation: Fondazione Parco Tecnologico Padano, Via Einstein Albert, 26900, Lodi, LO, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Giannico
authors.affiliation: Fondazione Parco Tecnologico Padano, Via Einstein Albert, 26900, Lodi, LO, Italy.|DIVET, Università di Milano, Via Celoria 10, 20133, Milan, Italy.
authors.forename: Giulietta
authors.initials: G
authors.lastname: Minozzi
authors.affiliation: Fondazione Parco Tecnologico Padano, Via Einstein Albert, 26900, Lodi, LO, Italy.
authors.forename: Ezequiel L
authors.initials: EL
authors.lastname: Nicolazzi
authors.affiliation: Institute of Animal Genetics, University of Warmia and Mazury, Oczapowskiego 2, Olsztyn, 10-719, Poland.
authors.forename: Stanislaw
authors.initials: S
authors.lastname: Kamiński
authors.affiliation: West Pomeranian University of Technology, Piastów 17, 70-310, Szczecin, Poland.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Wojdak-Maksymiec
mesh_terms: D000818:Animals; D016022:Case-Control Studies; D002417:Cattle; D056915:DNA Copy Number Variations; D005260:Female; D016678:Genome; D054643:INDEL Mutation; D008414:Mastitis, Bovine / Q000235:genetics*; D020125:Mutation, Missense; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA