The assessment of inter-individual variation of whole-genome DNA sequence in 32 cows. 2015

Joanna Szyda, and Magdalena Frąszczak, and Magda Mielczarek, and Riccardo Giannico, and Giulietta Minozzi, and Ezequiel L Nicolazzi, and Stanislaw Kamiński, and Katarzyna Wojdak-Maksymiec
Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland. joanna.szyda@up.wroc.pl.

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.

UI MeSH Term Description Entries
D008414 Mastitis, Bovine INFLAMMATION of the UDDER in cows. Bovine Mastitides,Bovine Mastitis,Mastitides, Bovine
D002417 Cattle Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor. Beef Cow,Bos grunniens,Bos indicus,Bos indicus Cattle,Bos taurus,Cow,Cow, Domestic,Dairy Cow,Holstein Cow,Indicine Cattle,Taurine Cattle,Taurus Cattle,Yak,Zebu,Beef Cows,Bos indicus Cattles,Cattle, Bos indicus,Cattle, Indicine,Cattle, Taurine,Cattle, Taurus,Cattles, Bos indicus,Cattles, Indicine,Cattles, Taurine,Cattles, Taurus,Cow, Beef,Cow, Dairy,Cow, Holstein,Cows,Dairy Cows,Domestic Cow,Domestic Cows,Indicine Cattles,Taurine Cattles,Taurus Cattles,Yaks,Zebus
D005260 Female Females
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D016022 Case-Control Studies Comparisons that start with the identification of persons with the disease or outcome of interest and a control (comparison, referent) group without the disease or outcome of interest. The relationship of an attribute is examined by comparing both groups with regard to the frequency or levels of outcome over time. Case-Base Studies,Case-Comparison Studies,Case-Referent Studies,Matched Case-Control Studies,Nested Case-Control Studies,Case Control Studies,Case-Compeer Studies,Case-Referrent Studies,Case Base Studies,Case Comparison Studies,Case Control Study,Case Referent Studies,Case Referrent Studies,Case-Comparison Study,Case-Control Studies, Matched,Case-Control Studies, Nested,Case-Control Study,Case-Control Study, Matched,Case-Control Study, Nested,Case-Referent Study,Case-Referrent Study,Matched Case Control Studies,Matched Case-Control Study,Nested Case Control Studies,Nested Case-Control Study,Studies, Case Control,Studies, Case-Base,Studies, Case-Comparison,Studies, Case-Compeer,Studies, Case-Control,Studies, Case-Referent,Studies, Case-Referrent,Studies, Matched Case-Control,Studies, Nested Case-Control,Study, Case Control,Study, Case-Comparison,Study, Case-Control,Study, Case-Referent,Study, Case-Referrent,Study, Matched Case-Control,Study, Nested Case-Control
D016678 Genome The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA. Genomes
D017422 Sequence Analysis, DNA A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis. DNA Sequence Analysis,Sequence Determination, DNA,Analysis, DNA Sequence,DNA Sequence Determination,DNA Sequence Determinations,DNA Sequencing,Determination, DNA Sequence,Determinations, DNA Sequence,Sequence Determinations, DNA,Analyses, DNA Sequence,DNA Sequence Analyses,Sequence Analyses, DNA,Sequencing, DNA
D054643 INDEL Mutation A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION. INDELs Mutation,Insertions-Deletions Mutation,Insertion-Deletion Mutation,INDEL Mutations,INDELs Mutations,Insertion Deletion Mutation,Insertion-Deletion Mutations,Insertions Deletions Mutation,Insertions-Deletions Mutations,Mutation, INDEL,Mutation, INDELs,Mutation, Insertion-Deletion,Mutation, Insertions-Deletions
D056915 DNA Copy Number Variations Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease. Copy Number Polymorphism,DNA Copy Number Variant,Copy Number Changes, DNA,Copy Number Polymorphisms,Copy Number Variants, DNA,Copy Number Variation, DNA,DNA Copy Number Change,DNA Copy Number Changes,DNA Copy Number Polymorphism,DNA Copy Number Polymorphisms,DNA Copy Number Variants,DNA Copy Number Variation,Polymorphism, Copy Number,Polymorphisms, Copy Number
D020125 Mutation, Missense A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed) Missense Mutation,Missense Mutations,Mutations, Missense

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