title: A 0.5-Mbp deletion on bovine chromosome 23 is a strong candidate for stillbirth in Nordic Red cattle.
abstract: BACKGROUND
  A whole-genome association study of 4631 progeny-tested Nordic Red dairy cattle bulls using imputed next-generation sequencing data revealed a major quantitative trait locus (QTL) that affects birth index (BI) on Bos taurus autosome (BTA) 23. We analyzed this QTL to identify which of the component traits of BI are affected and understand its molecular basis.
  
  
  RESULTS
  A genome-wide scan of BI in Nordic Red dairy cattle detected major QTL on BTA6, 14 and 23. The strongest associated single nucleotide polymorphism (SNP) on BTA23 was located at 13,313,896 bp with [Formula: see text]. Analyses of component traits showed that the QTL had a large effect on stillbirth. Based on the 10 most strongly associated SNPs with stillbirth, we constructed a haplotype. Among this haplotype's alleles, HAPQTL had a large negative effect on stillbirth. No animals were found to be homozygous for HAPQTL. Analysis of stillbirth records that were categorized by carrier status for HAPQTL of the sire and maternal grandsire suggested that this haplotype had a recessive mode of inheritance. Illumina BovineHD BeadChip genotypes and genotype intensity data indicated a chromosomal deletion between 12.28 and 12.81 Mbp on BTA23. An independent set of Illumina Bovine50k BeadChip genotypes identified a recessive lethal haplotype that spanned the deleted region.
  
  
  CONCLUSIONS
  A deleted region of approximately 500 kb that spans three genes on BTA23 was identified and is a strong candidate QTL with a large effect on BI by increasing stillbirth.
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark. goutam.sahana@mbg.au.dk.
authors.forename: Goutam
authors.identifier: http://orcid.org/0000-0001-7608-7577
authors.initials: G
authors.lastname: Sahana
authors.affiliation: Natural Resources Institute Finland, 31600, Jokioinen, Finland.
authors.forename: Terhi
authors.initials: T
authors.lastname: Iso-Touru
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Wu
authors.affiliation: Danish Agricultural Advisory Service, 8200, Århus N, Denmark.
authors.forename: Ulrik Sander
authors.initials: US
authors.lastname: Nielsen
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden.
authors.forename: Dirk-Jan
authors.initials: DJ
authors.lastname: de Koning
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.
authors.forename: Mogens Sandø
authors.initials: MS
authors.lastname: Lund
authors.affiliation: Natural Resources Institute Finland, 31600, Jokioinen, Finland.
authors.forename: Johanna
authors.initials: J
authors.lastname: Vilkki
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.
authors.forename: Bernt
authors.initials: B
authors.lastname: Guldbrandtsen
mesh_terms: D000483:Alleles; D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D033481:Chromosomes, Mammalian; D003198:Computer Simulation; D017353:Gene Deletion; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes; D008297:Male; D015233:Models, Statistical; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D050497:Stillbirth / Q000235:genetics*