Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature

Nat Genet. 2011 May;43(5):405-13. doi: 10.1038/ng.814. Epub 2011 Apr 24.

Abstract

We report mapping of a quantitative trait locus (QTL) with a major effect on bovine stature to a ∼780-kb interval using a Hidden Markov Model-based approach that simultaneously exploits linkage and linkage disequilibrium. We re-sequenced the interval in six sires with known QTL genotype and identified 13 clustered candidate quantitative trait nucleotides (QTNs) out of >9,572 discovered variants. We eliminated five candidate QTNs by studying the phenotypic effect of a recombinant haplotype identified in a breed diversity panel. We show that the QTL influences fetal expression of seven of the nine genes mapping to the ∼780-kb interval. We further show that two of the eight candidate QTNs, mapping to the PLAG1-CHCHD7 intergenic region, influence bidirectional promoter strength and affect binding of nuclear factors. By performing expression QTL analyses, we identified a splice site variant in CHCHD7 and exploited this naturally occurring null allele to exclude CHCHD7 as single causative gene.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • Base Sequence
  • Cattle / anatomy & histology*
  • Cattle / genetics*
  • Chromosome Mapping
  • Crosses, Genetic
  • DNA Primers / genetics
  • Female
  • Genetic Variation*
  • Genome-Wide Association Study
  • Haplotypes
  • Linkage Disequilibrium
  • Male
  • Open Reading Frames
  • Polymorphism, Single Nucleotide
  • Promoter Regions, Genetic
  • Quantitative Trait Loci
  • RNA Splice Sites
  • Regulon
  • Sequence Homology, Nucleic Acid

Substances

  • DNA Primers
  • RNA Splice Sites