Alleles; Animals; Base Sequence; Cattle/anatomy & histology/genetics; Chromosome Mapping; Crosses, Genetic; DNA Primers/genetics; Female; Genetic Variation; Genome-Wide Association Study; Haplotypes; Linkage Disequilibrium; Open Reading Frames; Male; Polymorphism, Single Nucleotide; Promoter Regions, Genetic; Quantitative Trait Loci; RNA Splice Sites; Regulon; Sequence Homology, Nucleic Acid
Abstract :
[en] We report mapping of a quantitative trait locus (QTL) with a major effect on bovine stature to a approximately 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 approximately 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.
Disciplines :
Genetics & genetic processes
Author, co-author :
Karim, Latifa ✱; Université de Liège - ULiège > Département des sciences de la vie > GIGA-R : Biologie et génétique moléculaire
Takeda, Haruko ✱; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Lin, Li ✱
Druet, Tom ✱; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Arias, Juan A C
Baurain, Denis ; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Cambisano, Nadine ; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Davis, Stephen R
Farnir, Frédéric ; Université de Liège - ULiège > Département de productions animales > Biostatistiques et bioinformatique appliquées aux sc. vétér.
Grisart, Bernard
Harris, Bevin L
Keehan, Mike D
Littlejohn, Mathew D
Spelman, Richard J
Georges, Michel ✱; Université de Liège - ULiège > Département de productions animales > Département de productions animales
Coppieters, Wouter ✱; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
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