Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression.
BACKGROUND
In mammals, an important source of genomic variation is insertion polymorphism of retrotransposons. These may acquire a functional role when inserted inside genes or in their proximity. The aim of this work was to carry out a genome wide analysis of ERE1 retrotransposons in the horse and to analyze insertion polymorphism in relation to evolution and function. The effect of an ERE1 insertion in the promoter of the myostatin gene, which is involved in muscle development, was also investigated.


RESULTS
In the horse population, the fraction of ERE1 polymorphic loci is related to the degree of similarity to their consensus sequence. Through the analysis of ERE1 conservation in seven equid species, we established that the level of identity to their consensus is indicative of evolutionary age of insertion. The position of ERE1s relative to genes suggests that some elements have acquired a functional role. Reporter gene assays showed that the ERE1 insertion within the horse myostatin promoter affects gene expression. The frequency of this variant promoter correlates with sport aptitude and racing performance.


CONCLUSIONS
Sequence conservation and insertion polymorphism of ERE1 elements are related to the time of their appearance in the horse lineage, therefore, ERE1s are a useful tool for evolutionary and population studies. Our results suggest that the ERE1 insertion at the myostatin locus has been unwittingly selected by breeders to obtain horses with specific racing abilities. Although a complex combination of environmental and genetic factors contributes to athletic performance, breeding schemes may take into account ERE1 insertion polymorphism at the myostatin promoter.
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy. marco.santagostino@unipv.it.
Marco
M
Santagostino
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy. lela.khoriauli@unipv.it.
Lela
L
Khoriauli
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy. riccardo.gamba@iusspavia.it.
Riccardo
R
Gamba
Laboratorio di Genetica Forense Veterinaria, UNIRELAB srl, Via A. Gramsci 70, 20019, Settimo Milanese (MI), Italy. mar.bonuglia@gmail.com.
Margherita
M
Bonuglia
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy. klipsteinori@hotmail.com.
Ori
O
Klipstein
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy. mfrancesca.piras@unipv.it.
Francesca M
FM
Piras
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy. Francesco.Vella@unipv.it.
Francesco
F
Vella
Laboratorio di Genetica Forense Veterinaria, UNIRELAB srl, Via A. Gramsci 70, 20019, Settimo Milanese (MI), Italy. russoalessandra.76@gmail.com.
Alessandra
A
Russo
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy. claudia.badiale01@universitadipavia.it.
Claudia
C
Badiale
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy. alice.mazzagatti01@universitadipavia.it.
Alice
A
Mazzagatti
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy. elena.raimondi@unipv.it.
Elena
E
Raimondi
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy. solomon.nergadze@unipv.it.
Solomon G
SG
Nergadze
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy. elena.giulotto@unipv.it.
Elena
E
Giulotto
D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D017930:Genes, Reporter; D056426:Genetic Loci; D016678:Genome; D005838:Genotype; D006736:Horses / Q000235:genetics*; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional / Q000235:genetics*; D055435:Myostatin / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D018626:Retroelements / Q000235:genetics
D055435:Myostatin; D018626:Retroelements