Method to predict the pattern of locomotion in horses

Abstract

The present invention provides methods for predicting the pattern of locomotion in a horse including the ability of a horse to use different gaits and the ability to trot at a fast speed. The methods comprise determining in a sample of DNA obtained from a horse the presence or absence of at least one genetic marker, wherein said at least one genetic marker is located on horse chromosome 23, said marker being associated with the ability to use different gaits. The invention further provides primers that amplify markers being associated with the ability to use different gaits and hybridization probes to detect markers being associated with the ability to use different gaits and the ability to trot at a fast speed.

1 - 11 . (canceled) 
     
     
         12 . A method of selecting a horse for breeding based on a prediction of a pattern of locomotion in the horse including an ability to use alternative gaits, to trot or pace at a fast speed, and/or to perform in dressage, the method comprising steps of:
 extracting a plurality of DNA from a plurality of samples obtained from a plurality of horses to form a plurality of extracted DNA;   determining in the extracted DNA the presence or absence of the nonsense mutation in exon 2 of the DMRT3 gene at nucleotide position 22,999,655 on horse chromosome 23, said nucleotide position corresponding to nucleotide position 939 in SEQ ID NO:3, and position 51 in SEQ ID NO:23, by contacting a nucleotide primer that specifically binds to the extracted DNA sequence between nucleotide positions 22,628,976 and 23,315,071 base pairs on horse chromosome 23, or to the complementary strand thereof, with said extracted DNA under hybridizing conditions and detecting the presence of a hybridization product comprising the primer and the DNA, wherein the nucleotide positions on horse chromosome 23 refer to the horse reference sequence according to the Sep. 2007  Equus caballus  draft assembly EquCab2;   selecting a first breeding horse from the plurality of horses based on the presence or absence of the nonsense mutation in the extracted DNA; and   breeding the first breeding horse with a second breeding horse to maximize a chance to obtain a progeny with a favored pattern of locomotion.   
     
     
         13 . The method according to  claim 12 , further comprising selecting the second breeding horse from the plurality of horses based on the presence or absence of the nonsense mutation in the extracted DNA. 
     
     
         14 . The method according to  claim 13 , wherein the favored pattern of locomotion is a type of gait. 
     
     
         15 . The method according to  claim 13 , wherein the first and second breeding horses both are homozygous or heterozygous for a gait allele (presence of nonsense mutation) to maximize the progeny having an ability to use alternative gaits and to trot at high speed. 
     
     
         16 . The method according to  claim 13 , wherein the first and second breeding horses both are homozygous or heterozygous for a wild type allele (absence of the nonsense mutation) to maximize the progeny having an ability to perform in showjumping, dressage, and completion racing in gallop. 
     
     
         17 . The method according to  claim 12 , wherein said nucleotide primer specifically binds to the DNA sequence between at least one genetic marker is located in the region between the flanking SNPs at nucleotide positions 22,919,878 and 23,011,289 base pairs on horse chromosome 23. 
     
     
         18 . The method according to  claim 12 , wherein said nucleotide probe specifically binds to the sequences SEQ ID NO:1, 3 and 5-25. 
     
     
         19 . The method according to  claim 12 , wherein said nucleotide probe is selected from SEQ NO:26, SEQ ID NO:27, SEQ ID NO:30, and SEQ ID NO:31. 
     
     
         20 . The method according to  claim 12 , further comprising determining a paternity of at least one of the plurality of horses. 
     
     
         21 . The method according to  claim 12 , wherein said nucleotide primer specifically binds to the DMRT3 gene. 
     
     
         22 . The method according to  claim 12 , wherein said detection of a hybridization product is performed by polymerase chain reaction (PCR), allele specific hybridization, the 3′exonuclease assay (Taqman assay), fluorescent dye and quenching agent-based PCR assay, allele-specific restriction enzymes (RFLP-based techniques), direct sequencing, the oligonucleotide ligation assay (OLA), pyrosequencing, the invader assay, minisequencing, DHPLC-based techniques, single strand conformational polymorphism (SSCP), allele-specific PCR, denaturating gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), chemical mismatch cleavage (CMC), heteroduplex analysis based system, techniques based on mass spectroscopy, invasive cleavage assay, polymorphism ratio sequencing (PRS), microarrays, a rolling circle extension assay, HPLC-based techniques, extension based assays, ARMS (Amplification Refractory Mutation System), ALEX (Amplification Refractory Mutation Linear Extension), SBCE (Single base chain extension), molecular beacon assays, invader (Third wave technologies), ligase chain reaction assays, 5′-nuclease assay-based techniques, hybridization capillary array electrophoresis (CAE), and solid phase hybridization (dot blot, reverse dot blot, chips). 
     
     
         23 . A method of selecting a horse for breeding based on a prediction of a pattern of locomotion in the horse including an ability to use alternative gaits, to trot or pace at a fast speed, and/or to perform in dressage, the method comprising steps of:
 extracting a plurality of protein from a plurality of samples obtained from a plurality of horses to form a plurality of extracted protein;   determining in the extracted protein the presence or absence of a truncated form of the DMRT3 protein;   selecting a first breeding horse from the plurality of horses based on the presence or absence of the truncated form of the DMRT3 protein; and   breeding the first breeding horse with a second breeding horse to maximize a chance to obtain a progeny with a favored pattern of locomotion.   
     
     
         24 . The method according to  claim 23 , further comprising selecting a second breeding horse from the plurality of horses based on the presence or absence of the nonsense mutation in the extracted DNA. 
     
     
         25 . The method according to  claim 24 , wherein the favored pattern of locomotion is a type of gait. 
     
     
         26 . The method according to  claim 24 , wherein both the first and second breeding horses express the truncated DMRT3 protein. 
     
     
         27 . The method according to  claim 24 , wherein both the first and second breeding horses express the truncated DMRT3 protein that lacks the last 174 amino acid sequences and maintains a funcntional DNA-binding domain.