Leptin promoter polymorphisms and uses thereof

Abstract

The present invention relates to single nucleotide polymorphisms (SNPs) in the leptin promoter, and to methods for the identification of animals carrying specific alleles of these SNPs that are associated with circulating leptin levels, feed intake, growth rate, body weight, carcass merit and carcass composition. The present invention provides oligonucleotides that can be used as primers and/or probes to amplify and/or detect these SNPs, and provides methods for selecting and grouping animals, in particular bovines, according to genotype.

1 . A method for identifying a bovine animal having a desirable phenotype relating to feed intake, growth rate, body weight, carcass merit or carcass composition, as compared to the general population of bovine animals, comprising detecting the presence of a single nucleotide polymorphism in the leptin gene, wherein the single nucleotide polymorphism is selected from the group consisting of UASMS1, UASMS2, UASMS3, and EXON2-FB, wherein the presence of a particular genotype at either the UASMS1, UASMS2, UASMS3 or EXON2-FB single nucleotide polymorphism is indicative of a phenotypic trait relating to circulating leptin levels, feed intake, growth rate, body weight, carcass merit and/or or carcass composition.  
     
     
         2 . The method according to  claim 1  wherein the single nucleotide polymorphism is the UASMS1 polymorphism, and wherein 
 a) animals having the CC genotype have lower final body weight, average body weight, slaughter weight, carcass weight, and/or dry matter intake as compared to animals having the CT or TT genotypes,    b) animals having the TT genotype have higher final body weight, average body weight, slaughter weight, carcass weight and/or dry matter intake compared to animals having the CT or CC genotypes, and    c) animals having the CT genotype have final body weights, average body weights, slaughter weights, carcass weights and dry matter intake levels that are intermediate to the levels in animals having the CC or TT genotypes.    
     
     
         3 . The method according to  claim 1  wherein the single nucleotide polymorphism is the UASMS2 polymorphism, and wherein 
 a) animals having the CC genotype have lower serum leptin levels, average daily gain, dry matter intake, marbling score and/or ultrasound back fat compared to animals having the CT or TT genotypes,b) animals having the TT genotype have intermediate serum leptin levels, marbling score and ultrasound back fat compared to animals having the CC or TT genotypes, and higher average daily gain and dry matter intake compared to animals having the CC genotype, and    c) animals having the CT genotype have higher serum leptin levels, marbling score and/or ultrasound back fat compared to animals having the CT or CC genotypes, and higher average daily gain and/or dry matter intake compared to animals having the CC genotype.    
     
     
         4 . The method according to  claim 1  wherein the single nucleotide polymorphism is the UASMS3 polymorphism, and wherein 
 a) animals having the CC genotype have lower final body weight, average body weight, slaughter weight, carcass weight, and/or dry matter intake compared to animals having the CG or GG genotypes,    b) animals having the GG genotype have higher final body weight, average body weight, slaughter weight, carcass weight and/or dry matter intake compared to animals having the CC or CG genotypes, and    c) animals having the CG genotype have intermediate final body weight, average body weight, slaughter weight, carcass weight and/or dry matter intake compared to animals with CC or GG genotypes.    
     
     
         5 . The method according to  claim 1  wherein the single nucleotide polymorphism is the EXON2-FB polymorphism, and wherein 
 a) animals having the CC genotype have lower ultrasound back fat and higher metabolic midweight, final body weight, slaughter weight and/or carcass weight, compared to animals having the CT or TT genotypes,    b) animals having the TT genotype have higher ultrasound back fat and lower metabolic midweight, final body weight, and/or slaughter weight compared to animals having the CT or CC genotypes, and    c) animals having the CT genotype have intermediate ultrasound back fat, metabolic midweight, slaughter weight and/or carcass weight, compared to animals having the CC or TT genotypes.    
     
     
         6 . The method according to  claim 1  wherein the UASMS1 and UASMS3 polymorphisms are in complete linkage such that 
 a) an animal with the CC genotype at the UASMS1 locus has the CC genotype at the UASMS3 locus,    b) an animal with the CT genotype at the UASMS1 locus has the CG genotype at the UASMS3 locus, and    c) an animal with the TT genotype at the UASMS1 locus has the GG genotype at the UASMS3 locus.    
     
     
         7 . An isolated oligonucleotide probe for detecting a single nucleotide polymorphism in the bovine ob gene, wherein the isolated oligonucleotide is selected from the group comprising: 
 a) 10 or more contiguous nucleotides of SEQ ID NO: 1 including nucleotide position 207 of SEQ ID NO: 1.    b) 10 or more contiguous nucleotides of SEQ ID NO: 2 including nucleotide position 207 of SEQ ID NO: 2.    c) 10 or more contiguous nucleotides of SEQ ID NO: 3 including nucleotide position 528 of SEQ ID NO: 3    d) 10 or more contiguous nucleotides of SEQ ID NO: 4 including nucleotide position 1759 of SEQ ID NO: 4    e) 10 or more contiguous nucleotides of SEQ ID NO: 5 including nucleotide position 305 of SEQ ID NO: 5    f) 10 or more contiguous nucleotides of SEQ ID NO: 6 including nucleotide position 305 of SEQ ID NO: 4    g) SEQ ID NO: 9    h) SEQ ID NO: 10    i) SEQ ID NO: 13    j) SEQ ID NO: 14    k) SEQ ID NO: 17    l) SEQ ID NO: 18    m) SEQ ID NO: 21    n) SEQ ID NO: 22    
     
     
         8 . A isolated primer pair useful in the amplification of a fragment of the bovine ob gene spanning the location of the UASMS1, UASMS2, UASMS3, or EXON2-FB single nucleotide polymorphisms, wherein the primer pair is selected from the group comprising: 
 a) a first primer that anneals to the ob gene promoter at a location upstream of nucleotide position 207 of SEQ ID NO: 1, and a second primer that anneals to the ob gene promoter at a location downstream of nucleotide position 207 of SEQ ID NO: 1.    b) a first primer that anneals to the ob gene promoter at a location upstream of nucleotide position 528 of SEQ ID NO: 1, and a second primer that anneals to the ob gene promoter at a location downstream of nucleotide position 528 of SEQ ID NO: 1.    c) a first primer that anneals to the ob gene promoter at a location upstream of nucleotide position 1759 of SEQ ID NO: 1, and a second primer that anneals to the ob gene promoter at a location downstream of nucleotide position 1759 of SEQ ID NO: 1.    d) a first primer that anneals to exon 2 of the ob gene at a location upstream of nucleotide position 305 of SEQ ID NO: 5, and a second primer that anneals to exon 2 of the ob gene at a location downstream of nucleotide position 305 of SEQ ID NO: 5.    e) a first primer having the sequence of SEQ ID NO: 7 and a second primer having the sequence of SEQ ID NO: 8.    f) a first primer having the sequence of SEQ ID NO: 11 and a second primer having the sequence of SEQ ID NO: 12.    g) a first primer having the sequence of SEQ ID NO: 15 and a second primer having the sequence of SEQ ID NO: 16.    h) a first primer having the sequence of SEQ ID NO: 19 and a second primer having the sequence of SEQ ID NO: 20.