Methods and Compositions for Testing and Breeding Cattle for Improved Fertility and Embryonic Survival

Abstract

Disclosed are arrays of nucleic acid molecules, kits, methods of genotyping and marker assisted bovine breeding methods using SNPs on genes of the bovine interferon tau signaling pathway for improved bovine fertilization rate, or embryo survival, or both.

1 . A collection of at least two of isolated polynucleotide molecule species selected from the group consisting of (1) an isolated polynucleotide comprising at least 12 consecutive nucleotides surrounding position of 1296 of SEQ ID NO:1; (2) an isolated polynucleotide comprising at least 12 consecutive nucleotides surrounding position of 213 of SEQ ID NO:2; (3) an isolated polynucleotide comprising at least 12 consecutive nucleotides surrounding position of 8504 of SEQ ID NO:3; (4) an isolated polynucleotide comprising at least 12 consecutive nucleotides surrounding position of 154963 of SEQ ID NO:4; (5) an isolated polynucleotide comprising at least 12 consecutive nucleotides surrounding position of 577 of SEQ ID NO:5; (6) an isolated polynucleotide comprising at least 12 consecutive nucleotides surrounding position of 23 of SEQ ID NO:6; (7) an isolated polynucleotide comprising at least 12 consecutive nucleotides surrounding position of 11646 of SEQ ID NO:6; and (8) an isolated polynucleotide comprising at least 12 consecutive nucleotides surrounding position of 12195 of SEQ ID NO:7. 
     
     
         2 . The collection according to  claim 1 , comprising at least three species. 
     
     
         3 . The collection of  claim 2 , comprising all eight species. 
     
     
         4 . The collection of  claim 1 , wherein the nucleotide species are on a solid support. 
     
     
         5 . The collection of  claim 1 , wherein the nucleotide species are arranged in an addressable array. 
     
     
         6 . The collection of  claim 4 , wherein the nucleotide species are arranged in an array on a solid support. 
     
     
         7 . The collection of  claim 6 , wherein the array is made of silicon, glass, plastic, or paper. 
     
     
         8 . The method of  claim 6 , wherein the array is formed into wells on plates, slides, sheets, membranes, fibers, chips, dishes, and beads. 
     
     
         9 . The collection of  claim 6 , wherein array is treated, coated or derivatized to facilitate the immobilization of the nucleotide molecules. 
     
     
         10 . A method for genotyping a bovine cell, comprising obtaining a nucleic acid sample from said cell and determining the identity of the nucleotide of eight SNP positions in the cell, wherein the eight SNP positions are (1) position 1296 of SEQ ID NO:1; (2) position 213 of SEQ ID NO:2; (3) position 8504 of SEQ ID NO:3; (4) position 154963 of SEQ ID NO:4; (5) position 577 of SEQ ID NO:5; (6) position of 23 SEQ ID NO:6; (7) position 11646 of SEQ ID NO:6; and (8) position 12195 of SEQ ID NO:7, the method, comprising
 (1) Determining the identity of a nucleotide at each of the eight SNP positions, and   (2) comparing the identity to the nucleotide identity at a corresponding position of in SEQ ID NOs: 1-7, respectively.   
     
     
         11 . The method according to  claim 10 , wherein the bovine cell is an adult cell, an embryo cell, a sperm, an egg, a fertilized egg, or a zygote. 
     
     
         12 . The method according to  claim 10 , wherein the identity of the nucleotide is determined by sequencing or a relevant fragment of the respective gene isolated from the cell. 
     
     
         13 . A method according to  claim 12 , wherein relevant fragment of the respective gene is isolated from the cell via amplification by the polymerase chain reaction (PCR) of genomic DNA of the cell, or by RT-PCR of the mRNA of the cell. 
     
     
         14 . A method according to  claim 10 , wherein both copies of the respective gene in the cell are genotyped. 
     
     
         15 . A method for progeny testing of cattle, the method comprising collecting a nucleic acid sample from said progeny, and genotyping said nucleic sample according to  claim 10 . 
     
     
         16 . A method for selectively breeding of cattle using a multiple ovulation and embryo transfer procedure (MOET), the method comprising superovulating a female animal, collecting eggs from said superovulated female, in vitro fertilizing said eggs from a suitable male animal, implanting said fertilized eggs into other females allowing for an embryo to develop, and genotyping said developing embryo according to  claim 10 , and terminating pregnancy if said developing embryo does not all have a corresponding desired polymorphic nucleotide as shown in Table 1A. 
     
     
         17 . A method according to  claim 16 , wherein pregnancy is terminated if the embryo is not homozygous with regard to all of the corresponding desired polymorphic nucleotide. 
     
     
         18 . A method for selectively breeding dairy cattle, comprising selecting a bull that is homozygous with regard to all desired polymorphic nucleotides as shown in Table 1A and using its semen for fertilizing a female animal. 
     
     
         19 . A method according to  claim 18 , wherein the female animal is in vitro fertilized. 
     
     
         20 . A method according to  claim 18 , wherein MOET procedure is used. 
     
     
         21 . A method according to  claim 18 , wherein said female animal is also homozygous with regard to all desired polymorphic nucleotides as shown in Table 1A. 
     
     
         22 . A method for testing a dairy cattle for its fertility, comprising genotyping its cells according to  claim 13 , wherein a cattle homozygous with regard to all desired polymorphic nucleotides as shown in Table 1A indicates that the cattle has fertility rate.