GENETIC VARIANTS ASSOCIATED WITH HUMAN-DIRECTED HYPER-SOCIAL BEHAVIOR IN DOMESTIC DOGS

• US 20200131573A1
• Filed: 06/29/2018
• Published: 04/30/2020
• Est. Priority Date: 06/30/2017
• Status: Active Application

• Current Assignee: Oregon State University (Oregon University System), Regents of the University of California (University of California)
• Original Assignee: The Trustees of Princeton University (Princeton University)
• Inventors: vonHOLDT, Bridgett, UDELL, Monique, SINSHEIMER, Janet
• Application Number:
  US16/626,374
• Publication Number:
  US 20200131573A1
• Time in Patent Office: Days
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2600/124 Animal traits, i.e. production traits, including athletic performance or the like
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

Disclosed herein are structural variants in the Williams-Beuren Syndrome locuse of the dog genome that are associated with hyper-social behavior in dogs relative to wolves, and that are informative regarding the nature of social behavior in dogs. Disclosed also is a commercial test with these loci as indicators along the spectrum of sociality. Methods of breeding dogs to select for dogs having increased sociability are also disclosed.

Claims

1. A method for predicting the probability of a canine exhibiting a sociable behavior comprising:

(a) genotyping a biological sample from a canine;

(b) counting the number of structural variants within the Williams-Beuren Syndrome (WBS) locus on canine chromosome 6; and

(c) predicting the probability of the canine exhibiting a sociable behavior based on the number of structural variants.

2. A method of ranking dogs or wolves according to their likely level of exhibiting a sociable behavior comprising:

(a) obtaining a biological sample from a first dog or wolf;

(b) determining the number of structural variants within the Williams-Beuren Syndrome (WBS) locus on chromosome 6 of the first dog or wolf;

(c) obtaining a biological sample from a second dog or wolf;

(d) determining the number of structural variants within the Williams-Beuren Syndrome (WBS) locus on chromosome 6 of the second dog or wolf; and

(e) ranking the first dog as being more likely to exhibit a sociable behavior than the second dog if the number of structural variants determined in step (b) is greater than the number of structural variants determined in step (d);

or

(f) ranking the second dog as being more likely to exhibit a sociable behavior than the first dog if the number of structural variants determined in step (d) is greater than the number of structural variants determined in step (b).

3. The method of claim 2 wherein the biological sample is blood, saliva, cerebrospinal fluid, skin, or urine.

4. The method of claim 2 wherein genotyping the biological sample includes PCR amplification and agarose gel electrophoresis.

5. The method of claim 2 wherein genotyping the biological sample utilizes at least one primer selected from the group consisting of:

6. The method of claim 2 wherein the structural variants are transposable elements that interrupt a gene in the WBS locus.

7. The method of claim 6 wherein the transposable elements are retrotransposons.

8. The method of claim 7 wherein the retrotransposons are short interspersed nuclear elements (SINEs) or a long interspersed nuclear elements (LINEs).

9. The method of claim 2 wherein at least one structural variant occurs within at least one gene selected from the group consisting of GTF2I, GTF2IRD1, and WBSCR17.

10. The method of claim 2 wherein the social behavior is selected from the group consisting of attentional bias to social stimuli (ABS), hyper-sociability (HYP), and social interest in strangers (SIS).

11. The method of claim 2 wherein at least one structural variant is found at Cfa6.6, Cfa6.7, Cfa6.66, or Cfa6.83.

12. A method of screening a dog or wolf library comprising:

(a) obtaining a genomic library from a dog or wolf that contains the Williams-Beuren Syndrome (WBS) locus on canine chromosome 6;

(b) determining the number of structural variants in the WBS locus.

13. The method of claim 12 wherein the locations of the structural variants are also determined.

14. The method of claim 12 wherein step (b) comprises determining the number of structural variants in at least one of GTF2I, GTF2IRD1, and WBSCR17.

15. The method of claim 12 wherein step (b) comprises determining the number of structural variants in all of GTF2I, GTF2IRD1, and WBSCR17.

16. The method of claim 12 wherein step (b) comprises the use of the polymerase chain reaction (PCR) to amplify at least one DNA fragment from the WBS locus.

17. The method of claim 16 wherein the DNA fragment comprises at least one of the loci Cfa6.6, Cfa6.7, Cfa6.66, or Cfa6.83.

18. The method of claim 12 wherein step (b) comprises the use of PCR to amplify the locus Cfa6.6 using the primers CCCCTTCAGCCAGCATATAA (SEQ ID NO:

1) (forward) and TTCTCTGGGCTGTCTGGACT (SEQ ID NO;

     2) (reverse).

19. The method of claim 12 wherein step (b) comprises the use of PCR to amplify the locus Cfa6.6 using the primers AAGTTTCTCTGATGGAAAACACA (SEQ ID NO:

3) (forward) and GGTGGCTGGAAATTTCAGTAG (SEQ ID NO;

     4) (reverse).

20. The method of claim 12 wherein step (b) comprises the use of PCR to amplify the locus Cfa6.7 using the primers TGGAGCCATGATTAGGAAGG (SEQ ID NO:

5) (forward) and TAAGGAAGGACCCCATTTCC (SEQ ID NO;

     6) (reverse).

21. The method of claim 12 wherein step (b) comprises the use of PCR to amplify the locus Cfa6.66 using the primers TGCTGCTTCATGTTCTGTGA (SEQ ID NO:

7) (forward) and TGGTGCATTAGCTTTGGTTG (SEQ ID NO;

     8) (reverse).

22. The method of claim 12 wherein step (b) comprises the use of PCR to amplify the locus Cfa6.83 using the primers AACCACAGGAACAAAACCTCA (SEQ ID NO:

9) (forward) and CCTCCTGTTGGACATTTGGA (SEQ ID NO;

     10) (reverse).

23. The method of claim 12 wherein step (b) comprises the use of agarose gel electrophoresis to identify DNA fragments from the WBS locus that have altered mobility compared to the corresponding fragments from the dog reference genome and that are indicative of structural variants in the WBS locus from the library.

24. The method of claim 12 wherein step (b) comprises a hybridization step using at least one probe from the WBS locus that identifies structural variants in the WBS locus. In some embodiments, the hybridization step comprises fluorescence in-situ hybridization (FISH).

25. A method of producing dogs that are more likely to exhibit a sociable behavior comprising:

(a) selecting a male and female dog for breeding that each are known to have at least one structural variant within Cfa6.6, Cfa6.7, Cfa6.66, or Cfa6.83 in the Williams-Beuren Syndrome (WBS) locus; and

(b) mating the dogs of step (a) to produce offspring.

26. The method of claim 25 wherein the male and female dogs are genotyped for the presence of structural variants within the Williams-Beuren Syndrome (WBS) locus.

27. The method of claim 25 wherein the at least one structural variant occurs within at least one gene selected from the group consisting of GTF2I, GTF2IRD1, and WBSCR17.

28. A method of editing the genome of a dog comprising:

(a) obtaining a dog;

(b) using clustered regularly interspaced short palindromic repeats (CRISPRs)/CRISPR-associated (Cas) 9 to inactivate a gene in the Williams-Beuren Syndrome (WBS) locus on canine chromosome 6.

29. The method of claim 28 wherein the gene is GTF2I, GTF2IRD1, or WBSCR17.

30. A kit for detecting the presence of structural variants within the Williams-Beuren Syndrome (WBS) locus of canines comprising one or more primers selected from the group consisting of:

31. The kit of claim 30 wherein the kit comprises the primers CCCCTTCAGCCAGCATATAA (SEQ ID NO:

1) and TTCTCTGGGCTGTCTGGACT (SEQ ID NO;

     2).

32. The kit of claim 30 wherein the kit comprises the primers AAGTTTCTCTGATGGAAAACACA (SEQ ID NO:

3) and GGTGGCTGGAAATTTCAGTAG (SEQ ID NO;

     4).

33. The kit of claim 30 wherein the kit comprises the primers TGGAGCCATGATTAGGAAGG (SEQ ID NO:

5) and TAAGGAAGGACCCCATTTCC (SEQ ID NO;

     6).

34. The kit of claim 30 wherein the kit comprises the primers TGCTGCTTCATGTTCTGTGA (SEQ ID NO:

7) and TGGTGCATTAGCTTTGGTTG (SEQ ID NO;

     8).

35. The kit of claim 30 wherein the kit comprises the primers AACCACAGGAACAAAACCTCA (SEQ ID NO:

9) and CCTCCTGTTGGACATTTGGA (SEQ ID NO;

     10).

36. The kit of claim 30 further comprising instructions for use.

37. The kit of claim 30 wherein the primers are labeled using a detectable marker.

38. The kit of claim 30 further comprising at least one of a buffer, dNTPs, a DNA polymerase, a DNA ligase, or a restriction enzyme.