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Bengalness UM 2016
- 1. Hasan Alhaddad, Ph.D. KuwaitUniversity January 2016 - University of Missouri Degree of Bengalness: A measure of the genomic contribution of Asian Leopard Cats into Bengal breed cats
- 2. Barbara Gandolfi Hasan Alhaddad MikeMontague Mona Abdi Erica K Creighton Bianca Haase Maria Longeri Rashid Saif Carlyn Peterson Brian Davis William Murphy Ettore Randi Shannon Joslin Grace Lan Jeff Brockman Mike Hamilton Nick Dodman Richard Malik Clare Rusbridge Nick Gustafson Diane Shelton Robert A Grahn Jens Haggstrom Serina Filler Hannes Lohi James C Mullikin Chris Helps Niels C Pedersen Wes Warren Leslie A Lyons A work team & a teamwork
- 3. Outline • Introduction •Aim1 -Diagnostic panel •Aim2 - Degree of Bengalness •Aim3 - Bengal breed •Conclusion and significance
- 4. Outline • Introduction • AsianLeopard cat and the domestic cat • Hybridization and Bengal breed • Aims • Aim1 - Diagnostic panel • Aim2 - Degree of Bengalness • Aim3 - Bengal breed • Conclusion and significance • Introduction • Asian Leopard cat and the domestic cat • Hybridization and Bengal breed • Aims
- 5. Introduction Fig. 5. Relationshipsamong species of Felidae, continued from Fig. 4. Numbers are posterior probability values with a second number representing sup I. Agnarsson et al. / Molecular Phylogenetics and Evolution 54 (2010) 726–745 I. Agnarsson et al. / Molecular Phylogenetics and Evolution 54 (2010) 726–745 737 P. bengalensis and F.s. catus Fig. 5. Relationships among species of Felidae, continued from Fig. 4. Numbers are posterior probability values with a second number representing sup I. Agnarsson et al. / Molecular Phylogenetics and Evolution 54 (2010) 726–745
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- 7. AIMS 1- Diagnostic panel Identifydiagnostic markers of Asian Leopard Cat (ALC) alleles in the Feline SNP array 2 - Degree of Bengalness Estimate ALC allele proportions in known pedigree, Bengal breed, and other cat breeds 3 - Bengal breed Use “Degree of Bengalness” to understand and maintain Bengal cat breed
- 8. AIMS Aim1- Diagnostic panel Identifydiagnostic markers of Asian Leopard Cat (ALC) alleles in the Feline SNP array Dataset-Analysis -Findings Aim2 - Degree of Bengalness Aim3 - Bengal breed Aim1- Diagnostic panel Identify diagnostic markers of Asian Leopard Cat (ALC) alleles in the Feline SNP array Dataset-Analysis -Findings
- 9. Data and Analysis ALC N= 9 63K SNPs DOM* N = 1765 63K SNPs * Non-Bengal, 41 Breeds • Select markers from the 63K array that are: 1.Fixed with allele 1 (A1) in ALC 2.A1 frequency in domestic cats = 0 or MAF <= 0.05.
- 10. Findings SNP Relative Position(Mb) A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 X 0 25 50 75 100 125 150 175 200 225 250 674 markers identified
- 11. Findings • To beconcerned about: • Number of markers • Inter-marker distances • Linkage disequilibrium
- 12. SNP Relative Position(Mb) 0 25 50 75 100 125 150 175 200 225 250 A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 X Findings 287 markers (~ 5Mb apart)
- 13. AIMS Aim1- Diagnostic panel Aim2- Degree of Bengalness Estimate ALC allele proportions in known pedigree, Bengal breed, and other cat breeds Dataset-Analysis -Findings Aim3 - Bengal breed Aim2 - Degree of Bengalness Estimate ALC allele proportions in known pedigree, Bengal breed, and other cat breeds Dataset-Analysis -Findings
- 14. Data and Analysis ALC-DOM pedigree N= 98 Bengal cats N = 98 33 cat breeds N = 1452 • Use only autosomal markers (262 SNPs). • Calculate % ALC alleles in each individual (degree bengalness). • Use pedigree to validate degree of bengalness.
- 15. Pedigree A Genetic LinkageMap of Microsatellites in the Domestic Cat (Felis catus) Marilyn Menotti-Raymond,*,1 Victor A. David,* Leslie A. Lyons,* Alejandro A. Scha¨ ffer,† James F. Tomlin,‡ Michelle K. Hutton,§ and Stephen J. O’Brien* *Laboratory of Genomic Diversity, NCI–FCRDC, Frederick, Maryland 21702; †NHGRI/IDRB and ‡CIT/CBEL/BIMAS, National Institutes of Health, Bethesda, Maryland 20892; and §PE AgGen, Inc., Davis, California 95616 Received September 18, 1998; accepted January 6, 1999 Of the nonprimate mammalian species with devel- oping comparative gene maps, the feline gene map (Felis catus, Order Carnivora, 2N ؍ 38) displays the highest level of syntenic conservation with humans, with as few as 10 translocation exchanges discriminat- ing the human and feline genome organization. To extend this model, a genetic linkage map of microsat- ellite loci in the feline genome has been constructed including 246 autosomal and 7 X-linked loci. Two hun- dred thirty-five dinucleotide (dC ⅐ dA)n ⅐ (dG ⅐ dT)n and 18 tetranucleotide repeat loci were identified and genotyped in a two-family, 108-member multigenera- tion interspecies backcross pedigree between the do- mestic cat (F. catus) and the Asian leopard cat (Prio- nailurus bengalensis). Two hundred twenty-nine loci were linked to at least one other marker with a lod score >3.0, identifying 34 linkage groups. Representa- tive markers from each linkage group were assigned to specific cat chromosomes by somatic cell hybrid analysis, resulting in chromosomal assignments to 16 of the 19 feline chromosomes. Genome coverage spans approximately 2900 cM, and we estimate a genetic length for the sex-averaged map as 3300 cM. The map has an average intragroup intermarker spacing of 11 cM and provides a valuable resource for mapping phe- notypic variation in the species and relating it to gene maps of other mammals, including human. © 1999 Academic Press Cyprus and Jordan (Davis, 1989). Within the 33 regis- tered domestic cat breeds recognized in the United States (Cat Fancy Association, Manasquan, NJ), some 100 disorders that demonstrate Mendelian patterns of inheritance have been identified and characterized (Nicholas et al., 1998; Migaki, 1982; Robinson, 1977). Many of these pathologies are analogous to human inherited disorders, including autosomal dominant polycystic kidney disease (Biller et al., 1996), retinal atrophy (Narfstro¨m, 1983), primary hyperoxaluria Type 2 (Danpure et al., 1989), glycogen storage disease Type IV (Fyfe et al., 1992), and hypothyroidism (Ta- nase et al., 1991). Genes associated with some of these feline disorders have been genetically mapped and characterized including loci for glycogen branching en- zyme, arylsulfatase B, and lipoprotein lipase (Gilbert et al., 1988; Fyfe et al., 1992; Jackson et al., 1992; Ginz- inger et al., 1996), and corrective gene therapy strate- gies have even been examined for some disorders, including feline arylsulfatase B deficiency and mucopolysaccharidosis Type VI (Gasper et al., 1984; Peters et al., 1991; Byers et al., 1997). Nonetheless, genes associated with the majority of feline disorders have yet to be identified. The value of animal models has been demonstrated repeatedly with hundreds of characterized mouse mu- tations. Model animal systems serve to elucidate mo- Genomics 57, 9–23 (1999) Article ID geno.1999.5743, available online at http://www.idealibrary.com on FIG. 1. Domestic cat/Asian leopard cat interspecific backcross pedigree. Fca, domestic cat (Felis catus); Pbe, Asian leopard cat (Prionailurus bengalensis); LXD, progeny of Asian leopard cat ϫ domestic cat cross; BXD, progeny of F1 female backcrossed to domestic cat; BXL, progeny of F1 female backcrossed to Asian leopard cat. 17FELINELINKAGEMAP FIG. 1—Continued 18MENOTTI-RAYMONDETAL.
- 16. Pedigree simplified ALC DOM LxDBxLBxD Pedigree provides expected values of ALC alleles
- 17. Findings ALC % ALC Allele frequency 020 40 60 80 100 02468 BxL % ALC Allele frequency 0 20 40 60 80 100 01234 LxD % ALC Allele frequency 0 20 40 60 80 100 0246810 BxD % ALC Allele frequency 0 20 40 60 80 100 0246810 Bengal % ALC Allele frequency 0 20 40 60 80 100 05101520253035 Other Domestic % ALC Allele frequency 0 20 40 60 80 100 0200400600800 Theoretical and Observed degree of bengalness are in agreement
- 18. %Bengalness 0255075100 ALC LxD BENACURL BOM BUR CREX EGY MANEE PERM MCOON MUNCH ORI PBALD RBLUE SREX SIR SPH VAN BxL BxD ABY BIR BSH CHR DREX JBOB KOR LYK MANX NFC PER RAG SFOLD SIA SOM TREX WIR Findings • Bengal breed and its unique degree of bengalness. • Turkish Van (probably T. Angora) and high degree bengalness (?).
- 19. AIMS Aim1- Diagnostic panel Aim2- Degree of Bengalness Aim3 - Bengal breed Use “Degree of Bengalness” to understand and maintain Bengal cat breed Dataset-Analysis -Findings Aim3 - Bengal breed Use “Degree of Bengalness” to understand and maintain Bengal cat breed Dataset-Analysis -Findings
- 20. Data and Analysis Bengalcats N = 98 • Use degree of bengalness to understand breeding history of Bengal breed. • % Bengalness = 100 x (1/2)#generations ALC-DOM pedigree N = 98
- 21. Findings 0 1 23 4 5 10 15 20 25 0 1.6875 3.375 6.75 12.5 25 50 100 Generation Crossed to Domestic %Bengalness Theoritical Asian Leopard Cats BxL LxD BxD Random Bengal Breed cats 10 15 20 25 Generation Crossed to Domestic Theoritical Asian Leopard Cats BxL LxD BxD Random Bengal Breed cats • Variation in backcrosses. • Less variation in Bengals cats. • Generation 4 (6.75%). • Bengalness equilibrium in Bengal cats.
- 22. Conclusion and Significance •Genome-wide SNP panel is selected to measure degree of bengalness in Bengal cat breed. • The panel can be used to study the genetics of ALC-DOM hybrid zones and the conservation genetics of ALC.
- 23. Leslie A. Lyons,PhD Barbara Gandolfi, PhD Department of Veterinary Medicine and Surgery Acknowledgment Mona Abdi, M.Sc. student Department of Biological Sciences Robert A Grahn, PhD Veterinary Genetics Laboratory
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- 25. Disclaimer Figures, photos, andgraphs in my lectures are collected using google searches. I do not claim to have personally produced all the material (except for some). I do cite only articles or books used. I thank all owners of the visual aid that I use and apologize for not citing each individual item. If anybody finds the inclusion of their material into my lectures a violation of their copy rights, please contact me via email. hhalhaddad@gmail.com